From 1cbeb9227cc35b86acbbb766880ca703d0d1d9e8 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 5 Apr 2024 13:08:04 +0100 Subject: [PATCH] Refresh imports in preparation of CL release 2024-04-05 (#2325) Refresh imports in preparation of CL release 2024-04-05 --- src/ontology/imports/merged_import.owl | 16178 +++++++++------- src/ontology/mappings/fbbt-mappings.sssom.tsv | 1 - 2 files changed, 8806 insertions(+), 7373 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 70bc4e9bd..9ef4c72ba 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-30") + +Annotation(owl:versionInfo "2024-04-05") Declaration(Class()) Declaration(Class()) @@ -214,6 +214,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -488,7 +489,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11332,7 +11332,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12378,7 +12377,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12734,7 +12732,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12851,6 +12848,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12989,9 +12987,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13355,7 +13350,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13424,7 +13418,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13995,25 +13988,12 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14021,41 +14001,10 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14081,7 +14030,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14135,33 +14083,14 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14169,57 +14098,25 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(owl:deprecated)) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ # Annotation Property: (definition) -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) AnnotationAssertion( "2012-04-05: Barry Smith @@ -14241,47 +14138,25 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) -AnnotationAssertion( "editor note"@en) -AnnotationAssertion( ) AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "IAO:0000116") -AnnotationAssertion( "uberon") -AnnotationAssertion( "editor_note") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "editor_note") AnnotationAssertion(rdfs:label "editor note"@en) -AnnotationAssertion(rdfs:label "editor note") # Annotation Property: (has obsolescence reason) -AnnotationAssertion( "has obsolescence reason"@en) AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) AnnotationAssertion(rdfs:label "has obsolescence reason"@en) # Annotation Property: (term tracker item) -AnnotationAssertion( "term tracker item"@en) -AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) -AnnotationAssertion( ) AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion( "IAO:0000233") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "term_tracker_item") -AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) @@ -14290,25 +14165,15 @@ AnnotationAssertion(rdfs:label "ter # Annotation Property: (expand expression to) -AnnotationAssertion( "expand expression to"@en) -AnnotationAssertion( "ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" -"@en) AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) -AnnotationAssertion( "Chris Mungall"@en) AnnotationAssertion(rdfs:label "expand expression to"@en) # Annotation Property: (has ontology root term) -AnnotationAssertion( "has ontology root term"@en) AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) -AnnotationAssertion( "Nicolas Matentzoglu"@en) AnnotationAssertion( "IAO:0000700") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion(rdfs:label "has ontology root term"@en) @@ -14316,35 +14181,13 @@ AnnotationAssertion(rdfs:label "has # Annotation Property: (term replaced by) -AnnotationAssertion( "term replaced by"@en) -AnnotationAssertion( ) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (defined by construct) -AnnotationAssertion( "'part disjoint with' 'defined by construct' \"\"\" - PREFIX owl: - PREFIX : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.") AnnotationAssertion( ) AnnotationAssertion( ) @@ -14353,11 +14196,9 @@ AnnotationAssertion(rdfs:label "def # Annotation Property: (abbreviation) -AnnotationAssertion( "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") AnnotationAssertion( "A synonym type for describing abbreviations or initalisms") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "abbreviation") SubAnnotationPropertyOf( ) @@ -14371,11 +14212,9 @@ SubAnnotationPropertyOf( (plural form) -AnnotationAssertion( "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)") AnnotationAssertion( "A synonym type for describing pluralization synonyms") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "plural form") SubAnnotationPropertyOf( ) @@ -14385,14 +14224,7 @@ SubAnnotationPropertyOf( (never in taxon) -AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") -AnnotationAssertion(Annotation( "PMID:20973947") "S never_in_taxon T iff: S SubClassOf in_taxon only not T.") AnnotationAssertion( "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)") -AnnotationAssertion( "Class: ?X DisjointWith: RO_0002162 some ?Y ") AnnotationAssertion( "PREFIX rdfs: PREFIX owl: PREFIX in_taxon: @@ -14416,22 +14248,12 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . }") -AnnotationAssertion( "RO:0002161") -AnnotationAssertion( "uberon") -AnnotationAssertion( "never_in_taxon") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "never_in_taxon") AnnotationAssertion(rdfs:label "never in taxon") -AnnotationAssertion(rdfs:label "never_in_taxon") AnnotationAssertion(rdfs:seeAlso ) -# Annotation Property: (present_in_taxon) +# Annotation Property: (present in taxon) AnnotationAssertion( "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "PREFIX rdfs: PREFIX owl: PREFIX in_taxon: @@ -14456,32 +14278,14 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label) }") -AnnotationAssertion( "RO:0002175") -AnnotationAssertion( "applicable for taxon") -AnnotationAssertion( "uberon") -AnnotationAssertion( "present_in_taxon") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "present_in_taxon") AnnotationAssertion(rdfs:comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.") AnnotationAssertion(rdfs:label "present in taxon"@en) -AnnotationAssertion(rdfs:label "present_in_taxon") AnnotationAssertion(rdfs:seeAlso ) # Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - -# Annotation Property: (is a defining property chain axiom where second argument is reflexive) - -AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") -AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") - # Annotation Property: (is negative form of) AnnotationAssertion( ) @@ -14778,60 +14582,6 @@ SubAnnotationPropertyOf( SubAnnotationPropertyOf( ) -# Annotation Property: (creator) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/creator") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-creator") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-creator") -AnnotationAssertion(rdfs:label "creator") - -# Annotation Property: (description) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/description") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-description") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-description") -AnnotationAssertion(rdfs:label "description") - -# Annotation Property: (title) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/title") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-title") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-title") -AnnotationAssertion(rdfs:label "title") - -# Annotation Property: (contributor) - -AnnotationAssertion( "http://purl.org/dc/terms/contributor") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-contributor") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-contributor") -AnnotationAssertion(rdfs:label "contributor") - -# Annotation Property: (date) - -AnnotationAssertion( "http://purl.org/dc/terms/date") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dcterms-date") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dcterms-date") -AnnotationAssertion(rdfs:label "date") - -# Annotation Property: (license) - -AnnotationAssertion( "http://purl.org/dc/terms/license") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dcterms-license") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dcterms-license") -AnnotationAssertion(rdfs:label "license") - # Annotation Property: (subset_property) AnnotationAssertion(rdfs:label "subset_property") @@ -14859,7 +14609,6 @@ AnnotationAssertion(rdfs:label (has_broad_synonym) AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") @@ -14872,7 +14621,6 @@ AnnotationAssertion(rdfs:label (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") @@ -14881,7 +14629,6 @@ AnnotationAssertion(rdfs:seeAlso (has narrow synonym) AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") AnnotationAssertion(rdfs:label "has narrow synonym"@en) AnnotationAssertion(rdfs:label "has_narrow_synonym") @@ -14894,7 +14641,6 @@ AnnotationAssertion(rdfs:label (has_related_synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") @@ -14916,54 +14662,22 @@ AnnotationAssertion(rdfs:label "shorthand") -# Annotation Property: rdfs:seeAlso (see also) - -AnnotationAssertion( rdfs:seeAlso "http://www.w3.org/2000/01/rdf-schema#seeAlso") -AnnotationAssertion( rdfs:seeAlso "uberon") -AnnotationAssertion( rdfs:seeAlso "seeAlso") -AnnotationAssertion( rdfs:seeAlso "true"^^xsd:boolean) -AnnotationAssertion( rdfs:seeAlso "seeAlso") -AnnotationAssertion(rdfs:label rdfs:seeAlso "see also") - -# Annotation Property: (depiction) - -AnnotationAssertion( "http://xmlns.com/foaf/0.1/depiction") -AnnotationAssertion( "uberon") -AnnotationAssertion( "depiction") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "depiction") -AnnotationAssertion(rdfs:label "depiction") - ############################ # Object Properties ############################ -# Object Property: (part_of) +# Object Property: (part of) -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a part and its whole"@en) AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "BFO:0000050") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "part_of") AnnotationAssertion( ) AnnotationAssertion( ) @@ -14983,22 +14697,15 @@ TransitiveObjectProperty() # Object Property: (has part) -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a whole and its part"@en) AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) AnnotationAssertion( "BFO:0000051") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_part") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15012,15 +14719,10 @@ TransitiveObjectProperty() # Object Property: (preceded by) -AnnotationAssertion( "preceded by"@en) AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) -AnnotationAssertion( "is preceded by"@en) -AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( "BFO:0000062") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") @@ -15034,11 +14736,9 @@ ObjectPropertyRange( (precedes) -AnnotationAssertion( "precedes"@en) AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) AnnotationAssertion( "BFO:0000063") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") @@ -15051,11 +14751,7 @@ ObjectPropertyRange( (occurs in) -AnnotationAssertion( "occurs in"@en) AnnotationAssertion( "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "occurs_in"@en) -AnnotationAssertion( "unfolds in"@en) -AnnotationAssertion( "unfolds_in"@en) AnnotationAssertion( "BFO:0000066") AnnotationAssertion( "external") AnnotationAssertion( "occurs_in") @@ -15064,7 +14760,6 @@ AnnotationAssertion( ) AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) @@ -15074,208 +14769,9 @@ ObjectPropertyRange( (contains process) -AnnotationAssertion( "site of"@en) AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "BFO:0000067") -AnnotationAssertion( "uberon") -AnnotationAssertion( "contains_process") -AnnotationAssertion( "contains_process") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "contains process"@en) -AnnotationAssertion(rdfs:label "contains process") - -# Object Property: (anterior to) - -AnnotationAssertion( "BSPO:0000096") -AnnotationAssertion( "uberon") -AnnotationAssertion( "anterior_to") -AnnotationAssertion( "anterior_to") -AnnotationAssertion(rdfs:label "anterior to") - -# Object Property: (distal to) - -AnnotationAssertion( "BSPO:0000097") -AnnotationAssertion( "uberon") -AnnotationAssertion( "distal_to") -AnnotationAssertion( "distal_to") -AnnotationAssertion(rdfs:label "distal to") - -# Object Property: (dorsal to) - -AnnotationAssertion( "BSPO:0000098") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dorsal_to") -AnnotationAssertion( "dorsal_to") -AnnotationAssertion(rdfs:label "dorsal to") - -# Object Property: (posterior to) - -AnnotationAssertion( "BSPO:0000099") -AnnotationAssertion( "uberon") -AnnotationAssertion( "posterior_to") -AnnotationAssertion( "posterior_to") -AnnotationAssertion(rdfs:label "posterior to") - -# Object Property: (proximal to) - -AnnotationAssertion( "BSPO:0000100") -AnnotationAssertion( "uberon") -AnnotationAssertion( "proximal_to") -AnnotationAssertion( "proximal_to") -AnnotationAssertion(rdfs:label "proximal to") - -# Object Property: (ventral to) - -AnnotationAssertion( "BSPO:0000102") -AnnotationAssertion( "uberon") -AnnotationAssertion( "ventral_to") -AnnotationAssertion( "ventral_to") -AnnotationAssertion(rdfs:label "ventral to") - -# Object Property: (deep to) - -AnnotationAssertion( "BSPO:0000107") -AnnotationAssertion( "uberon") -AnnotationAssertion( "deep_to") -AnnotationAssertion( "deep_to") -AnnotationAssertion(rdfs:label "deep to") - -# Object Property: (superficial to) - -AnnotationAssertion( "BSPO:0000108") -AnnotationAssertion( "uberon") -AnnotationAssertion( "superficial_to") -AnnotationAssertion( "superficial_to") -AnnotationAssertion(rdfs:label "superficial to") - -# Object Property: (in left side of) - -AnnotationAssertion( "BSPO:0000120") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_left_side_of") -AnnotationAssertion( "in_left_side_of") -AnnotationAssertion(rdfs:label "in left side of") - -# Object Property: (in right side of) - -AnnotationAssertion( "BSPO:0000121") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_right_side_of") -AnnotationAssertion( "in_right_side_of") -AnnotationAssertion(rdfs:label "in right side of") - -# Object Property: (in posterior side of) - -AnnotationAssertion( "BSPO:0000122") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_posterior_side_of") -AnnotationAssertion( "in_posterior_side_of") -AnnotationAssertion(rdfs:label "in posterior side of") - -# Object Property: (in anterior side of) - -AnnotationAssertion( "BSPO:0000123") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_anterior_side_of") -AnnotationAssertion( "in_anterior_side_of") -AnnotationAssertion(rdfs:label "in anterior side of") - -# Object Property: (in proximal side of) - -AnnotationAssertion( "BSPO:0000124") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_proximal_side_of") -AnnotationAssertion( "in_proximal_side_of") -AnnotationAssertion(rdfs:label "in proximal side of") - -# Object Property: (in lateral side of) - -AnnotationAssertion( "BSPO:0000126") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_lateral_side_of") -AnnotationAssertion( "in_lateral_side_of") -AnnotationAssertion(rdfs:label "in lateral side of") - -# Object Property: (in superficial part of) - -AnnotationAssertion( "BSPO:0001100") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_superficial_part_of") -AnnotationAssertion( "in_superficial_part_of") -AnnotationAssertion(rdfs:label "in superficial part of") - -# Object Property: (in deep part of) - -AnnotationAssertion( "BSPO:0001101") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_deep_part_of") -AnnotationAssertion( "in_deep_part_of") -AnnotationAssertion(rdfs:label "in deep part of") - -# Object Property: (proximalmost part of) - -AnnotationAssertion( "BSPO:0001106") -AnnotationAssertion( "uberon") -AnnotationAssertion( "proximalmost_part_of") -AnnotationAssertion( "proximalmost_part_of") -AnnotationAssertion(rdfs:label "proximalmost part of") - -# Object Property: (immediately deep to) - -AnnotationAssertion( "BSPO:0001107") -AnnotationAssertion( "uberon") -AnnotationAssertion( "immediately_deep_to") -AnnotationAssertion( "immediately_deep_to") -AnnotationAssertion(rdfs:label "immediately deep to") - -# Object Property: (distalmost part of) - -AnnotationAssertion( "BSPO:0001108") -AnnotationAssertion( "uberon") -AnnotationAssertion( "distalmost_part_of") -AnnotationAssertion( "distalmost_part_of") -AnnotationAssertion(rdfs:label "distalmost part of") - -# Object Property: (preaxialmost part of) - -AnnotationAssertion( "BSPO:0001113") -AnnotationAssertion( "uberon") -AnnotationAssertion( "preaxialmost_part_of") -AnnotationAssertion( "preaxialmost_part_of") -AnnotationAssertion(rdfs:label "preaxialmost part of") - -# Object Property: (postaxialmost part of) - -AnnotationAssertion( "BSPO:0001115") -AnnotationAssertion( "uberon") -AnnotationAssertion( "postaxialmost_part_of") -AnnotationAssertion( "postaxialmost_part_of") -AnnotationAssertion(rdfs:label "postaxialmost part of") - -# Object Property: (intersects midsagittal plane of) - -AnnotationAssertion( "BSPO:0005001") -AnnotationAssertion( "uberon") -AnnotationAssertion( "intersects_midsagittal_plane_of") -AnnotationAssertion( "intersects_midsagittal_plane_of") -AnnotationAssertion(rdfs:label "intersects midsagittal plane of") - -# Object Property: (immediately superficial to) - -AnnotationAssertion( "BSPO:0015014") -AnnotationAssertion( "uberon") -AnnotationAssertion( "immediately_superficial_to") -AnnotationAssertion( "immediately_superficial_to") -AnnotationAssertion(rdfs:label "immediately superficial to") - -# Object Property: (in dorsal side of) - -AnnotationAssertion( "BSPO:0015101") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_dorsal_side_of") -AnnotationAssertion( "in_dorsal_side_of") -AnnotationAssertion(rdfs:label "in dorsal side of") # Object Property: (results in distribution of) @@ -15298,12 +14794,7 @@ SubObjectPropertyOf( (characteristic of) -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility is a characteristic of this vase"@en) -AnnotationAssertion( "this red color is a characteristic of this apple"@en) AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) -AnnotationAssertion( "inheres_in"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") AnnotationAssertion(rdfs:label "characteristic of"@en) SubObjectPropertyOf( ) @@ -15312,14 +14803,8 @@ FunctionalObjectProperty() # Object Property: (bearer of) -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) AnnotationAssertion( "Inverse of characteristic_of"@en) AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) AnnotationAssertion( "RO:0000053") AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") @@ -15331,15 +14816,9 @@ ObjectPropertyRange( (participates in) -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) AnnotationAssertion( "RO:0000056") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") AnnotationAssertion(rdfs:label "participates in"@en) @@ -15350,14 +14829,8 @@ ObjectPropertyRange( (has participant) -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) -AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion( "RO:0000057") AnnotationAssertion( "external") AnnotationAssertion( "has_participant") @@ -15369,11 +14842,8 @@ ObjectPropertyRange( (function of) -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "function_of"@en) -AnnotationAssertion( "is function of"@en) AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "function of"@en) SubObjectPropertyOf( ) @@ -15382,11 +14852,8 @@ ObjectPropertyDomain( (quality of) -AnnotationAssertion( "this red color is a quality of this apple"@en) AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) -AnnotationAssertion( "is quality of"@en) -AnnotationAssertion( "quality_of"@en) AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "quality of"@en) SubObjectPropertyOf( ) @@ -15394,11 +14861,8 @@ InverseObjectProperties( (role of) -AnnotationAssertion( "this investigator role is a role of this person"@en) AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "is role of"@en) -AnnotationAssertion( "role_of"@en) AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") AnnotationAssertion(rdfs:label "role of"@en) SubObjectPropertyOf( ) @@ -15406,10 +14870,8 @@ InverseObjectProperties( (has function) -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "has_function"@en) AnnotationAssertion(rdfs:label "has function"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15417,25 +14879,16 @@ ObjectPropertyRange( (has quality) -AnnotationAssertion( "this apple has quality this red color"@en) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) -AnnotationAssertion( "has_quality"@en) -AnnotationAssertion( "RO:0000086") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_quality") -AnnotationAssertion( "has_quality") AnnotationAssertion(rdfs:label "has quality"@en) -AnnotationAssertion(rdfs:label "has quality") SubObjectPropertyOf( ) ObjectPropertyRange( ) # Object Property: (has role) -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "has_role"@en) AnnotationAssertion(rdfs:label "has role"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15460,64 +14913,34 @@ SubObjectPropertyOf( (derives from) -AnnotationAssertion( "this cell derives from this parent cell (cell division)"@en) -AnnotationAssertion( "this nucleus derives from this parent nucleus (nuclear division)"@en) -AnnotationAssertion( ) AnnotationAssertion( "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'."@en) -AnnotationAssertion( "derives_from"@en) -AnnotationAssertion( "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "derives from"@en) InverseObjectProperties( ) # Object Property: (derives into) -AnnotationAssertion( "this parent cell derives into this cell (cell division)"@en) -AnnotationAssertion( "this parent nucleus derives into this nucleus (nuclear division)"@en) -AnnotationAssertion( ) AnnotationAssertion( "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'."@en) -AnnotationAssertion( "derives_into"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "derives into"@en) # Object Property: (location of) -AnnotationAssertion( "is location of"@en) -AnnotationAssertion( "my head is the location of my brain"@en) -AnnotationAssertion( "this cage is the location of this rat"@en) AnnotationAssertion( "a relation between two independent continuants, the location and the target, in which the target is entirely within the location"@en) AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "location_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0001015") -AnnotationAssertion( "uberon") -AnnotationAssertion( "location_of") -AnnotationAssertion( "location_of") AnnotationAssertion(rdfs:label "location of"@en) -AnnotationAssertion(rdfs:label "location of") InverseObjectProperties( ) TransitiveObjectProperty() # Object Property: (located in) -AnnotationAssertion( "located in"@en) -AnnotationAssertion( "my brain is located in my head"@en) -AnnotationAssertion( "this rat is located in this cage"@en) AnnotationAssertion( "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en) AnnotationAssertion( "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"@en) AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "located_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") -AnnotationAssertion( "RO:0001025") -AnnotationAssertion( "uberon") -AnnotationAssertion( "located_in") AnnotationAssertion( ) -AnnotationAssertion( "located_in") AnnotationAssertion(rdfs:label "located in"@en) -AnnotationAssertion(rdfs:label "located in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Located_in"^^xsd:anyURI) TransitiveObjectProperty() ObjectPropertyDomain(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) @@ -15527,58 +14950,32 @@ ObjectPropertyRange( ObjectIntersecti # Object Property: (2D boundary of) -AnnotationAssertion( "the surface of my skin is a 2D boundary of my body"@en) AnnotationAssertion( "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity"@en) AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) -AnnotationAssertion( "2D_boundary_of"@en) -AnnotationAssertion( "boundary of"@en) -AnnotationAssertion( "is 2D boundary of"@en) -AnnotationAssertion( "is boundary of"@en) -AnnotationAssertion( "surface of"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "2D boundary of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (has 2D boundary) -AnnotationAssertion( "my body has 2D boundary the surface of my skin"@en) AnnotationAssertion( "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en) AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) -AnnotationAssertion( ) -AnnotationAssertion( "has boundary"@en) -AnnotationAssertion( "has_2D_boundary"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002002") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_boundary") -AnnotationAssertion( "has_boundary") AnnotationAssertion(rdfs:label "has 2D boundary"@en) -AnnotationAssertion(rdfs:label "has 2D boundary") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (innervated_by) -AnnotationAssertion( ) -AnnotationAssertion( "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^xsd:anyURI) -AnnotationAssertion( "RO:0002005") -AnnotationAssertion( "uberon") -AnnotationAssertion( "innervated_by") -AnnotationAssertion( "innervated_by") AnnotationAssertion(rdfs:label "innervated_by"@en) -AnnotationAssertion(rdfs:label "innervated_by") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (has synaptic terminal of) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has synaptic terminal of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15594,10 +14991,8 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002007") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "bounding_layer_of") AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") @@ -15710,8 +15105,6 @@ FunctionalObjectProperty() # Object Property: (before or simultaneous with) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "<="@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Primitive instance level timing relation between events") AnnotationAssertion(rdfs:label "before or simultaneous with"@en) @@ -15720,23 +15113,15 @@ SubObjectPropertyOf( (simultaneous with) AnnotationAssertion( "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.") -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "RO:0002082") -AnnotationAssertion( "uberon") -AnnotationAssertion( "simultaneous_with") AnnotationAssertion( ) -AnnotationAssertion( "simultaneous_with") AnnotationAssertion(rdfs:comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en) AnnotationAssertion(rdfs:label "simultaneous with"@en) -AnnotationAssertion(rdfs:label "simultaneous with") SubObjectPropertyOf( ) SymmetricObjectProperty() TransitiveObjectProperty() # Object Property: (ends after) -AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) AnnotationAssertion(rdfs:label "ends after"@en) @@ -15745,11 +15130,8 @@ TransitiveObjectProperty() # Object Property: (immediately preceded by) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "starts_at_end_of") AnnotationAssertion( "RO:0002087") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) @@ -15760,11 +15142,6 @@ InverseObjectProperties( (immediately precedes) -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "ends_at_start_of") -AnnotationAssertion( "meets") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002090") AnnotationAssertion( "external") AnnotationAssertion( "immediately_precedes") @@ -15777,12 +15154,9 @@ SubObjectPropertyOf( (has soma location) -AnnotationAssertion( ) AnnotationAssertion( "Relation between a neuron and a material anatomical entity that its soma is part of."@en) -AnnotationAssertion( ) AnnotationAssertion( " some ( and some ?Y)") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has soma location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15790,33 +15164,8 @@ ObjectPropertyRange( (fasciculates with) -AnnotationAssertion( ) AnnotationAssertion( "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. "@en) -AnnotationAssertion( ) -AnnotationAssertion( "fasciculates with") -AnnotationAssertion( "(forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - (\"neuron ; CL_0000540\" ?x) - (\"neuron projection bundle ; CARO_0001001\" ?y) - (\"neuron projection segment ; CARO_0001502\" ?nps) - (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - ))))))") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fasciculates with"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15825,50 +15174,28 @@ ObjectPropertyRange( (axon synapses in) -AnnotationAssertion( ) AnnotationAssertion( "Relation between a neuron and some structure its axon forms (chemical) synapses in."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( and some ( and some ( and some ?Y)))") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "axon synapses in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (synapsed by) -AnnotationAssertion( ) AnnotationAssertion( "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that has_part some ( that some Y?)))") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002103") -AnnotationAssertion( "uberon") -AnnotationAssertion( "synapsed_by") -AnnotationAssertion( "synapsed_by") AnnotationAssertion(rdfs:label "synapsed by"@en) -AnnotationAssertion(rdfs:label "synapsed by") SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( ))) # Object Property: (has plasma membrane part) -AnnotationAssertion( "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]"@en) -AnnotationAssertion( ) AnnotationAssertion( "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( and some ?Y)") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has plasma membrane part"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15876,16 +15203,10 @@ ObjectPropertyRange( (has postsynaptic terminal in) -AnnotationAssertion( ) AnnotationAssertion( "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "synapsed in"@en) AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has postsynaptic terminal in"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15893,26 +15214,17 @@ ObjectPropertyDomain( (has presynaptic terminal in) -AnnotationAssertion( ) AnnotationAssertion( "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input."@en) -AnnotationAssertion( "synapses in"@en) AnnotationAssertion( " some ( that some ( that some Y?)"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has presynaptic terminal in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (synapsed to) -AnnotationAssertion( ) AnnotationAssertion( " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that some ( that some Y?)))") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -15926,26 +15238,18 @@ ObjectPropertyDomain( ObjectUnionOf(< # Object Property: (has synaptic terminal in) -AnnotationAssertion( ) AnnotationAssertion( "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.") -AnnotationAssertion( ) -AnnotationAssertion( "has synapse in") AnnotationAssertion( " some ( that some Y?)") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has synaptic terminal in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (overlaps) -AnnotationAssertion( ) AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002131") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "overlaps") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15958,35 +15262,7 @@ SymmetricObjectProperty() # Object Property: (has fasciculating neuron projection) -AnnotationAssertion( ) AnnotationAssertion( "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it."@en) -AnnotationAssertion( ) -AnnotationAssertion( "has fasciculating component"@en) -AnnotationAssertion( "(forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - (\"neuron projection bundle ; CARO_0001001\" ?x) - (\"neuron projection ; GO0043005\" ?y) - (\"neuron projection segment ; CARO_0001502\" ?nps) - (\"neuron projection bundle segment ; CARO_0001500\" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - -") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has fasciculating neuron projection"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15994,36 +15270,17 @@ ObjectPropertyRange( ObjectUnionOf( (innervates) -AnnotationAssertion( ) AnnotationAssertion( "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."@en) -AnnotationAssertion( ) AnnotationAssertion( " some ( that ( some ( that some Y?)))") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002134") -AnnotationAssertion( "uberon") -AnnotationAssertion( "innervates") -AnnotationAssertion( "innervates") AnnotationAssertion(rdfs:label "innervates"@en) -AnnotationAssertion(rdfs:label "innervates") ObjectPropertyDomain( ) # Object Property: (continuous with) -AnnotationAssertion( ) AnnotationAssertion( "X continuous_with Y if and only if X and Y share a fiat boundary.") -AnnotationAssertion( ) -AnnotationAssertion( "connected to") -AnnotationAssertion( "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002150") -AnnotationAssertion( "uberon") -AnnotationAssertion( "continuous_with") -AnnotationAssertion( "continuous_with") AnnotationAssertion(rdfs:label "continuous with"@en) -AnnotationAssertion(rdfs:label "continuous with") AnnotationAssertion(rdfs:seeAlso "FMA:85972") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -16032,13 +15289,7 @@ ObjectPropertyRange( (shares ancestor with) -AnnotationAssertion( ) AnnotationAssertion( "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.") -AnnotationAssertion( "Consider obsoleting and merging with child relation, 'in homology relationship with'") -AnnotationAssertion( "RO:0002158") -AnnotationAssertion( "uberon") -AnnotationAssertion( "homologous_to") -AnnotationAssertion( "homologous_to") AnnotationAssertion(rdfs:comment "VBO calls this homologous_to") AnnotationAssertion(rdfs:label "shares ancestor with") SubObjectPropertyOf( ) @@ -16047,36 +15298,18 @@ TransitiveObjectProperty() # Object Property: (only in taxon) -AnnotationAssertion( "lactation SubClassOf 'only in taxon' some 'Mammalia'") -AnnotationAssertion( ) AnnotationAssertion( "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.") AnnotationAssertion( "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002160") -AnnotationAssertion( "uberon") -AnnotationAssertion( "only_in_taxon") -AnnotationAssertion( "only_in_taxon") AnnotationAssertion(rdfs:label "only in taxon") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (in taxon) -AnnotationAssertion( ) AnnotationAssertion( "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002162") -AnnotationAssertion( "uberon") -AnnotationAssertion( "in_taxon") AnnotationAssertion( ) -AnnotationAssertion( "in_taxon") AnnotationAssertion(rdfs:comment "Connects a biological entity to its taxon of origin.") AnnotationAssertion(rdfs:label "in taxon") AnnotationAssertion(rdfs:seeAlso ) @@ -16084,14 +15317,9 @@ SubObjectPropertyOf( (spatially disjoint from) -AnnotationAssertion( ) AnnotationAssertion( "A is spatially_disjoint_from B if and only if they have no parts in common") AnnotationAssertion( "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy") AnnotationAssertion( "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spatially disjoint from") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) @@ -16099,15 +15327,8 @@ SubObjectPropertyOf( (connected to) -AnnotationAssertion( "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).") AnnotationAssertion( "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002170") -AnnotationAssertion( "uberon") -AnnotationAssertion( "connected_to") -AnnotationAssertion( "connected_to") AnnotationAssertion(rdfs:label "connected to"@en) -AnnotationAssertion(rdfs:label "connected to") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16116,16 +15337,8 @@ ObjectPropertyRange( ObjectSomeValues # Object Property: (connects) -AnnotationAssertion( "The M8 connects Glasgow and Edinburgh") -AnnotationAssertion( "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).") AnnotationAssertion( "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002176") -AnnotationAssertion( "uberon") -AnnotationAssertion( "connects") -AnnotationAssertion( "connects") AnnotationAssertion(rdfs:label "connects"@en) -AnnotationAssertion(rdfs:label "connects") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16135,13 +15348,7 @@ ObjectPropertyRange( ObjectSomeValues # Object Property: (attached to part of) AnnotationAssertion( "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.") -AnnotationAssertion( "attached to part of (anatomical structure to anatomical structure)") -AnnotationAssertion( "RO:0002177") -AnnotationAssertion( "uberon") -AnnotationAssertion( "attaches_to_part_of") -AnnotationAssertion( "attaches_to_part_of") AnnotationAssertion(rdfs:label "attached to part of"@en) -AnnotationAssertion(rdfs:label "attached to part of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16151,40 +15358,22 @@ ObjectPropertyRange( "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.") AnnotationAssertion( "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002178") -AnnotationAssertion( "uberon") -AnnotationAssertion( "supplies") -AnnotationAssertion( "supplies") AnnotationAssertion(rdfs:label "supplies"@en) -AnnotationAssertion(rdfs:label "supplies") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) # Object Property: (drains) AnnotationAssertion( "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.") AnnotationAssertion( "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002179") -AnnotationAssertion( "uberon") -AnnotationAssertion( "drains") -AnnotationAssertion( "drains") AnnotationAssertion(rdfs:label "drains"@en) -AnnotationAssertion(rdfs:label "drains") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) # Object Property: (has component) -AnnotationAssertion( ) AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") -AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002180") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") @@ -16195,19 +15384,9 @@ SubObjectPropertyOf( (develops from) -AnnotationAssertion( ) AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002202") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_from") -AnnotationAssertion( "develops_from") AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label "develops from"@en) -AnnotationAssertion(rdfs:label "develops from") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16217,18 +15396,9 @@ ObjectPropertyRange( (develops into) -AnnotationAssertion( ) AnnotationAssertion( "inverse of develops from") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002203") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_into") AnnotationAssertion( ) -AnnotationAssertion( "develops_into") AnnotationAssertion(rdfs:label "develops into"@en) -AnnotationAssertion(rdfs:label "develops into") SubObjectPropertyOf( ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16236,10 +15406,7 @@ TransitiveObjectProperty() # Object Property: (expressed in) -AnnotationAssertion( "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'") -AnnotationAssertion( ) AnnotationAssertion( "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "expressed in"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16249,20 +15416,10 @@ ObjectPropertyRange( (directly develops from) -AnnotationAssertion( ) AnnotationAssertion( "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "FBbt") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002207") AnnotationAssertion( "has developmental precursor") -AnnotationAssertion( "uberon") -AnnotationAssertion( "directly_develops_from") -AnnotationAssertion( "directly_develops_from") AnnotationAssertion(rdfs:comment "TODO - add child relations from DOS") AnnotationAssertion(rdfs:label "directly develops from"@en) -AnnotationAssertion(rdfs:label "directly develops from") SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ObjectUnionOf( )) @@ -16270,9 +15427,7 @@ ObjectPropertyRange( ObjectUnionOf( (directly develops into) -AnnotationAssertion( ) AnnotationAssertion( "inverse of directly develops from") -AnnotationAssertion( "developmental precursor of") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly develops into"@en) SubObjectPropertyOf( ) @@ -16280,14 +15435,6 @@ SubObjectPropertyOf( (regulates) AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "RO:0002211") AnnotationAssertion( "external") AnnotationAssertion( "regulates") @@ -16306,9 +15453,6 @@ ObjectPropertyRange( (negatively regulates) AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002212") AnnotationAssertion( "external") @@ -16326,10 +15470,6 @@ InverseObjectProperties( (positively regulates) AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "positively regulates (process to process)") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002213") AnnotationAssertion( "external") AnnotationAssertion( "positively_regulates") @@ -16346,17 +15486,9 @@ TransitiveObjectProperty() # Object Property: (capable of) -AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") -AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") -AnnotationAssertion( ) -AnnotationAssertion( "has function realized in") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") AnnotationAssertion( "RO:0002215") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") @@ -16369,11 +15501,8 @@ ObjectPropertyRange( (capable of part of) AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") -AnnotationAssertion( ) -AnnotationAssertion( "has function in") AnnotationAssertion( "RO:0002216") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion(rdfs:label "capable of part of"@en) @@ -16384,33 +15513,17 @@ SubObjectPropertyOf( (surrounded by) -AnnotationAssertion( ) AnnotationAssertion( "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002219") -AnnotationAssertion( "uberon") -AnnotationAssertion( "surrounded_by") -AnnotationAssertion( "surrounded_by") AnnotationAssertion(rdfs:label "surrounded by"@en) -AnnotationAssertion(rdfs:label "surrounded by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (adjacent to) -AnnotationAssertion(Annotation(rdfs:seeAlso ) "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.") -AnnotationAssertion( "The epidermis layer of a vertebrate is adjacent to the dermis.") -AnnotationAssertion( "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.") -AnnotationAssertion( "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.") -AnnotationAssertion( ) AnnotationAssertion( "x adjacent to y if and only if x and y share a boundary.") AnnotationAssertion( "This relation acts as a join point with BSPO") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002220") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "adjacent_to") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16424,26 +15537,13 @@ ObjectPropertyRange( (surrounds) -AnnotationAssertion( ) AnnotationAssertion( "inverse of surrounded by") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002221") -AnnotationAssertion( "uberon") -AnnotationAssertion( "surrounds") AnnotationAssertion( ) -AnnotationAssertion( "surrounds") AnnotationAssertion(rdfs:label "surrounds"@en) -AnnotationAssertion(rdfs:label "surrounds") SubObjectPropertyOf( ) # Object Property: (temporally related to) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") AnnotationAssertion(rdfs:label "temporally related to"@en) @@ -16452,33 +15552,18 @@ ObjectPropertyRange( (starts) -AnnotationAssertion( ) AnnotationAssertion( "inverse of starts with") -AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "Allen") -AnnotationAssertion( "RO:0002223") -AnnotationAssertion( "uberon") -AnnotationAssertion( "starts") AnnotationAssertion( ) -AnnotationAssertion( "starts") AnnotationAssertion(rdfs:label "starts"@en) -AnnotationAssertion(rdfs:label "starts") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (starts with) -AnnotationAssertion( "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor") -AnnotationAssertion( ) AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") -AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "started by") AnnotationAssertion( "RO:0002224") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") @@ -16490,60 +15575,31 @@ TransitiveObjectProperty() # Object Property: (develops from part of) -AnnotationAssertion( ) AnnotationAssertion( "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002225") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_from_part_of") -AnnotationAssertion( "develops_from_part_of") AnnotationAssertion(rdfs:label "develops from part of"@en) -AnnotationAssertion(rdfs:label "develops from part of") SubObjectPropertyOf( ) # Object Property: (develops in) -AnnotationAssertion( ) AnnotationAssertion( "x develops_in y if x is located in y whilst x is developing") -AnnotationAssertion( ) -AnnotationAssertion( "EHDAA2") -AnnotationAssertion( "Jonathan Bard, EHDAA2") -AnnotationAssertion( "RO:0002226") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_in") -AnnotationAssertion( "develops_in") AnnotationAssertion(rdfs:label "develops in"@en) -AnnotationAssertion(rdfs:label "develops in") SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (ends) -AnnotationAssertion( ) AnnotationAssertion( "inverse of ends with") -AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "RO:0002229") -AnnotationAssertion( "uberon") -AnnotationAssertion( "ends") AnnotationAssertion( ) -AnnotationAssertion( "ends") AnnotationAssertion(rdfs:label "ends"@en) -AnnotationAssertion(rdfs:label "ends") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (ends with) -AnnotationAssertion( ) AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") -AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "finished by") AnnotationAssertion( "RO:0002230") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") @@ -16555,10 +15611,7 @@ TransitiveObjectProperty() # Object Property: (has start location) -AnnotationAssertion( ) AnnotationAssertion( "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y") -AnnotationAssertion( ) -AnnotationAssertion( "starts with process that occurs in") AnnotationAssertion( "RO:0002231") AnnotationAssertion( "external") AnnotationAssertion( "has_start_location") @@ -16572,10 +15625,7 @@ ObjectPropertyRange( (has end location) -AnnotationAssertion( ) AnnotationAssertion( "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y") -AnnotationAssertion( ) -AnnotationAssertion( "ends with process that occurs in") AnnotationAssertion( "RO:0002232") AnnotationAssertion( "external") AnnotationAssertion( "has_end_location") @@ -16589,10 +15639,7 @@ ObjectPropertyRange( (has input) -AnnotationAssertion( ) AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") -AnnotationAssertion( ) -AnnotationAssertion( "consumes") AnnotationAssertion( "RO:0002233") AnnotationAssertion( "external") AnnotationAssertion( "has_input") @@ -16610,10 +15657,7 @@ ObjectPropertyDomain( (has output) -AnnotationAssertion( ) AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") -AnnotationAssertion( ) -AnnotationAssertion( "produces") AnnotationAssertion( "RO:0002234") AnnotationAssertion( "external") AnnotationAssertion( "has_output") @@ -16630,13 +15674,7 @@ InverseObjectProperties( (connecting branch of) -AnnotationAssertion( "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.") AnnotationAssertion( "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002252") -AnnotationAssertion( "uberon") -AnnotationAssertion( "connecting_branch_of") -AnnotationAssertion( "connecting_branch_of") AnnotationAssertion(rdfs:label "connecting branch of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -16646,23 +15684,14 @@ InverseObjectProperties( (has connecting branch) AnnotationAssertion( "inverse of connecting branch of") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has connecting branch") SubObjectPropertyOf( ) # Object Property: (has developmental contribution from) -AnnotationAssertion( "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]") -AnnotationAssertion( ) AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002254") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_developmental_contribution_from") -AnnotationAssertion( "has_developmental_contribution_from") AnnotationAssertion(rdfs:label "has developmental contribution from"@en) -AnnotationAssertion(rdfs:label "has developmental contribution from") SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -16670,9 +15699,7 @@ ObjectPropertyRange( (developmentally contributes to) -AnnotationAssertion( ) AnnotationAssertion( "inverse of has developmental contribution from") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmentally contributes to"@en) SubObjectPropertyOf( ) @@ -16680,22 +15707,8 @@ SubObjectPropertyOf( (developmentally induced by) -AnnotationAssertion( ) AnnotationAssertion( "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "induced by") -AnnotationAssertion( ) -AnnotationAssertion( " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)") -AnnotationAssertion( "GO:0001759") -AnnotationAssertion( "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]") -AnnotationAssertion( "RO:0002256") -AnnotationAssertion( "uberon") -AnnotationAssertion( "developmentally_induced_by") -AnnotationAssertion( "developmentally_induced_by") AnnotationAssertion(rdfs:label "developmentally induced by"@en) -AnnotationAssertion(rdfs:label "developmentally induced by") SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -16703,20 +15716,15 @@ ObjectPropertyRange( (developmentally induces) -AnnotationAssertion( ) AnnotationAssertion( "Inverse of developmentally induced by"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmentally induces"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (developmentally preceded by) -AnnotationAssertion( ) AnnotationAssertion( "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p") AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( ) -AnnotationAssertion( "In general you should not use this relation to make assertions - use one of the more specific relations below this one") AnnotationAssertion(rdfs:comment "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from") AnnotationAssertion(rdfs:label "developmentally preceded by"@en) SubObjectPropertyOf( ) @@ -16726,7 +15734,6 @@ ObjectPropertyRange( (acts upstream of) -AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of") @@ -16735,7 +15742,6 @@ SubObjectPropertyOf( (acts upstream of or within) -AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") AnnotationAssertion( "affects") AnnotationAssertion( ) @@ -16745,49 +15751,32 @@ SubObjectPropertyOf( (developmentally replaces) -AnnotationAssertion( ) AnnotationAssertion( "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else") AnnotationAssertion( "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage") -AnnotationAssertion( ) -AnnotationAssertion( "replaces") -AnnotationAssertion( "RO:0002285") -AnnotationAssertion( "uberon") -AnnotationAssertion( "developmentally_replaces") -AnnotationAssertion( "developmentally_replaces") AnnotationAssertion(rdfs:label "developmentally replaces"@en) -AnnotationAssertion(rdfs:label "developmentally replaces") SubObjectPropertyOf( ) # Object Property: (developmentally succeeded by) -AnnotationAssertion( ) AnnotationAssertion( "Inverse of developmentally preceded by") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) SubObjectPropertyOf( ) # Object Property: (part of developmental precursor of) -AnnotationAssertion( "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of developmental precursor of"@en) SubObjectPropertyOf( ) # Object Property: (expresses) -AnnotationAssertion( ) AnnotationAssertion( "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "expresses"@en) SubObjectPropertyOf( ) # Object Property: (results in developmental progression of) -AnnotationAssertion( ) AnnotationAssertion( "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).") AnnotationAssertion( "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002295") AnnotationAssertion( "external") AnnotationAssertion( "results_in_developmental_progression_of") @@ -16801,11 +15790,7 @@ ObjectPropertyRange( (results in development of) -AnnotationAssertion( "every flower development (GO:0009908) results in development of some flower (PO:0009046)"@en) -AnnotationAssertion( ) AnnotationAssertion( "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.") -AnnotationAssertion( ) -AnnotationAssertion( "http://www.geneontology.org/GO.doc.development.shtml"^^xsd:anyURI) AnnotationAssertion( "RO:0002296") AnnotationAssertion( "external") AnnotationAssertion( "results_in_development_of") @@ -16820,11 +15805,6 @@ SubObjectPropertyOf( (results in formation of) -AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) -AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002297") AnnotationAssertion( "external") AnnotationAssertion( "results_in_formation_of") @@ -16832,7 +15812,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of"@en) +AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) AnnotationAssertion(rdfs:label "results in formation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16840,12 +15820,7 @@ InverseObjectProperties( (results in morphogenesis of) -AnnotationAssertion( "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"@en) -AnnotationAssertion( "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.") -AnnotationAssertion( ) AnnotationAssertion( "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.") -AnnotationAssertion( ) -AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002298") AnnotationAssertion( "external") AnnotationAssertion( "results_in_morphogenesis_of") @@ -16860,12 +15835,7 @@ SubObjectPropertyOf( (results in maturation of) -AnnotationAssertion( "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)"@en) -AnnotationAssertion( " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process") -AnnotationAssertion( ) AnnotationAssertion( "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.") -AnnotationAssertion( ) -AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002299") AnnotationAssertion( "external") AnnotationAssertion( "results_in_maturation_of") @@ -16881,8 +15851,6 @@ SubObjectPropertyOf( (causally upstream of, positive effect) AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002304") AnnotationAssertion( "external") AnnotationAssertion( "causally_upstream_of,_positive_effect") @@ -16899,7 +15867,6 @@ SubObjectPropertyOf( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002305") AnnotationAssertion( "external") AnnotationAssertion( "causally_upstream_of,_negative_effect") @@ -16915,20 +15882,13 @@ SubObjectPropertyOf( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") -AnnotationAssertion( ) -AnnotationAssertion( "inheres in part of") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "characteristic of part of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (results in acquisition of features of) -AnnotationAssertion( "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.") AnnotationAssertion( "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity") -AnnotationAssertion( ) -AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002315") AnnotationAssertion( "external") AnnotationAssertion( "results_in_acquisition_of_features_of") @@ -16945,36 +15905,21 @@ ObjectPropertyRange( (evolutionarily related to) AnnotationAssertion( "A relationship that holds via some environmental process") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.") AnnotationAssertion(rdfs:label "evolutionarily related to"@en) # Object Property: (mereotopologically related to) AnnotationAssertion( "A mereological relationship or a topological relationship") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mereotopologically related to"@en) # Object Property: (developmentally related to) AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") AnnotationAssertion(rdfs:label "developmentally related to"@en) # Object Property: (enables) -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -AnnotationAssertion( "is catalyzing") -AnnotationAssertion( "is executing") -AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enables"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) @@ -16984,28 +15929,17 @@ InverseObjectProperties( (functionally related to) AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion( ) -AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion( "RO:0002328") -AnnotationAssertion( "uberon") -AnnotationAssertion( "functionally_related_to") -AnnotationAssertion( "functionally_related_to") AnnotationAssertion(rdfs:label "functionally related to"@en) -AnnotationAssertion(rdfs:label "functionally related to") # Object Property: (part of structure that is capable of) AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion( ) -AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) SubObjectPropertyOf( ) # Object Property: (genomically related to) AnnotationAssertion( "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism") AnnotationAssertion(rdfs:label "genomically related to"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -17013,9 +15947,6 @@ ObjectPropertyRange( (involved in) AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") AnnotationAssertion(rdfs:label "involved in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -17023,11 +15954,7 @@ SubObjectPropertyOf( (regulates levels of) -AnnotationAssertion( "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid") AnnotationAssertion( "p regulates levels of c if p regulates some amount (PATO:0000070) of c") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "regulates levels of (process to entity)") AnnotationAssertion( "RO:0002332") AnnotationAssertion( "external") AnnotationAssertion( "regulates_levels_of") @@ -17041,7 +15968,6 @@ ObjectPropertyRange( (enabled by) AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) @@ -17051,8 +15977,6 @@ SubObjectPropertyOf( (regulated by) AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion( "regulated by (processual)") AnnotationAssertion( "RO:0002334") AnnotationAssertion( "external") AnnotationAssertion( "regulated_by") @@ -17068,7 +15992,6 @@ ObjectPropertyRange( (negatively regulated by) AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002335") AnnotationAssertion( "external") AnnotationAssertion( "negatively_regulated_by") @@ -17081,7 +16004,6 @@ SubObjectPropertyOf( (positively regulated by) AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002336") AnnotationAssertion( "external") AnnotationAssertion( "positively_regulated_by") @@ -17094,8 +16016,6 @@ SubObjectPropertyOf( (related via localization to) AnnotationAssertion( "A relationship that holds via some process of localization") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is a grouping relation.") AnnotationAssertion(rdfs:label "related via localization to"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -17103,7 +16023,6 @@ ObjectPropertyRange( (has target start location) AnnotationAssertion( "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002338") AnnotationAssertion( "external") AnnotationAssertion( "has_target_start_location") @@ -17118,7 +16037,6 @@ SubObjectPropertyOf( (has target end location) AnnotationAssertion( "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002339") AnnotationAssertion( "external") AnnotationAssertion( "has_target_end_location") @@ -17133,7 +16051,6 @@ SubObjectPropertyOf( (results in transport along) AnnotationAssertion( "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l ") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002341") AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_along") @@ -17145,7 +16062,6 @@ SubObjectPropertyOf( (results in transport across) AnnotationAssertion( "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002342") AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_across") @@ -17158,8 +16074,6 @@ SubObjectPropertyOf( (results in growth of) -AnnotationAssertion( "'pollen tube growth' results_in growth_of some 'pollen tube'") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002343") AnnotationAssertion( "external") AnnotationAssertion( "results_in_growth_of") @@ -17171,8 +16085,6 @@ SubObjectPropertyOf( (results in transport to from or in) -AnnotationAssertion( "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002344") AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_to_from_or_in") @@ -17183,12 +16095,7 @@ SubObjectPropertyOf( (member of) -AnnotationAssertion( "An organism that is a member of a population of organisms") AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") -AnnotationAssertion( "is member of") -AnnotationAssertion( "member part of") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "member of"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -17196,39 +16103,24 @@ InverseObjectProperties( (has member) AnnotationAssertion( "has member is a mereological relation between a collection and an item.") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002351") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_member") -AnnotationAssertion( "has_member") AnnotationAssertion(rdfs:label "has member"@en) -AnnotationAssertion(rdfs:label "has member") SubObjectPropertyOf( ) IrreflexiveObjectProperty() # Object Property: (input of) AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002352") -AnnotationAssertion( "uberon") -AnnotationAssertion( "input_of") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "input_of") AnnotationAssertion(rdfs:label "input of"@en) -AnnotationAssertion(rdfs:label "input of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (output of) AnnotationAssertion( "inverse of has output") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002353") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "output_of") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17240,29 +16132,19 @@ SubObjectPropertyOf( (formed as result of) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "formed as result of"@en) SubObjectPropertyOf( ) # Object Property: (has dendrite location) -AnnotationAssertion( ) -AnnotationAssertion( "http://neurolex.org/wiki/Property:DendriteLocation"^^xsd:anyURI) AnnotationAssertion(rdfs:label "has dendrite location"@en) SubObjectPropertyOf( ) # Object Property: (attached to) AnnotationAssertion( "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a") -AnnotationAssertion( ) -AnnotationAssertion( "attached to (anatomical structure to anatomical structure)") -AnnotationAssertion( "RO:0002371") -AnnotationAssertion( "uberon") -AnnotationAssertion( "attaches_to") AnnotationAssertion( ) -AnnotationAssertion( "attaches_to") AnnotationAssertion(rdfs:label "attached to"@en) -AnnotationAssertion(rdfs:label "attached to") SubObjectPropertyOf( ) SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -17270,14 +16152,7 @@ SymmetricObjectProperty() # Object Property: (has muscle origin) AnnotationAssertion( "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to."@en) -AnnotationAssertion( ) -AnnotationAssertion( "Wikipedia:Insertion_(anatomy)"@en) -AnnotationAssertion( "RO:0002372") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_muscle_origin") -AnnotationAssertion( "has_muscle_origin") AnnotationAssertion(rdfs:label "has muscle origin"@en) -AnnotationAssertion(rdfs:label "has muscle origin") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17286,14 +16161,7 @@ ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to # Object Property: (has muscle insertion) AnnotationAssertion( "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone."@en) -AnnotationAssertion( ) -AnnotationAssertion( "Wikipedia:Insertion_(anatomy)"@en) -AnnotationAssertion( "RO:0002373") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_muscle_insertion") -AnnotationAssertion( "has_muscle_insertion") AnnotationAssertion(rdfs:label "has muscle insertion"@en) -AnnotationAssertion(rdfs:label "has muscle insertion") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17301,12 +16169,7 @@ ObjectPropertyDomain(Annotation( "We # Object Property: (in branching relationship with) -AnnotationAssertion( ) AnnotationAssertion( "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships") -AnnotationAssertion( "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "in branching relationship with"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/170"^^xsd:anyURI) @@ -17316,24 +16179,9 @@ ObjectPropertyRange( (tributary of) -AnnotationAssertion( "Deschutes River tributary_of Columbia River") -AnnotationAssertion( "inferior epigastric vein tributary_of external iliac vein") -AnnotationAssertion( ) AnnotationAssertion( "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.") -AnnotationAssertion( ) -AnnotationAssertion( "drains into") -AnnotationAssertion( "drains to") -AnnotationAssertion( "tributary channel of") -AnnotationAssertion( "http://en.wikipedia.org/wiki/Tributary") -AnnotationAssertion( "http://www.medindia.net/glossary/venous_tributary.htm") -AnnotationAssertion( "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^xsd:anyURI) -AnnotationAssertion( "RO:0002376") -AnnotationAssertion( "uberon") -AnnotationAssertion( "tributary_of") AnnotationAssertion( ) -AnnotationAssertion( "tributary_of") AnnotationAssertion(rdfs:label "tributary of"@en) -AnnotationAssertion(rdfs:label "tributary of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "http://en.wikipedia.org/wiki/Tributary"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -17341,25 +16189,15 @@ SubObjectPropertyOf( (spatially coextensive with) -AnnotationAssertion( "A lump of clay and a statue") AnnotationAssertion( "x spatially_coextensive_with y if and inly if x and y have the same location") -AnnotationAssertion( ) -AnnotationAssertion( "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios") AnnotationAssertion(rdfs:label "spatially coextensive with"@en) SubObjectPropertyOf( ) # Object Property: (branching part of) -AnnotationAssertion( "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S") AnnotationAssertion( "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002380") -AnnotationAssertion( "uberon") -AnnotationAssertion( "branching_part_of") AnnotationAssertion( ) -AnnotationAssertion( "branching_part_of") AnnotationAssertion(rdfs:label "branching part of"@en) -AnnotationAssertion(rdfs:label "branching part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "FMA:85994") SubObjectPropertyOf( ) @@ -17369,9 +16207,7 @@ ObjectPropertyRange( ObjectSomeValues # Object Property: (has developmental potential involving) -AnnotationAssertion( ) AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has developmental potential involving"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17379,51 +16215,31 @@ ObjectPropertyRange( (has potential to developmentally contribute to) -AnnotationAssertion( ) AnnotationAssertion( "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002385") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_potential_to_developmentally_contribute_to") -AnnotationAssertion( "has_potential_to_developmentally_contribute_to") AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) -AnnotationAssertion(rdfs:label "has potential to developmentally contribute to") SubObjectPropertyOf( ) # Object Property: (has potential to developmentally induce) -AnnotationAssertion( ) AnnotationAssertion( "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has potential to developmentally induce"@en) SubObjectPropertyOf( ) # Object Property: (has potential to develop into) -AnnotationAssertion( ) AnnotationAssertion( "x has the potential to develop into y iff x develops into y or if x is capable of developing into y"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002387") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_potential_to_develop_into") -AnnotationAssertion( "has_potential_to_develop_into") AnnotationAssertion(rdfs:label "has potential to develop into"@en) -AnnotationAssertion(rdfs:label "has potential to develop into") SubObjectPropertyOf( ) # Object Property: (has potential to directly develop into) -AnnotationAssertion( ) AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) SubObjectPropertyOf( ) # Object Property: (causally downstream of) -AnnotationAssertion( ) AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002404") AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of") @@ -17436,8 +16252,6 @@ InverseObjectProperties( (immediately causally downstream of) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002405") AnnotationAssertion( "external") AnnotationAssertion( "immediately_causally_downstream_of") @@ -17451,9 +16265,6 @@ InverseObjectProperties( (indirectly positively regulates) AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -17463,9 +16274,6 @@ TransitiveObjectProperty() # Object Property: (indirectly negatively regulates) AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -17490,14 +16298,11 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") AnnotationAssertion(rdfs:label "causally related to"@en) # Object Property: (causally upstream of) AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002411") AnnotationAssertion( "external") AnnotationAssertion( "causally_upstream_of") @@ -17513,8 +16318,6 @@ TransitiveObjectProperty() # Object Property: (immediately causally upstream of) AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002412") AnnotationAssertion( "external") AnnotationAssertion( "immediately_causally_upstream_of") @@ -17528,8 +16331,6 @@ SubObjectPropertyOf( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") -AnnotationAssertion( ) -AnnotationAssertion( "influences (processual)") AnnotationAssertion( "RO:0002418") AnnotationAssertion( "external") AnnotationAssertion( "affects") @@ -17543,8 +16344,6 @@ TransitiveObjectProperty() # Object Property: (causally downstream of or within) AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "RO:0002427") AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of_or_within") @@ -17557,7 +16356,6 @@ TransitiveObjectProperty() # Object Property: (involved in regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17565,15 +16363,12 @@ SubObjectPropertyOf( (involved in positive regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in positive regulation of") SubObjectPropertyOf( ) # Object Property: (involved in negative regulation of) AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "involved in negative regulation of") SubObjectPropertyOf( ) @@ -17582,8 +16377,6 @@ SubObjectPropertyOf( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") AnnotationAssertion(rdfs:label "involved in or involved in regulation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17591,10 +16384,7 @@ SubObjectPropertyOf( (is active in) -AnnotationAssertion( "A protein that enables activity in a cytosol.") AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") -AnnotationAssertion( ) -AnnotationAssertion( "executes activity in") AnnotationAssertion( "enables activity in") AnnotationAssertion(rdfs:comment "") AnnotationAssertion(rdfs:label "is active in") @@ -17605,11 +16395,6 @@ SubObjectPropertyOf( (contributes to morphology of) AnnotationAssertion( "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002433") -AnnotationAssertion( "uberon") -AnnotationAssertion( "contributes_to_morphology_of") -AnnotationAssertion( "contributes_to_morphology_of") AnnotationAssertion(rdfs:label "contributes to morphology of") SubObjectPropertyOf( ) @@ -17618,13 +16403,10 @@ SubObjectPropertyOf( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") -AnnotationAssertion( ) -AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion( "in pairwise interaction with") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interacts with") AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) SymmetricObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -17632,20 +16414,14 @@ ObjectPropertyRange( (molecularly interacts with) AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") AnnotationAssertion(rdfs:label "molecularly interacts with") AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) SubObjectPropertyOf( ) SymmetricObjectProperty() # Object Property: (phosphorylates) AnnotationAssertion( "Axiomatization to GO to be added later") -AnnotationAssertion( ) -AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") AnnotationAssertion(rdfs:label "phosphorylates") SubObjectPropertyOf( ) @@ -17654,8 +16430,6 @@ SubObjectPropertyOf( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "molecularly controls") AnnotationAssertion(rdfs:label "directly regulates activity of") SubObjectPropertyOf( ) @@ -17667,9 +16441,6 @@ ObjectPropertyRange( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") AnnotationAssertion( "molecularly decreases activity of") AnnotationAssertion(rdfs:label "directly negatively regulates activity of") SubObjectPropertyOf( ) @@ -17680,9 +16451,6 @@ ObjectPropertyRange( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") AnnotationAssertion( "molecularly increases activity of") AnnotationAssertion(rdfs:label "directly positively regulates activity of") SubObjectPropertyOf( ) @@ -17691,22 +16459,12 @@ ObjectPropertyRange( (helper property (not for use in curation)) -AnnotationAssertion( ) -AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") AnnotationAssertion(rdfs:label "helper property (not for use in curation)") # Object Property: (composed primarily of) -AnnotationAssertion( "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'") AnnotationAssertion( "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002473") -AnnotationAssertion( "uberon") -AnnotationAssertion( "composed_primarily_of") AnnotationAssertion( ) -AnnotationAssertion( "composed_primarily_of") AnnotationAssertion(rdfs:label "composed primarily of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17715,7 +16473,6 @@ ObjectPropertyRange( (has part that occurs in) AnnotationAssertion( "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part that occurs in") ObjectPropertyDomain( ) @@ -17723,14 +16480,12 @@ ObjectPropertyRange( (is kinase activity) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "is kinase activity") SubObjectPropertyOf( ) # Object Property: (receives input from) AnnotationAssertion( "See notes for inverse relation") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "receives input from") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -17738,14 +16493,11 @@ InverseObjectProperties( (sends output to) AnnotationAssertion( "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sends output to") SubObjectPropertyOf( ) # Object Property: (relation between physical entity and a process or stage) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.") AnnotationAssertion(rdfs:label "relation between physical entity and a process or stage") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -17753,11 +16505,6 @@ ObjectPropertyRange( (existence starts during) AnnotationAssertion( "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002488") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_during") -AnnotationAssertion( "existence_starts_during") AnnotationAssertion(rdfs:label "existence starts during") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17765,18 +16512,12 @@ SubObjectPropertyOf( (existence starts with) AnnotationAssertion( "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002489") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_with") -AnnotationAssertion( "existence_starts_with") AnnotationAssertion(rdfs:label "existence starts with") SubObjectPropertyOf( ) # Object Property: (existence overlaps) AnnotationAssertion( "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence overlaps") SubObjectPropertyOf( ) @@ -17784,12 +16525,7 @@ SubObjectPropertyOf( (existence starts and ends during) AnnotationAssertion( "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002491") AnnotationAssertion( "exists during") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_and_ends_during") -AnnotationAssertion( "existence_starts_and_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence starts and ends during") SubObjectPropertyOf( ) @@ -17797,14 +16533,7 @@ SubObjectPropertyOf( (existence ends during) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.") AnnotationAssertion( "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002492") -AnnotationAssertion( "ceases_to_exist_during") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_ends_during") -AnnotationAssertion( "existence_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during") SubObjectPropertyOf( ) @@ -17813,11 +16542,6 @@ SubObjectPropertyOf( (existence ends with) AnnotationAssertion( "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002493") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_ends_with") -AnnotationAssertion( "existence_ends_with") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends with") SubObjectPropertyOf( ) @@ -17825,11 +16549,6 @@ SubObjectPropertyOf( (transformation of) AnnotationAssertion( "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002494") -AnnotationAssertion( "uberon") -AnnotationAssertion( "transformation_of") -AnnotationAssertion( "transformation_of") AnnotationAssertion(rdfs:label "transformation of") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -17837,12 +16556,6 @@ TransitiveObjectProperty() # Object Property: (immediate transformation of) AnnotationAssertion( "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002495") -AnnotationAssertion( "uberon") -AnnotationAssertion( "immediate_transformation_of") -AnnotationAssertion( "immediate_transformation_of") AnnotationAssertion(rdfs:label "immediate transformation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17850,11 +16563,6 @@ SubObjectPropertyOf( (existence starts during or after) AnnotationAssertion( "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002496") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_during_or_after") -AnnotationAssertion( "existence_starts_during_or_after") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence starts during or after") SubObjectPropertyOf( ) @@ -17862,11 +16570,6 @@ SubObjectPropertyOf( (existence ends during or before) AnnotationAssertion( "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002497") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_ends_during_or_before") -AnnotationAssertion( "existence_ends_during_or_before") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during or before") SubObjectPropertyOf( ) @@ -17874,7 +16577,6 @@ SubObjectPropertyOf( (causal agent in process) AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causal agent in process") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -17882,9 +16584,6 @@ InverseObjectProperties( (causal relation between processes) AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") AnnotationAssertion(rdfs:label "causal relation between processes") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17892,16 +16591,12 @@ ObjectPropertyRange( (depends on) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "depends on") AnnotationAssertion(rdfs:seeAlso ) # Object Property: (causal relation between entities) AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") AnnotationAssertion(rdfs:label "causal relation between entities") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17909,37 +16604,23 @@ ObjectPropertyRange( (has skeleton) -AnnotationAssertion( "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'") AnnotationAssertion( "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.") -AnnotationAssertion( ) -AnnotationAssertion( "has supporting framework") -AnnotationAssertion( "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).") -AnnotationAssertion( "RO:0002551") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_skeleton") -AnnotationAssertion( "has_skeleton") AnnotationAssertion(rdfs:label "has skeleton") SubObjectPropertyOf( ) InverseObjectProperties( ) AsymmetricObjectProperty() IrreflexiveObjectProperty() ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange(Annotation( "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") ) -ObjectPropertyRange( ) # Object Property: (causally influenced by) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") AnnotationAssertion(rdfs:label "causally influenced by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (interaction relation helper property) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interaction relation helper property") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) @@ -17947,15 +16628,12 @@ SubObjectPropertyOf( (molecular interaction relation helper property) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "molecular interaction relation helper property") SubObjectPropertyOf( ) # Object Property: (results in movement of) AnnotationAssertion( "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c") -AnnotationAssertion( ) -AnnotationAssertion( "") AnnotationAssertion( "RO:0002565") AnnotationAssertion( "external") AnnotationAssertion( "results_in_movement_of") @@ -17969,10 +16647,6 @@ SubObjectPropertyOf( (causally influences) AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") AnnotationAssertion(rdfs:label "causally influences") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17981,8 +16655,6 @@ ObjectPropertyRange( (biomechanically related to) AnnotationAssertion( "A relation that holds between elements of a musculoskeletal system or its analogs.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.") AnnotationAssertion(rdfs:label "biomechanically related to") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -17991,25 +16663,14 @@ ObjectPropertyRange( (has muscle antagonist) AnnotationAssertion( "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.") -AnnotationAssertion( ) -AnnotationAssertion( "Wikipedia:Antagonist_(muscle)") -AnnotationAssertion( "RO:0002568") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_muscle_antagonist") -AnnotationAssertion( "has_muscle_antagonist") AnnotationAssertion(rdfs:label "has muscle antagonist") SubObjectPropertyOf( ) # Object Property: (has branching part) AnnotationAssertion( "inverse of branching part of") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002569") -AnnotationAssertion( "uberon") -AnnotationAssertion( "has_branching_part") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "has_branching_part") AnnotationAssertion(rdfs:label "has branching part") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -18018,14 +16679,7 @@ TransitiveObjectProperty() # Object Property: (conduit for) AnnotationAssertion( "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.") -AnnotationAssertion( ) -AnnotationAssertion( "UBERON:cjm") -AnnotationAssertion( "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.") -AnnotationAssertion( "RO:0002570") -AnnotationAssertion( "uberon") -AnnotationAssertion( "conduit_for") AnnotationAssertion( ) -AnnotationAssertion( "conduit_for") AnnotationAssertion(rdfs:label "conduit for") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -18034,13 +16688,7 @@ ObjectPropertyRange( (lumen of) AnnotationAssertion( "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002571") -AnnotationAssertion( "uberon") -AnnotationAssertion( "lumen_of") AnnotationAssertion( ) -AnnotationAssertion( "lumen_of") AnnotationAssertion(rdfs:label "lumen of") SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -18048,12 +16696,7 @@ ObjectPropertyRange( (luminal space of) AnnotationAssertion( "s is luminal space of x iff s is lumen_of x and s is an immaterial entity") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002572") -AnnotationAssertion( "uberon") -AnnotationAssertion( "luminal_space_of") AnnotationAssertion( ) -AnnotationAssertion( "luminal_space_of") AnnotationAssertion(rdfs:label "luminal space of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -18061,12 +16704,7 @@ ObjectPropertyDomain( (skeleton of) AnnotationAssertion( "inverse of has skeleton") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002576") -AnnotationAssertion( "uberon") -AnnotationAssertion( "skeleton_of") AnnotationAssertion( ) -AnnotationAssertion( "skeleton_of") AnnotationAssertion(rdfs:label "skeleton of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -18075,10 +16713,6 @@ ObjectPropertyRange( (directly regulates) AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002578") AnnotationAssertion( "external") AnnotationAssertion( "directly_regulates") @@ -18092,9 +16726,7 @@ SubObjectPropertyOf( (has part structure that is capable of) -AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part structure that is capable of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -18143,8 +16775,6 @@ SubObjectPropertyOf( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causal relation between material entity and a process") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -18152,31 +16782,25 @@ ObjectPropertyRange( (capable of regulating) -AnnotationAssertion( "pyrethroid -> growth") AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of regulating") SubObjectPropertyOf( ) # Object Property: (capable of negatively regulating) AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of negatively regulating") SubObjectPropertyOf( ) # Object Property: (capable of positively regulating) -AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of positively regulating") SubObjectPropertyOf( ) # Object Property: (process has causal agent) AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002608") AnnotationAssertion( "external") AnnotationAssertion( "process_has_causal_agent") @@ -18187,9 +16811,6 @@ SubObjectPropertyOf( (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) AnnotationAssertion( "RO:0002629") AnnotationAssertion( "external") AnnotationAssertion( "directly_positively_regulates") @@ -18205,8 +16826,6 @@ SubObjectPropertyOf( (directly negatively regulates) AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002630") AnnotationAssertion( "external") @@ -18222,12 +16841,9 @@ SubObjectPropertyOf( (produces) -AnnotationAssertion( ) AnnotationAssertion( "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0003000") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "produces") AnnotationAssertion( ) AnnotationAssertion( "produces") @@ -18240,12 +16856,9 @@ ObjectPropertyRange( (produced by) -AnnotationAssertion( ) AnnotationAssertion( "a produced_by b iff some process that occurs_in b has_output a.") -AnnotationAssertion( ) AnnotationAssertion( "RO:0003001") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") @@ -18305,7 +16918,6 @@ SubObjectPropertyOf( (acts upstream of or within, positive effect) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) AnnotationAssertion( ) @@ -18326,7 +16938,6 @@ SubObjectPropertyOf( (acts upstream of, positive effect) AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) AnnotationAssertion( ) @@ -18358,7 +16969,6 @@ SubObjectPropertyOf( (causally upstream of or within, positive effect) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") @@ -18368,7 +16978,6 @@ SubObjectPropertyOf( (regulates activity of) AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -18521,7 +17130,6 @@ AnnotationAssertion(rdfs:label "has # Object Property: (has high plasma membrane amount) -AnnotationAssertion( "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')") AnnotationAssertion(Annotation( "PMID:19243617") "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.") AnnotationAssertion( ) AnnotationAssertion( ) @@ -18531,7 +17139,6 @@ ObjectPropertyDomain( (has low plasma membrane amount) -AnnotationAssertion( "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')") AnnotationAssertion(Annotation( "PMID:19243617") "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.") AnnotationAssertion( ) AnnotationAssertion( ) @@ -18541,12 +17148,7 @@ ObjectPropertyDomain( (device utilizes material) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") -AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -18614,22 +17216,18 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "channel_for") AnnotationAssertion(rdfs:label "channel for") -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (channels_from) AnnotationAssertion( "uberon") AnnotationAssertion( "channels_from") AnnotationAssertion(rdfs:label "channels_from") -TransitiveObjectProperty() # Object Property: (channels_into) AnnotationAssertion( "uberon") AnnotationAssertion( "channels_into") AnnotationAssertion(rdfs:label "channels_into") -TransitiveObjectProperty() # Object Property: (distally connected to) @@ -18640,7 +17238,6 @@ AnnotationAssertion(rdfs:label ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) -InverseObjectProperties( ) # Object Property: (extends_fibers_into) @@ -18649,7 +17246,6 @@ AnnotationAssertion( "extends_fibers_into") AnnotationAssertion(rdfs:label "extends_fibers_into") SubObjectPropertyOf( ) -SymmetricObjectProperty() # Object Property: (filtered through) @@ -18666,7 +17262,6 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "indirectly_supplies") AnnotationAssertion(rdfs:label "indirectly_supplies") -TransitiveObjectProperty() # Object Property: (layer part of) @@ -18728,7 +17323,6 @@ AnnotationAssertion( "transitively_anteriorly_connected_to") AnnotationAssertion(rdfs:label "transitively anteriorly connected to") AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^xsd:anyURI) -TransitiveObjectProperty() # Object Property: (transitively distally connected to) @@ -18736,7 +17330,6 @@ AnnotationAssertion( "transitively_distally_connected_to") AnnotationAssertion(rdfs:label "transitively distally connected to") AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^xsd:anyURI) -TransitiveObjectProperty() # Object Property: (transitively proximally connected to) @@ -18744,7 +17337,6 @@ AnnotationAssertion( "transitively_proximally_connected_to") AnnotationAssertion(rdfs:label "transitively proximally connected to") AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^xsd:anyURI) -TransitiveObjectProperty() # Object Property: (trunk_part_of) @@ -20895,7 +19487,7 @@ AnnotationAssertion( "GO:0001956") AnnotationAssertion(rdfs:label "positive regulation of neurotransmitter secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intramembranous ossification) @@ -20929,7 +19521,7 @@ AnnotationAssertion( "GO:0001959") AnnotationAssertion(rdfs:label "regulation of cytokine-mediated signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cytokine-mediated signaling pathway) @@ -20945,7 +19537,7 @@ AnnotationAssertion( "GO:0001960") AnnotationAssertion(rdfs:label "negative regulation of cytokine-mediated signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cytokine-mediated signaling pathway) @@ -20962,7 +19554,7 @@ AnnotationAssertion( "GO:0001961") AnnotationAssertion(rdfs:label "positive regulation of cytokine-mediated signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (synaptic transmission, dopaminergic) @@ -21542,7 +20134,7 @@ AnnotationAssertion( "GO:0002225") AnnotationAssertion(rdfs:label "positive regulation of antimicrobial peptide production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (innate immune response in mucosa) @@ -23965,7 +22557,7 @@ AnnotationAssertion( "GO:0002622") AnnotationAssertion(rdfs:label "regulation of B cell antigen processing and presentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of B cell antigen processing and presentation) @@ -23981,7 +22573,7 @@ AnnotationAssertion( "GO:0002623") AnnotationAssertion(rdfs:label "negative regulation of B cell antigen processing and presentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of B cell antigen processing and presentation) @@ -24009,7 +22601,7 @@ AnnotationAssertion( "GO:0002625") AnnotationAssertion(rdfs:label "regulation of T cell antigen processing and presentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T cell antigen processing and presentation) @@ -24025,7 +22617,7 @@ AnnotationAssertion( "GO:0002626") AnnotationAssertion(rdfs:label "negative regulation of T cell antigen processing and presentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T cell antigen processing and presentation) @@ -24042,7 +22634,7 @@ AnnotationAssertion( "GO:0002627") AnnotationAssertion(rdfs:label "positive regulation of T cell antigen processing and presentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of proteolysis associated with antigen processing and presentation) @@ -24065,7 +22657,7 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of proteolysis associated with antigen processing and presentation) @@ -24081,7 +22673,7 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of granuloma formation) @@ -24090,7 +22682,7 @@ AnnotationAssertion( "GO:0002631") AnnotationAssertion(rdfs:label "regulation of granuloma formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of granuloma formation) @@ -24103,7 +22695,7 @@ AnnotationAssertion( "GO:0002632") AnnotationAssertion(rdfs:label "negative regulation of granuloma formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of granuloma formation) @@ -24117,7 +22709,7 @@ AnnotationAssertion( "GO:0002633") AnnotationAssertion(rdfs:label "positive regulation of granuloma formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of germinal center formation) @@ -24126,7 +22718,7 @@ AnnotationAssertion( "GO:0002634") AnnotationAssertion(rdfs:label "regulation of germinal center formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of germinal center formation) @@ -24222,8 +22814,8 @@ AnnotationAssertion( "GO:0002644") AnnotationAssertion(rdfs:label "negative regulation of tolerance induction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of tolerance induction) @@ -24237,7 +22829,7 @@ AnnotationAssertion( "GO:0002645") AnnotationAssertion(rdfs:label "positive regulation of tolerance induction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of tolerance induction dependent upon immune response) @@ -25371,7 +23963,7 @@ AnnotationAssertion( "GO:0002784") AnnotationAssertion(rdfs:label "regulation of antimicrobial peptide production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of antimicrobial peptide production) @@ -25384,7 +23976,7 @@ AnnotationAssertion( "GO:0002785") AnnotationAssertion(rdfs:label "negative regulation of antimicrobial peptide production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peptide secretion) @@ -25442,7 +24034,7 @@ AnnotationAssertion( "GO:0002794") AnnotationAssertion(rdfs:label "regulation of antimicrobial peptide secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of antimicrobial peptide secretion) @@ -25455,7 +24047,7 @@ AnnotationAssertion( "GO:0002795") AnnotationAssertion(rdfs:label "negative regulation of antimicrobial peptide secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of antimicrobial peptide secretion) @@ -25469,7 +24061,7 @@ AnnotationAssertion( "GO:0002796") AnnotationAssertion(rdfs:label "positive regulation of antimicrobial peptide secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of adaptive immune response) @@ -25685,7 +24277,7 @@ AnnotationAssertion( "GO:0002867") AnnotationAssertion(rdfs:label "regulation of B cell deletion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of B cell deletion) @@ -25702,7 +24294,7 @@ AnnotationAssertion( "negative regulation of B cell deletion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of B cell deletion) @@ -25720,7 +24312,7 @@ AnnotationAssertion( "positive regulation of B cell deletion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (T cell anergy) @@ -25913,7 +24505,7 @@ AnnotationAssertion( "GO:0002905") AnnotationAssertion(rdfs:label "regulation of mature B cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mature B cell apoptotic process) @@ -25941,7 +24533,7 @@ AnnotationAssertion( "GO:0002907") AnnotationAssertion(rdfs:label "positive regulation of mature B cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of lymphocyte anergy) @@ -26420,7 +25012,7 @@ AnnotationAssertion( "GO:0003156") AnnotationAssertion(rdfs:label "regulation of animal organ formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocardium development) @@ -29139,7 +27731,7 @@ AnnotationAssertion( "GO:0005319") AnnotationAssertion(rdfs:label "lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurotransmitter transmembrane transporter activity) @@ -29150,7 +27742,7 @@ AnnotationAssertion( "neurotransmitter transporter activity") AnnotationAssertion( "GO:0005326") AnnotationAssertion(rdfs:label "neurotransmitter transmembrane transporter activity") -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) @@ -30585,7 +29177,7 @@ AnnotationAssertion( "GO:0006446") AnnotationAssertion(rdfs:label "regulation of translational initiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of translational elongation) @@ -30594,7 +29186,7 @@ AnnotationAssertion( "GO:0006448") AnnotationAssertion(rdfs:label "regulation of translational elongation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of translational termination) @@ -30603,7 +29195,7 @@ AnnotationAssertion( "GO:0006449") AnnotationAssertion(rdfs:label "regulation of translational termination") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein phosphorylation) @@ -32068,7 +30660,7 @@ AnnotationAssertion( "GO:0007088") AnnotationAssertion(rdfs:label "regulation of mitotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nuclear migration) @@ -33278,7 +31870,7 @@ AnnotationAssertion( "GO:0007558") AnnotationAssertion(rdfs:label "regulation of juvenile hormone secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (imaginal disc morphogenesis) @@ -34052,7 +32644,7 @@ AnnotationAssertion( "GO:0008320") AnnotationAssertion(rdfs:label "protein transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (monoatomic cation transmembrane transporter activity) @@ -34195,14 +32787,13 @@ AnnotationAssertion(Annotation(rdfs:label "RhBG mediates ammonium effflux out of AnnotationAssertion(Annotation(rdfs:label "RhCG mediates ammonium efflux out of kidney collecting duct cells") "Reactome:R-HSA-446277") AnnotationAssertion(Annotation(rdfs:label "RhBG mediates ammonium influx into kidney collecting duct cells") "Reactome:R-HSA-446278") AnnotationAssertion(Annotation(rdfs:label "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)") "Reactome:R-HSA-5623051") -AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/23129") "TC:1.A.11") AnnotationAssertion( "molecular_function") AnnotationAssertion( "ammonia transmembrane transporter activity") AnnotationAssertion( "ammonium channel activity") AnnotationAssertion( "GO:0008519") AnnotationAssertion(rdfs:label "ammonium transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (G protein-coupled peptide receptor activity) @@ -36000,7 +34591,7 @@ AnnotationAssertion( "GO:0010632") AnnotationAssertion(rdfs:label "regulation of epithelial cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of epithelial cell migration) @@ -36009,7 +34600,7 @@ AnnotationAssertion( "GO:0010633") AnnotationAssertion(rdfs:label "negative regulation of epithelial cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of epithelial cell migration) @@ -36313,7 +34904,7 @@ AnnotationAssertion( "GO:0010718") AnnotationAssertion(rdfs:label "positive regulation of epithelial to mesenchymal transition") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of epithelial to mesenchymal transition) @@ -36322,7 +34913,7 @@ AnnotationAssertion( "GO:0010719") AnnotationAssertion(rdfs:label "negative regulation of epithelial to mesenchymal transition") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cell development) @@ -36819,7 +35410,7 @@ AnnotationAssertion( "GO:0010968") AnnotationAssertion(rdfs:label "regulation of microtubule nucleation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transport along microtubule) @@ -37217,7 +35808,7 @@ AnnotationAssertion( "GO:0014041") AnnotationAssertion(rdfs:label "regulation of neuron maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of neuron maturation) @@ -37369,7 +35960,7 @@ AnnotationAssertion( "regulation of acetylcholine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of acetylcholine secretion, neurotransmission) @@ -37384,7 +35975,7 @@ AnnotationAssertion( "positive regulation of acetylcholine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of acetylcholine secretion, neurotransmission) @@ -37398,7 +35989,7 @@ AnnotationAssertion( "negative regulation of acetylcholine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of dopamine secretion) @@ -37549,7 +36140,7 @@ AnnotationAssertion( "GO:0014717") AnnotationAssertion(rdfs:label "regulation of satellite cell activation involved in skeletal muscle regeneration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of satellite cell activation involved in skeletal muscle regeneration) @@ -37558,7 +36149,7 @@ AnnotationAssertion( "GO:0014718") AnnotationAssertion(rdfs:label "positive regulation of satellite cell activation involved in skeletal muscle regeneration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle satellite cell activation) @@ -37662,7 +36253,7 @@ AnnotationAssertion( "GO:0014807") AnnotationAssertion(rdfs:label "regulation of somitogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle cell migration) @@ -38074,7 +36665,7 @@ AnnotationAssertion( "GO:0015075") AnnotationAssertion(rdfs:label "monoatomic ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (calcium ion transmembrane transporter activity) @@ -38125,7 +36716,7 @@ AnnotationAssertion( "GO:0015144") AnnotationAssertion(rdfs:label "carbohydrate transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hexose transmembrane transporter activity) @@ -38136,7 +36727,7 @@ AnnotationAssertion( "GO:0015149") AnnotationAssertion(rdfs:label "hexose transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (polysaccharide transmembrane transporter activity) @@ -38206,7 +36797,7 @@ AnnotationAssertion( "GO:0015171") AnnotationAssertion(rdfs:label "amino acid transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acidic amino acid transmembrane transporter activity) @@ -39316,7 +37907,7 @@ AnnotationAssertion( "GO:0017148") AnnotationAssertion(rdfs:label "negative regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of exocytosis) @@ -41594,7 +40185,7 @@ AnnotationAssertion( "negative regulation of cell motility involved in cerebral cortex radial glia guided migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (substrate-independent telencephalic tangential migration) @@ -42579,7 +41170,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (signal transduction involved in regulation of gene expression) @@ -45065,7 +43656,7 @@ AnnotationAssertion( "GO:0031334") AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of vesicle fusion) @@ -45347,7 +43938,7 @@ AnnotationAssertion( "GO:0031641") AnnotationAssertion(rdfs:label "regulation of myelination") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of myelination) @@ -45827,7 +44418,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of deoxyribonuclease activity) @@ -45854,7 +44445,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of nuclease activity) @@ -45870,7 +44461,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of deoxyribonuclease activity) @@ -46094,7 +44685,7 @@ AnnotationAssertion(Annotation( "GO:0032231") AnnotationAssertion(rdfs:label "regulation of actin filament bundle assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of actin filament bundle assembly) @@ -46122,7 +44713,7 @@ AnnotationAssertion( "positive regulation of actin filament bundle assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of nucleobase-containing compound transport) @@ -46240,7 +44831,7 @@ AnnotationAssertion( "GO:0032276") AnnotationAssertion(rdfs:label "regulation of gonadotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of gonadotropin secretion) @@ -46254,7 +44845,7 @@ AnnotationAssertion( "GO:0032277") AnnotationAssertion(rdfs:label "negative regulation of gonadotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of gonadotropin secretion) @@ -46269,7 +44860,7 @@ AnnotationAssertion( "GO:0032278") AnnotationAssertion(rdfs:label "positive regulation of gonadotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myelin assembly) @@ -46592,7 +45183,7 @@ AnnotationAssertion( "regulation of lipid transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of lipid transport) @@ -46607,7 +45198,7 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lipid transport) @@ -46623,7 +45214,7 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of intracellular lipid transport) @@ -46795,7 +45386,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of ion transmembrane transporter activity) @@ -46811,7 +45402,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lysosome localization) @@ -48216,7 +46807,7 @@ AnnotationAssertion(Annotation( "GO:0032820") AnnotationAssertion(rdfs:label "regulation of natural killer cell proliferation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of natural killer cell proliferation involved in immune response) @@ -48231,7 +46822,7 @@ AnnotationAssertion(Annotation( "GO:0032821") AnnotationAssertion(rdfs:label "negative regulation of natural killer cell proliferation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of natural killer cell proliferation involved in immune response) @@ -48317,7 +46908,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of natural killer cell differentiation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of natural killer cell differentiation involved in immune response) @@ -48335,7 +46926,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "positive regulation of natural killer cell differentiation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation) @@ -48398,7 +46989,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response) @@ -48417,7 +47008,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response) @@ -48437,7 +47028,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerulus development) @@ -49034,7 +47625,7 @@ AnnotationAssertion( "regulation of mast cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mast cell activation involved in immune response) @@ -49044,7 +47635,7 @@ AnnotationAssertion(Annotation( "GO:0033007") AnnotationAssertion(rdfs:label "negative regulation of mast cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mast cell activation involved in immune response) @@ -49054,7 +47645,7 @@ AnnotationAssertion(Annotation( "GO:0033008") AnnotationAssertion(rdfs:label "positive regulation of mast cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mast cell homeostasis) @@ -49086,7 +47677,7 @@ AnnotationAssertion( "GO:0033025") AnnotationAssertion(rdfs:label "regulation of mast cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mast cell apoptotic process) @@ -49100,7 +47691,7 @@ AnnotationAssertion( "GO:0033026") AnnotationAssertion(rdfs:label "negative regulation of mast cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mast cell apoptotic process) @@ -49115,7 +47706,7 @@ AnnotationAssertion( "GO:0033027") AnnotationAssertion(rdfs:label "positive regulation of mast cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myeloid cell apoptotic process) @@ -49136,7 +47727,7 @@ AnnotationAssertion( "GO:0033029") AnnotationAssertion(rdfs:label "regulation of neutrophil apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of neutrophil apoptotic process) @@ -49164,7 +47755,7 @@ AnnotationAssertion( "GO:0033031") AnnotationAssertion(rdfs:label "positive regulation of neutrophil apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of myeloid cell apoptotic process) @@ -49385,7 +47976,7 @@ AnnotationAssertion( "GO:0033088") AnnotationAssertion(rdfs:label "negative regulation of immature T cell proliferation in thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T cell differentiation in thymus) @@ -49484,7 +48075,7 @@ AnnotationAssertion( "GO:0033157") AnnotationAssertion(rdfs:label "regulation of intracellular protein transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (melanosome membrane) @@ -49886,7 +48477,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of kinase activity) @@ -49901,7 +48492,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of luteinizing hormone secretion) @@ -50107,7 +48698,7 @@ AnnotationAssertion( "GO:0034107") AnnotationAssertion(rdfs:label "negative regulation of erythrocyte clearance") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of erythrocyte clearance) @@ -50119,7 +48710,7 @@ AnnotationAssertion( "GO:0034108") AnnotationAssertion(rdfs:label "positive regulation of erythrocyte clearance") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate transmembrane transport) @@ -50271,7 +48862,7 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) # Class: (regulation of ascospore formation) @@ -51113,7 +49704,7 @@ AnnotationAssertion( "GO:0035203") AnnotationAssertion(rdfs:label "regulation of lamellocyte differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of lamellocyte differentiation) @@ -53472,7 +52063,7 @@ AnnotationAssertion( "regulation of meiotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of development, heterochronic) @@ -54844,7 +53435,7 @@ AnnotationAssertion( "GO:0042478") AnnotationAssertion(rdfs:label "regulation of eye photoreceptor cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of eye photoreceptor cell development) @@ -54859,7 +53450,7 @@ AnnotationAssertion( "GO:0042479") AnnotationAssertion(rdfs:label "positive regulation of eye photoreceptor cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of eye photoreceptor cell development) @@ -56166,7 +54757,7 @@ AnnotationAssertion( "GO:0043254") AnnotationAssertion(rdfs:label "regulation of protein-containing complex assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of carbohydrate biosynthetic process) @@ -56358,7 +54949,7 @@ AnnotationAssertion( "GO:0043304") AnnotationAssertion(rdfs:label "regulation of mast cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mast cell degranulation) @@ -56372,7 +54963,7 @@ AnnotationAssertion( "GO:0043305") AnnotationAssertion(rdfs:label "negative regulation of mast cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mast cell degranulation) @@ -56416,8 +55007,8 @@ AnnotationAssertion( "GO:0043309") AnnotationAssertion(rdfs:label "regulation of eosinophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of eosinophil degranulation) @@ -56431,8 +55022,8 @@ AnnotationAssertion( "GO:0043310") AnnotationAssertion(rdfs:label "negative regulation of eosinophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of eosinophil degranulation) @@ -56447,8 +55038,8 @@ AnnotationAssertion( "GO:0043311") AnnotationAssertion(rdfs:label "positive regulation of eosinophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neutrophil degranulation) @@ -56471,8 +55062,8 @@ AnnotationAssertion( "GO:0043313") AnnotationAssertion(rdfs:label "regulation of neutrophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of neutrophil degranulation) @@ -56486,8 +55077,8 @@ AnnotationAssertion( "GO:0043314") AnnotationAssertion(rdfs:label "negative regulation of neutrophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of neutrophil degranulation) @@ -56502,8 +55093,8 @@ AnnotationAssertion( "GO:0043315") AnnotationAssertion(rdfs:label "positive regulation of neutrophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cytotoxic T cell degranulation) @@ -56537,7 +55128,7 @@ AnnotationAssertion( "GO:0043317") AnnotationAssertion(rdfs:label "regulation of cytotoxic T cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cytotoxic T cell degranulation) @@ -56557,7 +55148,7 @@ AnnotationAssertion( "GO:0043318") AnnotationAssertion(rdfs:label "negative regulation of cytotoxic T cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cytotoxic T cell degranulation) @@ -56578,7 +55169,7 @@ AnnotationAssertion( "GO:0043319") AnnotationAssertion(rdfs:label "positive regulation of cytotoxic T cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (natural killer cell degranulation) @@ -56604,7 +55195,7 @@ AnnotationAssertion( "GO:0043321") AnnotationAssertion(rdfs:label "regulation of natural killer cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of natural killer cell degranulation) @@ -56620,7 +55211,7 @@ AnnotationAssertion( "GO:0043322") AnnotationAssertion(rdfs:label "negative regulation of natural killer cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of natural killer cell degranulation) @@ -56637,7 +55228,7 @@ AnnotationAssertion( "GO:0043323") AnnotationAssertion(rdfs:label "positive regulation of natural killer cell degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enucleate erythrocyte differentiation) @@ -56869,7 +55460,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "regulation of memory T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of memory T cell differentiation) @@ -56887,7 +55478,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of memory T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of memory T cell differentiation) @@ -56906,7 +55497,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "positive regulation of memory T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pre-T cell receptor complex) @@ -57038,7 +55629,7 @@ AnnotationAssertion( "GO:0043417") AnnotationAssertion(rdfs:label "negative regulation of skeletal muscle tissue regeneration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (response to peptide hormone) @@ -57250,7 +55841,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (insulin binding) @@ -57573,7 +56164,7 @@ AnnotationAssertion( "GO:0043941") AnnotationAssertion(rdfs:label "positive regulation of sexual sporulation resulting in formation of a cellular spore") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of sexual sporulation resulting in formation of a cellular spore) @@ -57582,7 +56173,7 @@ AnnotationAssertion( "GO:0043942") AnnotationAssertion(rdfs:label "negative regulation of sexual sporulation resulting in formation of a cellular spore") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glucan metabolic process) @@ -58338,7 +56929,7 @@ AnnotationAssertion( "GO:0045124") AnnotationAssertion(rdfs:label "regulation of bone resorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meiotic chromosome segregation) @@ -58444,8 +57035,8 @@ AnnotationAssertion( "GO:0045191") AnnotationAssertion(rdfs:label "regulation of isotype switching") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (establishment or maintenance of neuroblast polarity) @@ -59150,7 +57741,7 @@ AnnotationAssertion( "GO:0045592") AnnotationAssertion(rdfs:label "regulation of cumulus cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cumulus cell differentiation) @@ -59541,7 +58132,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "regulation of T-helper cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper cell differentiation) @@ -59556,7 +58147,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of T-helper cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper cell differentiation) @@ -59572,7 +58163,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "positive regulation of T-helper cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of T-helper 1 cell differentiation) @@ -59583,7 +58174,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "regulation of T-helper 1 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper 1 cell differentiation) @@ -59598,7 +58189,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of T-helper 1 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper 1 cell differentiation) @@ -59624,7 +58215,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "regulation of T-helper 2 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper 2 cell differentiation) @@ -59639,7 +58230,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "negative regulation of T-helper 2 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper 2 cell differentiation) @@ -59655,7 +58246,7 @@ AnnotationAssertion( "Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.") AnnotationAssertion(rdfs:label "positive regulation of T-helper 2 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of mechanoreceptor differentiation) @@ -59733,7 +58324,7 @@ AnnotationAssertion( "GO:0045637") AnnotationAssertion(rdfs:label "regulation of myeloid cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of myeloid cell differentiation) @@ -60293,7 +58884,7 @@ AnnotationAssertion( "GO:0045700") AnnotationAssertion(rdfs:label "regulation of spermatid nuclear differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of spermatid nuclear differentiation) @@ -60308,7 +58899,7 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of spermatid nuclear differentiation) @@ -60426,7 +59017,7 @@ AnnotationAssertion( "GO:0045727") AnnotationAssertion(rdfs:label "positive regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory burst at fertilization) @@ -60671,7 +59262,7 @@ AnnotationAssertion( "GO:0045779") AnnotationAssertion(rdfs:label "negative regulation of bone resorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of bone resorption) @@ -60855,10 +59446,10 @@ AnnotationAssertion( "GO:0045829") AnnotationAssertion(rdfs:label "negative regulation of isotype switching") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of isotype switching) @@ -60875,10 +59466,10 @@ AnnotationAssertion( "GO:0045830") AnnotationAssertion(rdfs:label "positive regulation of isotype switching") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of lipid metabolic process) @@ -60956,7 +59547,7 @@ AnnotationAssertion( "negative regulation of mitotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mitotic nuclear division) @@ -61038,7 +59629,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of protein kinase activity) @@ -61673,7 +60264,7 @@ AnnotationAssertion( "GO:0045972") AnnotationAssertion(rdfs:label "negative regulation of juvenile hormone secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of juvenile hormone secretion) @@ -62146,7 +60737,7 @@ AnnotationAssertion( "GO:0046627") AnnotationAssertion(rdfs:label "negative regulation of insulin receptor signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of insulin receptor signaling pathway) @@ -62161,7 +60752,7 @@ AnnotationAssertion( "GO:0046628") AnnotationAssertion(rdfs:label "positive regulation of insulin receptor signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gamma-delta T cell activation) @@ -63045,7 +61636,7 @@ AnnotationAssertion( "GO:0046928") AnnotationAssertion(rdfs:label "regulation of neurotransmitter secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of neurotransmitter secretion) @@ -63318,7 +61909,7 @@ AnnotationAssertion( "GO:0048209") AnnotationAssertion(rdfs:label "regulation of vesicle targeting, to, from or within Golgi") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male gamete generation) @@ -64364,7 +62955,7 @@ AnnotationAssertion( "GO:0048633") AnnotationAssertion(rdfs:label "positive regulation of skeletal muscle tissue growth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of muscle organ development) @@ -64385,7 +62976,7 @@ AnnotationAssertion( "GO:0048635") AnnotationAssertion(rdfs:label "negative regulation of muscle organ development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of muscle organ development) @@ -64399,7 +62990,7 @@ AnnotationAssertion( "GO:0048636") AnnotationAssertion(rdfs:label "positive regulation of muscle organ development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of developmental growth) @@ -64788,7 +63379,7 @@ AnnotationAssertion( "GO:0048742") AnnotationAssertion(rdfs:label "regulation of skeletal muscle fiber development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of skeletal muscle fiber development) @@ -65121,7 +63712,7 @@ AnnotationAssertion( "GO:0048814") AnnotationAssertion(rdfs:label "regulation of dendrite morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of hair follicle maturation) @@ -66385,7 +64976,7 @@ AnnotationAssertion( "GO:0050770") AnnotationAssertion(rdfs:label "regulation of axonogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of axonogenesis) @@ -66399,7 +64990,7 @@ AnnotationAssertion( "negative regulation of axonogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of axonogenesis) @@ -66449,7 +65040,7 @@ AnnotationAssertion( "positive regulation of dendrite morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of immune response) @@ -67232,7 +65823,7 @@ AnnotationAssertion( "GO:0050920") AnnotationAssertion(rdfs:label "regulation of chemotaxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of chemotaxis) @@ -67246,7 +65837,7 @@ AnnotationAssertion( "GO:0050921") AnnotationAssertion(rdfs:label "positive regulation of chemotaxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of chemotaxis) @@ -67259,7 +65850,7 @@ AnnotationAssertion( "GO:0050922") AnnotationAssertion(rdfs:label "negative regulation of chemotaxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pigment cell differentiation) @@ -68939,7 +67530,7 @@ AnnotationAssertion( "GO:0051282") AnnotationAssertion(rdfs:label "regulation of sequestering of calcium ion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of sequestering of calcium ion) @@ -68960,7 +67551,7 @@ AnnotationAssertion( "GO:0051283") AnnotationAssertion(rdfs:label "negative regulation of sequestering of calcium ion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of sequestering of calcium ion) @@ -68982,7 +67573,7 @@ AnnotationAssertion( "GO:0051284") AnnotationAssertion(rdfs:label "positive regulation of sequestering of calcium ion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell division) @@ -69354,7 +67945,7 @@ AnnotationAssertion( "GO:0051459") AnnotationAssertion(rdfs:label "regulation of corticotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of corticotropin secretion) @@ -69373,7 +67964,7 @@ AnnotationAssertion( "GO:0051460") AnnotationAssertion(rdfs:label "negative regulation of corticotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of corticotropin secretion) @@ -69393,7 +67984,7 @@ AnnotationAssertion( "GO:0051461") AnnotationAssertion(rdfs:label "positive regulation of corticotropin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vesicle fusion with vacuole) @@ -70287,8 +68878,8 @@ AnnotationAssertion( "GO:0051797") AnnotationAssertion(rdfs:label "regulation of hair follicle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of hair follicle development) @@ -70677,7 +69268,7 @@ AnnotationAssertion( "GO:0051969") AnnotationAssertion(rdfs:label "regulation of transmission of nerve impulse") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of transmission of nerve impulse) @@ -70930,7 +69521,7 @@ AnnotationAssertion( "GO:0055018") AnnotationAssertion(rdfs:label "regulation of cardiac muscle fiber development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cardiac muscle fiber development) @@ -70962,7 +69553,7 @@ AnnotationAssertion( "positive regulation of cardiac muscle fiber development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiac muscle tissue growth) @@ -70971,7 +69562,7 @@ AnnotationAssertion( "GO:0055021") AnnotationAssertion(rdfs:label "regulation of cardiac muscle tissue growth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cardiac muscle tissue growth) @@ -71398,7 +69989,7 @@ AnnotationAssertion(Annotation( "GO:0060043") AnnotationAssertion(rdfs:label "regulation of cardiac muscle cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cardiac muscle cell proliferation) @@ -71410,7 +70001,7 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cardiac muscle cell proliferation) @@ -71422,7 +70013,7 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart contraction) @@ -72120,7 +70711,7 @@ AnnotationAssertion( "regulation of respiratory burst involved in inflammatory response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of respiratory burst involved in inflammatory response) @@ -72226,7 +70817,7 @@ AnnotationAssertion( "GO:0060281") AnnotationAssertion(rdfs:label "regulation of oocyte development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of oocyte development) @@ -72283,7 +70874,7 @@ AnnotationAssertion( "GO:0060295") AnnotationAssertion(rdfs:label "regulation of cilium movement involved in cell motility") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of sarcomere organization) @@ -72293,7 +70884,7 @@ AnnotationAssertion( "GO:0060297") AnnotationAssertion(rdfs:label "regulation of sarcomere organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of sarcomere organization) @@ -72303,8 +70894,8 @@ AnnotationAssertion( "GO:0060298") AnnotationAssertion(rdfs:label "positive regulation of sarcomere organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of sarcomere organization) @@ -72314,9 +70905,9 @@ AnnotationAssertion( "GO:0060299") AnnotationAssertion(rdfs:label "negative regulation of sarcomere organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of blood vessel remodeling) @@ -72707,7 +71298,7 @@ AnnotationAssertion( "regulation of heart growth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of heart growth) @@ -73227,7 +71818,7 @@ AnnotationAssertion(Annotation( "GO:0060491") AnnotationAssertion(rdfs:label "regulation of cell projection assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell-cell signaling involved in lung development) @@ -74119,7 +72710,7 @@ AnnotationAssertion( "GO:0060685") AnnotationAssertion(rdfs:label "regulation of prostatic bud formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of prostatic bud formation) @@ -74603,7 +73194,7 @@ AnnotationAssertion( "positive regulation of epithelial cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of epithelial cell proliferation involved in prostate gland development) @@ -74615,8 +73206,8 @@ AnnotationAssertion( "negative regulation of epithelial cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal cell proliferation involved in prostate gland development) @@ -75721,7 +74312,7 @@ AnnotationAssertion( "GO:0061050") AnnotationAssertion(rdfs:label "regulation of cell growth involved in cardiac muscle cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cell growth involved in cardiac muscle cell development) @@ -75907,7 +74498,7 @@ AnnotationAssertion( "GO:0061075") AnnotationAssertion(rdfs:label "positive regulation of neural retina development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of neural retina development) @@ -75918,7 +74509,7 @@ AnnotationAssertion( "GO:0061076") AnnotationAssertion(rdfs:label "negative regulation of neural retina development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right horn of sinus venosus development) @@ -75965,7 +74556,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein tyrosine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of protein tyrosine kinase activity) @@ -76288,7 +74879,7 @@ AnnotationAssertion( "GO:0061168") AnnotationAssertion(rdfs:label "regulation of hair follicle placode formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of hair placode formation) @@ -76309,7 +74900,7 @@ AnnotationAssertion( "GO:0061170") AnnotationAssertion(rdfs:label "negative regulation of hair follicle placode formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of insulin secretion involved in cellular response to glucose stimulus) @@ -76321,7 +74912,7 @@ AnnotationAssertion( "GO:0061178") AnnotationAssertion(rdfs:label "regulation of insulin secretion involved in cellular response to glucose stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of insulin secretion involved in cellular response to glucose stimulus) @@ -76334,7 +74925,7 @@ AnnotationAssertion(Annotation( "GO:0061179") AnnotationAssertion(rdfs:label "negative regulation of insulin secretion involved in cellular response to glucose stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland epithelium development) @@ -78465,7 +77056,7 @@ AnnotationAssertion( "GO:0061888") AnnotationAssertion(rdfs:label "regulation of astrocyte activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of astrocyte activation) @@ -78476,8 +77067,8 @@ AnnotationAssertion( "GO:0061889") AnnotationAssertion(rdfs:label "negative regulation of astrocyte activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of astrocyte activation) @@ -78488,8 +77079,8 @@ AnnotationAssertion( "GO:0061890") AnnotationAssertion(rdfs:label "positive regulation of astrocyte activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glial cell activation) @@ -82235,7 +80826,7 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of ureteric bud formation) @@ -82246,7 +80837,7 @@ AnnotationAssertion( "GO:0072107") AnnotationAssertion(rdfs:label "positive regulation of ureteric bud formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis) @@ -82257,7 +80848,7 @@ AnnotationAssertion( "GO:0072108") AnnotationAssertion(rdfs:label "positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular mesangium development) @@ -82872,8 +81463,8 @@ AnnotationAssertion(Annotation( "GO:0072200") AnnotationAssertion(rdfs:label "negative regulation of mesenchymal cell proliferation involved in ureter development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mesenchymal cell proliferation) @@ -84397,7 +82988,7 @@ AnnotationAssertion( "GO:0086004") AnnotationAssertion(rdfs:label "regulation of cardiac muscle cell contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventricular cardiac muscle cell action potential) @@ -84817,7 +83408,7 @@ AnnotationAssertion( "GO:0090063") AnnotationAssertion(rdfs:label "positive regulation of microtubule nucleation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cell cycle process) @@ -85173,7 +83764,7 @@ AnnotationAssertion( "GO:0090192") AnnotationAssertion(rdfs:label "regulation of glomerulus development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of glomerulus development) @@ -85365,7 +83956,7 @@ AnnotationAssertion( "GO:0090299") AnnotationAssertion(rdfs:label "regulation of neural crest formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of neural crest formation) @@ -85429,7 +84020,7 @@ AnnotationAssertion( "GO:0090317") AnnotationAssertion(rdfs:label "negative regulation of intracellular protein transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of superoxide metabolic process) @@ -87259,9 +85850,9 @@ AnnotationAssertion( "GO:0098815") AnnotationAssertion(rdfs:label "modulation of excitatory postsynaptic potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein transport along microtubule) @@ -87388,7 +85979,7 @@ AnnotationAssertion( "GO:0098904") AnnotationAssertion(rdfs:label "regulation of AV node cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of bundle of His cell action potential) @@ -87410,7 +86001,7 @@ AnnotationAssertion( "GO:0098906") AnnotationAssertion(rdfs:label "regulation of Purkinje myocyte action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of SA node cell action potential) @@ -87425,7 +86016,7 @@ AnnotationAssertion( "GO:0098907") AnnotationAssertion(rdfs:label "regulation of SA node cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of neuronal action potential) @@ -87435,7 +86026,7 @@ AnnotationAssertion(Annotation( "GO:0098908") AnnotationAssertion(rdfs:label "regulation of neuronal action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiac muscle cell action potential involved in regulation of contraction) @@ -87458,8 +86049,8 @@ AnnotationAssertion( "GO:0098910") AnnotationAssertion(rdfs:label "regulation of atrial cardiac muscle cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of ventricular cardiac muscle cell action potential) @@ -87470,7 +86061,7 @@ AnnotationAssertion( "GO:0098911") AnnotationAssertion(rdfs:label "regulation of ventricular cardiac muscle cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterograde trans-synaptic signaling) @@ -87593,7 +86184,7 @@ AnnotationAssertion( "regulation of postsynaptic neurotransmitter receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (exocytic insertion of neurotransmitter receptor to postsynaptic membrane) @@ -87900,10 +86491,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell-cell signaling via exosome) @@ -88002,7 +86593,7 @@ AnnotationAssertion( "regulation of presynapse organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of postsynapse organization) @@ -88016,7 +86607,7 @@ AnnotationAssertion( "regulation of postsynapse organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of trans-synaptic signaling) @@ -88697,7 +87288,7 @@ AnnotationAssertion( "GO:0106135") AnnotationAssertion(rdfs:label "negative regulation of cardiac muscle cell contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of vesicle fusion with Golgi apparatus) @@ -88799,7 +87390,7 @@ AnnotationAssertion( "regulation of actin filament organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of blood vessel endothelial cell differentiation) @@ -88867,7 +87458,7 @@ AnnotationAssertion( "GO:0110079") AnnotationAssertion(rdfs:label "regulation of placenta blood vessel development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of placenta blood vessel development) @@ -88959,7 +87550,7 @@ AnnotationAssertion( "GO:0110110") AnnotationAssertion(rdfs:label "positive regulation of animal organ morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of animal organ morphogenesis) @@ -88970,7 +87561,7 @@ AnnotationAssertion( "GO:0110111") AnnotationAssertion(rdfs:label "negative regulation of animal organ morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of lipid transporter activity) @@ -88982,7 +87573,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lipid transporter activity) @@ -88994,7 +87585,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of lipid transporter activity) @@ -89006,7 +87597,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of compound eye photoreceptor cell differentiation) @@ -89193,7 +87784,7 @@ AnnotationAssertion( "GO:0120034") AnnotationAssertion(rdfs:label "positive regulation of plasma membrane bounded cell projection assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of plasma membrane bounded cell projection organization) @@ -90268,7 +88859,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of postsynapse assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visual system development) @@ -90864,7 +89455,7 @@ AnnotationAssertion( "GO:1900118") AnnotationAssertion(rdfs:label "negative regulation of execution phase of apoptosis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of execution phase of apoptosis) @@ -90879,7 +89470,7 @@ AnnotationAssertion( "GO:1900119") AnnotationAssertion(rdfs:label "positive regulation of execution phase of apoptosis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of receptor binding) @@ -91060,8 +89651,8 @@ AnnotationAssertion( "GO:1900133") AnnotationAssertion(rdfs:label "regulation of renin secretion into blood stream") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of renin secretion into blood stream) @@ -91792,7 +90383,7 @@ AnnotationAssertion( "GO:1900248") AnnotationAssertion(rdfs:label "negative regulation of cytoplasmic translational elongation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cytoplasmic translational elongation) @@ -92060,7 +90651,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of calcium ion transmembrane transporter activity) @@ -92076,7 +90667,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of calcium ion transmembrane transporter activity) @@ -92092,7 +90683,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate derivative metabolic process) @@ -92272,7 +90863,7 @@ AnnotationAssertion( "negative regulation of trophoblast cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of trophoblast cell migration) @@ -92288,8 +90879,8 @@ AnnotationAssertion( "positive regulation of trophoblast cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest cell migration involved in autonomic nervous system development) @@ -92330,7 +90921,7 @@ AnnotationAssertion( "GO:1901191") AnnotationAssertion(rdfs:label "negative regulation of formation of translation initiation ternary complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of formation of translation initiation ternary complex) @@ -92383,7 +90974,7 @@ AnnotationAssertion( "GO:1901201") AnnotationAssertion(rdfs:label "regulation of extracellular matrix assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of extracellular matrix assembly) @@ -92412,7 +91003,7 @@ AnnotationAssertion( "GO:1901203") AnnotationAssertion(rdfs:label "positive regulation of extracellular matrix assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiac chamber formation) @@ -92462,7 +91053,7 @@ AnnotationAssertion( "GO:1901212") AnnotationAssertion(rdfs:label "positive regulation of cardiac chamber formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiac chamber morphogenesis) @@ -92474,7 +91065,7 @@ AnnotationAssertion( "GO:1901219") AnnotationAssertion(rdfs:label "regulation of cardiac chamber morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cardiac chamber morphogenesis) @@ -92537,7 +91128,7 @@ AnnotationAssertion( "GO:1901247") AnnotationAssertion(rdfs:label "negative regulation of lung ciliated cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lung ciliated cell differentiation) @@ -92552,7 +91143,7 @@ AnnotationAssertion( "GO:1901248") AnnotationAssertion(rdfs:label "positive regulation of lung ciliated cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of lung goblet cell differentiation) @@ -92583,7 +91174,7 @@ AnnotationAssertion( "GO:1901250") AnnotationAssertion(rdfs:label "negative regulation of lung goblet cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lung goblet cell differentiation) @@ -92603,7 +91194,7 @@ AnnotationAssertion( "GO:1901251") AnnotationAssertion(rdfs:label "positive regulation of lung goblet cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate derivative transport) @@ -92891,7 +91482,7 @@ AnnotationAssertion( "GO:1901505") AnnotationAssertion(rdfs:label "carbohydrate derivative transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of endothelial tube morphogenesis) @@ -92983,7 +91574,7 @@ AnnotationAssertion( "GO:1901550") AnnotationAssertion(rdfs:label "regulation of endothelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of endothelial cell development) @@ -92998,7 +91589,7 @@ AnnotationAssertion( "GO:1901551") AnnotationAssertion(rdfs:label "negative regulation of endothelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of endothelial cell development) @@ -93399,7 +91990,7 @@ AnnotationAssertion( "GO:1901627") AnnotationAssertion(rdfs:label "negative regulation of postsynaptic membrane organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of postsynaptic membrane organization) @@ -93515,7 +92106,7 @@ AnnotationAssertion( "GO:1901667") AnnotationAssertion(rdfs:label "negative regulation of skeletal muscle satellite cell activation involved in skeletal muscle regeneration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of compound eye retinal cell apoptotic process) @@ -94007,7 +92598,7 @@ AnnotationAssertion( "GO:1901888") AnnotationAssertion(rdfs:label "regulation of cell junction assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cell junction assembly) @@ -94036,7 +92627,7 @@ AnnotationAssertion( "GO:1901890") AnnotationAssertion(rdfs:label "positive regulation of cell junction assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dense core granule transport) @@ -94254,7 +92845,7 @@ AnnotationAssertion( "GO:1902034") AnnotationAssertion(rdfs:label "negative regulation of hematopoietic stem cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of hematopoietic stem cell proliferation) @@ -94493,7 +93084,7 @@ AnnotationAssertion( "GO:1902115") AnnotationAssertion(rdfs:label "regulation of organelle assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of organelle assembly) @@ -94522,7 +93113,7 @@ AnnotationAssertion( "GO:1902117") AnnotationAssertion(rdfs:label "positive regulation of organelle assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of keratinocyte apoptotic process) @@ -95032,7 +93623,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of water channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of water channel activity) @@ -95054,7 +93645,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of water channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of stem cell population maintenance) @@ -96070,7 +94661,7 @@ AnnotationAssertion( "GO:1902747") AnnotationAssertion(rdfs:label "negative regulation of lens fiber cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lens fiber cell differentiation) @@ -96090,7 +94681,7 @@ AnnotationAssertion( "GO:1902748") AnnotationAssertion(rdfs:label "positive regulation of lens fiber cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of chondrocyte development) @@ -96440,7 +95031,7 @@ AnnotationAssertion(Annotation( "GO:1902867") AnnotationAssertion(rdfs:label "negative regulation of retina development in camera-type eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of retina development in camera-type eye) @@ -96465,7 +95056,7 @@ AnnotationAssertion(Annotation( "GO:1902868") AnnotationAssertion(rdfs:label "positive regulation of retina development in camera-type eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of amacrine cell differentiation) @@ -96628,7 +95219,7 @@ AnnotationAssertion( "GO:1902908") AnnotationAssertion(rdfs:label "regulation of melanosome transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of melanosome transport) @@ -96643,7 +95234,7 @@ AnnotationAssertion( "GO:1902909") AnnotationAssertion(rdfs:label "negative regulation of melanosome transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of melanosome transport) @@ -96658,7 +95249,7 @@ AnnotationAssertion( "GO:1902910") AnnotationAssertion(rdfs:label "positive regulation of melanosome transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein kinase complex) @@ -97055,7 +95646,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of acetylcholine-gated cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of acetylcholine-gated cation channel activity) @@ -97700,7 +96291,7 @@ AnnotationAssertion( "An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype") AnnotationAssertion(rdfs:label "regulation of glutamate secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of glutamate secretion, neurotransmission) @@ -97716,7 +96307,7 @@ AnnotationAssertion( "An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype") AnnotationAssertion(rdfs:label "negative regulation of glutamate secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of glutamate secretion, neurotransmission) @@ -97732,7 +96323,7 @@ AnnotationAssertion( "An example of this is Rab3gap1 in mouse (Q80UJ7) in PMID:16782817 inferred from mutant phenotype") AnnotationAssertion(rdfs:label "positive regulation of glutamate secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of regulated secretory pathway) @@ -97822,7 +96413,7 @@ AnnotationAssertion( "GO:1903317") AnnotationAssertion(rdfs:label "regulation of protein maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of protein maturation) @@ -97837,7 +96428,7 @@ AnnotationAssertion( "GO:1903318") AnnotationAssertion(rdfs:label "negative regulation of protein maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of protein maturation) @@ -97852,7 +96443,7 @@ AnnotationAssertion( "GO:1903319") AnnotationAssertion(rdfs:label "positive regulation of protein maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of vacuolar transport) @@ -98477,7 +97068,7 @@ AnnotationAssertion( "GO:1903543") AnnotationAssertion(rdfs:label "positive regulation of exosomal secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of extracellular exosome assembly) @@ -98759,8 +97350,8 @@ AnnotationAssertion( "GO:1903581") AnnotationAssertion(rdfs:label "regulation of basophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of basophil degranulation) @@ -98775,8 +97366,8 @@ AnnotationAssertion( "GO:1903582") AnnotationAssertion(rdfs:label "negative regulation of basophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of basophil degranulation) @@ -98791,8 +97382,8 @@ AnnotationAssertion( "GO:1903583") AnnotationAssertion(rdfs:label "positive regulation of basophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of histamine secretion by mast cell) @@ -98803,8 +97394,8 @@ AnnotationAssertion( "GO:1903593") AnnotationAssertion(rdfs:label "regulation of histamine secretion by mast cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of histamine secretion by mast cell) @@ -98819,7 +97410,7 @@ AnnotationAssertion( "GO:1903594") AnnotationAssertion(rdfs:label "negative regulation of histamine secretion by mast cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of histamine secretion by mast cell) @@ -98834,9 +97425,9 @@ AnnotationAssertion( "GO:1903595") AnnotationAssertion(rdfs:label "positive regulation of histamine secretion by mast cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of DNA catabolic process) @@ -99441,7 +98032,7 @@ AnnotationAssertion( "GO:1903904") AnnotationAssertion(rdfs:label "negative regulation of establishment of T cell polarity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of establishment of T cell polarity) @@ -99486,7 +98077,7 @@ AnnotationAssertion( "GO:1903905") AnnotationAssertion(rdfs:label "positive regulation of establishment of T cell polarity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (estradiol binding) @@ -99592,7 +98183,7 @@ AnnotationAssertion( "GO:1903946") AnnotationAssertion(rdfs:label "negative regulation of ventricular cardiac muscle cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of ventricular cardiac muscle cell action potential) @@ -99607,7 +98198,7 @@ AnnotationAssertion( "GO:1903947") AnnotationAssertion(rdfs:label "positive regulation of ventricular cardiac muscle cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of atrial cardiac muscle cell action potential) @@ -99622,7 +98213,7 @@ AnnotationAssertion( "GO:1903948") AnnotationAssertion(rdfs:label "negative regulation of atrial cardiac muscle cell action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of atrial cardiac muscle cell action potential) @@ -99744,7 +98335,7 @@ AnnotationAssertion( "GO:1903978") AnnotationAssertion(rdfs:label "regulation of microglial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of microglial cell activation) @@ -99759,7 +98350,7 @@ AnnotationAssertion( "GO:1903979") AnnotationAssertion(rdfs:label "negative regulation of microglial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of microglial cell activation) @@ -99774,7 +98365,7 @@ AnnotationAssertion( "GO:1903980") AnnotationAssertion(rdfs:label "positive regulation of microglial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iron ion export across plasma membrane) @@ -100283,7 +98874,7 @@ AnnotationAssertion( "GO:1904073") AnnotationAssertion(rdfs:label "regulation of trophectodermal cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of trophectodermal cell proliferation) @@ -100468,8 +99059,8 @@ AnnotationAssertion( "GO:1904145") AnnotationAssertion(rdfs:label "negative regulation of meiotic cell cycle process involved in oocyte maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of meiotic cell cycle process involved in oocyte maturation) @@ -100484,7 +99075,7 @@ AnnotationAssertion( "GO:1904146") AnnotationAssertion(rdfs:label "positive regulation of meiotic cell cycle process involved in oocyte maturation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of microglial cell mediated cytotoxicity) @@ -100632,7 +99223,7 @@ AnnotationAssertion(Annotation( "GO:1904178") AnnotationAssertion(rdfs:label "negative regulation of adipose tissue development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of adipose tissue development) @@ -100652,7 +99243,7 @@ AnnotationAssertion(Annotation( "GO:1904179") AnnotationAssertion(rdfs:label "positive regulation of adipose tissue development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cholangiocyte apoptotic process) @@ -100881,7 +99472,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of iron ion transmembrane transporter activity) @@ -100908,7 +99499,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of iron ion transmembrane transporter activity) @@ -100936,7 +99527,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of Schwann cell chemotaxis) @@ -101162,7 +99753,7 @@ AnnotationAssertion( "GO:1904341") AnnotationAssertion(rdfs:label "regulation of colon smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of colon smooth muscle contraction) @@ -101177,7 +99768,7 @@ AnnotationAssertion( "GO:1904342") AnnotationAssertion(rdfs:label "negative regulation of colon smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of colon smooth muscle contraction) @@ -101192,7 +99783,7 @@ AnnotationAssertion( "GO:1904343") AnnotationAssertion(rdfs:label "positive regulation of colon smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of gastric mucosal blood circulation) @@ -101252,7 +99843,7 @@ AnnotationAssertion( "GO:1904347") AnnotationAssertion(rdfs:label "regulation of small intestine smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of small intestine smooth muscle contraction) @@ -101267,7 +99858,7 @@ AnnotationAssertion( "GO:1904348") AnnotationAssertion(rdfs:label "negative regulation of small intestine smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of small intestine smooth muscle contraction) @@ -101282,7 +99873,7 @@ AnnotationAssertion( "GO:1904349") AnnotationAssertion(rdfs:label "positive regulation of small intestine smooth muscle contraction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of protein catabolic process in the vacuole) @@ -101633,7 +100224,7 @@ AnnotationAssertion( "GO:1904413") AnnotationAssertion(rdfs:label "negative regulation of cardiac ventricle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cardiac ventricle development) @@ -101648,7 +100239,7 @@ AnnotationAssertion( "GO:1904414") AnnotationAssertion(rdfs:label "positive regulation of cardiac ventricle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of calcium ion transmembrane transport) @@ -101687,7 +100278,7 @@ AnnotationAssertion( "GO:1904438") AnnotationAssertion(rdfs:label "regulation of iron ion import across plasma membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of iron ion import across plasma membrane) @@ -101751,7 +100342,7 @@ AnnotationAssertion(Annotation( "GO:1904456") AnnotationAssertion(rdfs:label "negative regulation of neuronal action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of neuronal action potential) @@ -101771,7 +100362,7 @@ AnnotationAssertion(Annotation( "GO:1904457") AnnotationAssertion(rdfs:label "positive regulation of neuronal action potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal gland development) @@ -102009,7 +100600,7 @@ AnnotationAssertion( "GO:1904624") AnnotationAssertion(rdfs:label "regulation of glycine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of glycine secretion, neurotransmission) @@ -102024,7 +100615,7 @@ AnnotationAssertion( "GO:1904625") AnnotationAssertion(rdfs:label "negative regulation of glycine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of glycine secretion, neurotransmission) @@ -102039,7 +100630,7 @@ AnnotationAssertion( "GO:1904626") AnnotationAssertion(rdfs:label "positive regulation of glycine secretion, neurotransmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of podocyte apoptotic process) @@ -102265,7 +100856,7 @@ AnnotationAssertion( "GO:1904654") AnnotationAssertion(rdfs:label "negative regulation of lung alveolus development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of lung alveolus development) @@ -102290,7 +100881,7 @@ AnnotationAssertion( "GO:1904655") AnnotationAssertion(rdfs:label "positive regulation of lung alveolus development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glucose transmembrane transport) @@ -102902,7 +101493,7 @@ AnnotationAssertion( "U4PR86 in PMID:22801495 inferred from mutant phenotype") AnnotationAssertion(rdfs:label "negative regulation of apoptotic process involved in development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of apoptotic process involved in development) @@ -103058,7 +101649,7 @@ AnnotationAssertion( "U4PR86 in PMID:22801495 inferred from mutant phenotype") AnnotationAssertion(rdfs:label "positive regulation of apoptotic process involved in development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of apoptotic process involved in development) @@ -103098,7 +101689,7 @@ AnnotationAssertion( "Q10943 in PMID:22801495, inferred from mutant phenotype") AnnotationAssertion(rdfs:label "regulation of apoptotic process involved in development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of protein localization to nucleolus) @@ -103558,7 +102149,7 @@ AnnotationAssertion( "GO:1904838") AnnotationAssertion(rdfs:label "regulation of male germ-line stem cell asymmetric division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of male germ-line stem cell asymmetric division) @@ -103578,8 +102169,8 @@ AnnotationAssertion( "GO:1904839") AnnotationAssertion(rdfs:label "negative regulation of male germ-line stem cell asymmetric division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of male germ-line stem cell asymmetric division) @@ -103599,7 +102190,7 @@ AnnotationAssertion( "GO:1904840") AnnotationAssertion(rdfs:label "positive regulation of male germ-line stem cell asymmetric division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (excitatory synapse assembly) @@ -103851,7 +102442,7 @@ AnnotationAssertion( "GO:1904943") AnnotationAssertion(rdfs:label "negative regulation of cardiac ventricle formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cardiac ventricle formation) @@ -104269,7 +102860,7 @@ AnnotationAssertion( "GO:1905079") AnnotationAssertion(rdfs:label "regulation of cerebellar neuron development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cerebellar neuron development) @@ -104284,7 +102875,7 @@ AnnotationAssertion( "GO:1905080") AnnotationAssertion(rdfs:label "negative regulation of cerebellar neuron development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cerebellar neuron development) @@ -104299,7 +102890,7 @@ AnnotationAssertion( "GO:1905081") AnnotationAssertion(rdfs:label "positive regulation of cerebellar neuron development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of pulmonary blood vessel remodeling) @@ -104417,7 +103008,7 @@ AnnotationAssertion(Annotation( "GO:1905140") AnnotationAssertion(rdfs:label "regulation of apical ectodermal ridge formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of apical ectodermal ridge formation) @@ -104447,7 +103038,7 @@ AnnotationAssertion(Annotation( "GO:1905141") AnnotationAssertion(rdfs:label "negative regulation of apical ectodermal ridge formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of apical ectodermal ridge formation) @@ -104474,7 +103065,7 @@ AnnotationAssertion(Annotation( "GO:1905142") AnnotationAssertion(rdfs:label "positive regulation of apical ectodermal ridge formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (response to acetylcholine) @@ -104780,7 +103371,7 @@ AnnotationAssertion( "GO:1905208") AnnotationAssertion(rdfs:label "negative regulation of cardiocyte differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cardiocyte differentiation) @@ -104805,7 +103396,7 @@ AnnotationAssertion( "GO:1905209") AnnotationAssertion(rdfs:label "positive regulation of cardiocyte differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mitotic chromosome condensation) @@ -104868,7 +103459,7 @@ AnnotationAssertion( "GO:1905219") AnnotationAssertion(rdfs:label "regulation of platelet formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of platelet formation) @@ -104907,7 +103498,7 @@ AnnotationAssertion( "GO:1905221") AnnotationAssertion(rdfs:label "positive regulation of platelet formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicardium morphogenesis) @@ -105002,7 +103593,7 @@ AnnotationAssertion( "GO:1905269") AnnotationAssertion(rdfs:label "positive regulation of chromatin organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Meynert cell differentiation) @@ -105128,7 +103719,7 @@ AnnotationAssertion( "GO:1905293") AnnotationAssertion(rdfs:label "negative regulation of neural crest cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of neural crest cell differentiation) @@ -105143,7 +103734,7 @@ AnnotationAssertion( "GO:1905294") AnnotationAssertion(rdfs:label "positive regulation of neural crest cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of intestinal epithelial cell development) @@ -105154,7 +103745,7 @@ AnnotationAssertion( "GO:1905298") AnnotationAssertion(rdfs:label "regulation of intestinal epithelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of intestinal epithelial cell development) @@ -105169,8 +103760,8 @@ AnnotationAssertion( "GO:1905299") AnnotationAssertion(rdfs:label "negative regulation of intestinal epithelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of intestinal epithelial cell development) @@ -105185,7 +103776,7 @@ AnnotationAssertion( "GO:1905300") AnnotationAssertion(rdfs:label "positive regulation of intestinal epithelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiac myofibril assembly) @@ -105199,7 +103790,7 @@ AnnotationAssertion(Annotation( "GO:1905304") AnnotationAssertion(rdfs:label "regulation of cardiac myofibril assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cardiac myofibril assembly) @@ -105229,7 +103820,7 @@ AnnotationAssertion(Annotation( "GO:1905305") AnnotationAssertion(rdfs:label "negative regulation of cardiac myofibril assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cardiac myofibril assembly) @@ -106576,7 +105167,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of presynapse assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of presynapse assembly) @@ -106601,7 +105192,7 @@ AnnotationAssertion( "GO:1905607") AnnotationAssertion(rdfs:label "negative regulation of presynapse assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of presynapse assembly) @@ -107009,7 +105600,7 @@ AnnotationAssertion( "GO:1905787") AnnotationAssertion(rdfs:label "regulation of detection of mechanical stimulus involved in sensory perception of touch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of detection of mechanical stimulus involved in sensory perception of touch) @@ -107054,7 +105645,7 @@ AnnotationAssertion( "GO:1905788") AnnotationAssertion(rdfs:label "negative regulation of detection of mechanical stimulus involved in sensory perception of touch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of detection of mechanical stimulus involved in sensory perception of touch) @@ -107099,7 +105690,7 @@ AnnotationAssertion( "GO:1905789") AnnotationAssertion(rdfs:label "positive regulation of detection of mechanical stimulus involved in sensory perception of touch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (excitatory synapse pruning) @@ -107270,7 +105861,7 @@ AnnotationAssertion( "GO:1905833") AnnotationAssertion(rdfs:label "negative regulation of microtubule nucleation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epididymis development) @@ -107364,7 +105955,7 @@ AnnotationAssertion( "GO:1905879") AnnotationAssertion(rdfs:label "regulation of oogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of oogenesis) @@ -107384,7 +105975,7 @@ AnnotationAssertion( "GO:1905880") AnnotationAssertion(rdfs:label "negative regulation of oogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of oogenesis) @@ -107404,7 +105995,7 @@ AnnotationAssertion( "GO:1905881") AnnotationAssertion(rdfs:label "positive regulation of oogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of smooth muscle tissue development) @@ -107467,7 +106058,7 @@ AnnotationAssertion( "GO:1905903") AnnotationAssertion(rdfs:label "negative regulation of mesoderm formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mesoderm formation) @@ -107482,7 +106073,7 @@ AnnotationAssertion( "GO:1905904") AnnotationAssertion(rdfs:label "positive regulation of mesoderm formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of calcium ion export across plasma membrane) @@ -107627,7 +106218,7 @@ AnnotationAssertion( "GO:1905936") AnnotationAssertion(rdfs:label "regulation of germ cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of germ cell proliferation) @@ -107642,7 +106233,7 @@ AnnotationAssertion( "GO:1905937") AnnotationAssertion(rdfs:label "negative regulation of germ cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of germ cell proliferation) @@ -107657,7 +106248,7 @@ AnnotationAssertion( "GO:1905938") AnnotationAssertion(rdfs:label "positive regulation of germ cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of gonad development) @@ -107688,7 +106279,7 @@ AnnotationAssertion( "GO:1905940") AnnotationAssertion(rdfs:label "negative regulation of gonad development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of gonad development) @@ -107708,7 +106299,7 @@ AnnotationAssertion( "GO:1905941") AnnotationAssertion(rdfs:label "positive regulation of gonad development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of response to calcium ion) @@ -107836,7 +106427,7 @@ AnnotationAssertion( "GO:1905955") AnnotationAssertion(rdfs:label "negative regulation of endothelial tube morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of endothelial tube morphogenesis) @@ -107851,7 +106442,7 @@ AnnotationAssertion( "GO:1905956") AnnotationAssertion(rdfs:label "positive regulation of endothelial tube morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glutamatergic neuron differentiation) @@ -108094,7 +106685,7 @@ AnnotationAssertion( "regulation of cytoplasmic translational termination") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebum secreting cell proliferation) @@ -108386,7 +106977,7 @@ AnnotationAssertion( "GO:2000004") AnnotationAssertion(rdfs:label "regulation of metanephric S-shaped body morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of metanephric S-shaped body morphogenesis) @@ -108407,7 +106998,7 @@ AnnotationAssertion( "GO:2000006") AnnotationAssertion(rdfs:label "regulation of metanephric comma-shaped body morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of metanephric comma-shaped body morphogenesis) @@ -108521,7 +107112,7 @@ AnnotationAssertion( "GO:2000062") AnnotationAssertion(rdfs:label "negative regulation of ureter smooth muscle cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of ureter smooth muscle cell differentiation) @@ -108532,7 +107123,7 @@ AnnotationAssertion( "GO:2000063") AnnotationAssertion(rdfs:label "positive regulation of ureter smooth muscle cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of defense response to insect) @@ -108583,7 +107174,7 @@ AnnotationAssertion( "GO:2000077") AnnotationAssertion(rdfs:label "negative regulation of type B pancreatic cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of type B pancreatic cell development) @@ -108596,8 +107187,8 @@ AnnotationAssertion( "GO:2000078") AnnotationAssertion(rdfs:label "positive regulation of type B pancreatic cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of mesenchymal to epithelial transition involved in mesonephros morphogenesis) @@ -108641,7 +107232,7 @@ AnnotationAssertion( "GO:2000087") AnnotationAssertion(rdfs:label "regulation of mesonephric glomerulus development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of mesonephric glomerulus development) @@ -108890,7 +107481,7 @@ AnnotationAssertion( "GO:2000174") AnnotationAssertion(rdfs:label "regulation of pro-T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of pro-T cell differentiation) @@ -108902,7 +107493,7 @@ AnnotationAssertion( "GO:2000175") AnnotationAssertion(rdfs:label "negative regulation of pro-T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of pro-T cell differentiation) @@ -108914,7 +107505,7 @@ AnnotationAssertion( "GO:2000176") AnnotationAssertion(rdfs:label "positive regulation of pro-T cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of neural precursor cell proliferation) @@ -109131,7 +107722,7 @@ AnnotationAssertion( "GO:2000227") AnnotationAssertion(rdfs:label "negative regulation of pancreatic A cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of pancreatic A cell differentiation) @@ -109143,7 +107734,7 @@ AnnotationAssertion( "GO:2000228") AnnotationAssertion(rdfs:label "positive regulation of pancreatic A cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of pancreatic stellate cell proliferation) @@ -109220,8 +107811,8 @@ AnnotationAssertion( "GO:2000248") AnnotationAssertion(rdfs:label "negative regulation of establishment or maintenance of neuroblast polarity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of male germ cell proliferation) @@ -109432,7 +108023,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of synaptic vesicle exocytosis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of synaptic vesicle exocytosis) @@ -109453,7 +108044,7 @@ AnnotationAssertion( "GO:2000302") AnnotationAssertion(rdfs:label "positive regulation of synaptic vesicle exocytosis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of T-helper 17 type immune response) @@ -109498,7 +108089,7 @@ AnnotationAssertion(Annotation( "GO:2000319") AnnotationAssertion(rdfs:label "regulation of T-helper 17 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper 17 cell differentiation) @@ -109510,7 +108101,7 @@ AnnotationAssertion(Annotation( "GO:2000320") AnnotationAssertion(rdfs:label "negative regulation of T-helper 17 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper 17 cell differentiation) @@ -109522,7 +108113,7 @@ AnnotationAssertion(Annotation( "GO:2000321") AnnotationAssertion(rdfs:label "positive regulation of T-helper 17 cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of glucocorticoid receptor signaling pathway) @@ -110023,7 +108614,7 @@ AnnotationAssertion(Annotation( "GO:2000463") AnnotationAssertion(rdfs:label "positive regulation of excitatory postsynaptic potential") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of astrocyte chemotaxis) @@ -110458,7 +109049,7 @@ AnnotationAssertion( "GO:2000551") AnnotationAssertion(rdfs:label "regulation of T-helper 2 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper 2 cell cytokine production) @@ -110470,7 +109061,7 @@ AnnotationAssertion( "GO:2000552") AnnotationAssertion(rdfs:label "negative regulation of T-helper 2 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper 2 cell cytokine production) @@ -110482,7 +109073,7 @@ AnnotationAssertion( "GO:2000553") AnnotationAssertion(rdfs:label "positive regulation of T-helper 2 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of T-helper 1 cell cytokine production) @@ -110494,7 +109085,7 @@ AnnotationAssertion( "GO:2000554") AnnotationAssertion(rdfs:label "regulation of T-helper 1 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of T-helper 1 cell cytokine production) @@ -110506,7 +109097,7 @@ AnnotationAssertion( "GO:2000555") AnnotationAssertion(rdfs:label "negative regulation of T-helper 1 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of T-helper 1 cell cytokine production) @@ -110518,7 +109109,7 @@ AnnotationAssertion( "GO:2000556") AnnotationAssertion(rdfs:label "positive regulation of T-helper 1 cell cytokine production") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of CD4-positive, alpha-beta T cell proliferation) @@ -110647,7 +109238,7 @@ AnnotationAssertion(Annotation( "GO:2000595") AnnotationAssertion(rdfs:label "regulation of optic nerve formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of optic nerve formation) @@ -111041,7 +109632,7 @@ AnnotationAssertion(Annotation( "GO:2000729") AnnotationAssertion(rdfs:label "positive regulation of mesenchymal cell proliferation involved in ureter development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of stem cell differentiation) @@ -111162,8 +109753,8 @@ AnnotationAssertion( "GO:2000791") AnnotationAssertion(rdfs:label "negative regulation of mesenchymal cell proliferation involved in lung development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of mesenchymal cell proliferation involved in lung development) @@ -111174,8 +109765,8 @@ AnnotationAssertion( "GO:2000792") AnnotationAssertion(rdfs:label "positive regulation of mesenchymal cell proliferation involved in lung development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell proliferation involved in heart valve development) @@ -112096,7 +110687,7 @@ AnnotationAssertion(Annotation( "GO:2001191") AnnotationAssertion(rdfs:label "regulation of gamma-delta T cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of gamma-delta T cell activation involved in immune response) @@ -112111,7 +110702,7 @@ AnnotationAssertion(Annotation( "GO:2001192") AnnotationAssertion(rdfs:label "negative regulation of gamma-delta T cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of gamma-delta T cell activation involved in immune response) @@ -112126,7 +110717,7 @@ AnnotationAssertion(Annotation( "GO:2001193") AnnotationAssertion(rdfs:label "positive regulation of gamma-delta T cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of dendritic cell differentiation) @@ -112179,7 +110770,7 @@ AnnotationAssertion( "GO:2001205") AnnotationAssertion(rdfs:label "negative regulation of osteoclast development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of osteoclast development) @@ -112191,7 +110782,7 @@ AnnotationAssertion( "GO:2001206") AnnotationAssertion(rdfs:label "positive regulation of osteoclast development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of vasculogenesis) @@ -112277,7 +110868,7 @@ AnnotationAssertion( "GO:2001233") AnnotationAssertion(rdfs:label "regulation of apoptotic signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of apoptotic signaling pathway) @@ -112289,7 +110880,7 @@ AnnotationAssertion( "GO:2001234") AnnotationAssertion(rdfs:label "negative regulation of apoptotic signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of apoptotic signaling pathway) @@ -112301,7 +110892,7 @@ AnnotationAssertion( "GO:2001235") AnnotationAssertion(rdfs:label "positive regulation of apoptotic signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of chromosome organization) @@ -112343,7 +110934,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cation channel activity) @@ -112357,7 +110948,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cation channel activity) @@ -112371,60 +110962,43 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (data item) -AnnotationAssertion( "data item"@en) AnnotationAssertion(rdfs:label "data item"@en) SubClassOf( ) # Class: (information content entity) -AnnotationAssertion( "information content entity"@en) AnnotationAssertion(rdfs:label "information content entity"@en) SubClassOf( ) # Class: (curation status specification) -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) AnnotationAssertion(rdfs:label "curation status specification"@en) EquivalentClasses( ObjectOneOf( )) SubClassOf( ) # Class: (data about an ontology part) -AnnotationAssertion( "data about an ontology part"@en) AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "data about an ontology part"@en) SubClassOf( ) # Class: (obsolescence reason specification) -AnnotationAssertion( "obsolescence reason specification"@en) -AnnotationAssertion( ) AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) EquivalentClasses( ObjectOneOf( )) SubClassOf( ) # Class: (denotator type) -AnnotationAssertion( "denotator type"@en) -AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) AnnotationAssertion(rdfs:label "denotator type"@en) EquivalentClasses( ObjectOneOf( )) SubClassOf( ) @@ -112441,7 +111015,6 @@ AnnotationAssertion(rdfs:label "roo # Class: (Muridae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:15371245") AnnotationAssertion( "ncbi_taxonomy") @@ -112451,10 +111024,9 @@ SubClassOf( (Mus ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Mus") -AnnotationAssertion(Annotation( ) "mice") +AnnotationAssertion(Annotation( ) "mice") AnnotationAssertion(Annotation( ) "mouse") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:10088") @@ -112463,7 +111035,6 @@ SubClassOf( (Mus musculus) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:85055") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "house mouse") @@ -112475,7 +111046,6 @@ SubClassOf( (Teleostomi) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:117570") @@ -112484,7 +111054,6 @@ SubClassOf( (Euteleostomi) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:40673") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "bony vertebrates") @@ -112495,7 +111064,6 @@ SubClassOf( (Chromadorea) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:27837") AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") @@ -112506,7 +111074,6 @@ SubClassOf( (Ecdysozoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:1206794") @@ -112515,7 +111082,6 @@ SubClassOf( (Lophotrochozoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:1206795") @@ -112524,7 +111090,6 @@ SubClassOf( (Zygnemophyceae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "gamophytes") AnnotationAssertion( "ncbi_taxonomy") @@ -112538,7 +111103,6 @@ SubClassOf( (Streptophytina) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "charophyte/embryophyte group") AnnotationAssertion( "ncbi_taxonomy") @@ -112558,7 +111122,6 @@ SubClassOf( (Archelosauria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:22839753") AnnotationAssertion( "PMID:25450099") @@ -112571,7 +111134,6 @@ SubClassOf( (Dipnotetrapodomorpha) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:1338369") @@ -112580,7 +111142,6 @@ SubClassOf( (Eumycetozoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11062127") AnnotationAssertion( "PMID:9342353") @@ -112594,7 +111155,6 @@ SubClassOf( (Boreoeutheria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11743200") AnnotationAssertion( "PMID:11791233") @@ -112606,7 +111166,6 @@ SubClassOf( (Acrogymnospermae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:1437180") @@ -112615,7 +111174,6 @@ SubClassOf( (Gnetidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:1445966") @@ -112624,7 +111182,6 @@ SubClassOf( (Saccharomycotina) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "true yeasts") AnnotationAssertion( "ncbi_taxonomy") @@ -112634,7 +111191,6 @@ SubClassOf( (Schizosaccharomycetes) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Archiascomycota") @@ -112644,7 +111200,6 @@ SubClassOf( (Actinopteri) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:186623") @@ -112653,7 +111208,6 @@ SubClassOf( (Myomorpha) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "mice and others") AnnotationAssertion( "ncbi_taxonomy") @@ -112664,7 +111218,6 @@ SubClassOf( (Callithrix ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Callithrix") AnnotationAssertion( "ncbi_taxonomy") @@ -112674,7 +111227,6 @@ SubClassOf( (Pancrustacea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:10874751") AnnotationAssertion( "PMID:11557979") @@ -112685,7 +111237,6 @@ SubClassOf( (Mandibulata) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11557979") AnnotationAssertion( "PMID:9727836") @@ -112697,7 +111248,6 @@ SubClassOf( (Bacteria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:11") AnnotationAssertion( "PMID:10425795") AnnotationAssertion( "PMID:10425796") @@ -112741,7 +111291,6 @@ SubClassOf( (Dictyosteliaceae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:29367151") AnnotationAssertion( "ncbi_taxonomy") @@ -112751,7 +111300,6 @@ SubClassOf( (Dictyosteliales) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:29367151") AnnotationAssertion( "ncbi_taxonomy") @@ -112761,7 +111309,6 @@ SubClassOf( (Homininae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Homo/Pan/Gorilla group") @@ -112771,7 +111318,6 @@ SubClassOf( (Archaea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:11") AnnotationAssertion( "PMID:10425795") AnnotationAssertion( "PMID:10425796") @@ -112817,7 +111363,6 @@ SubClassOf( (Rhabditina) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2301116") @@ -112826,7 +111371,6 @@ SubClassOf( (Rhabditomorpha) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2301119") @@ -112835,7 +111379,6 @@ SubClassOf( (Evosea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2605435") @@ -112844,7 +111387,6 @@ SubClassOf( (Discoba) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2611352") @@ -112853,7 +111395,6 @@ SubClassOf( (Zygnematophycidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2684882") @@ -112862,7 +111403,6 @@ SubClassOf( (Spiralia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:2697495") @@ -112871,7 +111411,6 @@ SubClassOf( (Sar) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "SAR supergroup") @@ -112881,7 +111420,6 @@ SubClassOf( (Eukaryota) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:23020233") AnnotationAssertion( "PMID:30257078") @@ -112899,7 +111437,6 @@ SubClassOf( (Laurasiatheria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11214318") AnnotationAssertion( "PMID:11214319") @@ -112911,7 +111448,6 @@ SubClassOf( (Euarchontoglires) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11214319") AnnotationAssertion( "PMID:12082125") @@ -112924,7 +111460,6 @@ SubClassOf( (Glires) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11214319") AnnotationAssertion( "PMID:12082125") @@ -112937,7 +111472,6 @@ SubClassOf( (Simiiformes) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Anthropoidea") @@ -112947,7 +111481,6 @@ SubClassOf( (Hominoidea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "ape") AnnotationAssertion(Annotation( ) "apes") @@ -112958,7 +111491,6 @@ SubClassOf( (Zygnematales) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:3176") @@ -112967,7 +111499,6 @@ SubClassOf( (Embryophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "higher plants") AnnotationAssertion(Annotation( ) "land plants") @@ -112980,7 +111511,6 @@ SubClassOf( (Teleostei) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "teleost fishes") AnnotationAssertion( "ncbi_taxonomy") @@ -112990,7 +111520,6 @@ SubClassOf( (Tetrapoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "tetrapods") AnnotationAssertion( "ncbi_taxonomy") @@ -113000,7 +111529,6 @@ SubClassOf( (Amniota) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "amniotes") AnnotationAssertion( "ncbi_taxonomy") @@ -113010,7 +111538,6 @@ SubClassOf( (Theria ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Theria") AnnotationAssertion( "ncbi_taxonomy") @@ -113020,7 +111547,6 @@ SubClassOf( (Sauria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "diapsids") AnnotationAssertion( "ncbi_taxonomy") @@ -113031,7 +111557,6 @@ SubClassOf( (Dictyostelia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11062127") AnnotationAssertion( "PMID:29367151") @@ -113048,7 +111573,6 @@ SubClassOf( (Viridiplantae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:16248873") AnnotationAssertion( "PMID:30257078") @@ -113065,7 +111589,6 @@ SubClassOf( (Coniferophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "conifers") @@ -113075,7 +111598,6 @@ SubClassOf( (Opisthokonta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Fungi/Metazoa group") @@ -113086,7 +111608,6 @@ SubClassOf( (Metazoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "metazoans") AnnotationAssertion(Annotation( ) "multicellular animals") @@ -113099,7 +111620,6 @@ SubClassOf( (Bilateria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:33213") @@ -113108,7 +111628,6 @@ SubClassOf( (Protostomia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:33317") @@ -113117,7 +111636,6 @@ SubClassOf( (Deuterostomia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "deuterostomes") AnnotationAssertion( "ncbi_taxonomy") @@ -113127,7 +111645,6 @@ SubClassOf( (Carnivora) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "carnivores") AnnotationAssertion( "ncbi_taxonomy") @@ -113138,7 +111655,6 @@ SubClassOf( (Alveolata) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "alveolates") AnnotationAssertion( "ncbi_taxonomy") @@ -113148,7 +111664,6 @@ SubClassOf( (Euglenozoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Euglenozoans") @@ -113158,7 +111673,6 @@ SubClassOf( (Gnetopsida) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Chlamydospermopsida") @@ -113169,7 +111683,6 @@ SubClassOf( (Muroidea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:15019624") AnnotationAssertion( "PMID:15371245") @@ -113180,7 +111693,6 @@ SubClassOf( (Gnetales) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:3378") @@ -113189,7 +111701,6 @@ SubClassOf( (Felinae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:338152") @@ -113198,7 +111709,6 @@ SubClassOf( (Magnoliopsida) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:25249442") AnnotationAssertion(Annotation( ) "angiosperms") @@ -113213,7 +111723,6 @@ SubClassOf( (Schizosaccharomycetales) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:34346") @@ -113222,7 +111731,6 @@ SubClassOf( (Streptophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:35493") @@ -113231,7 +111739,6 @@ SubClassOf( (Haplorrhini) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:376913") @@ -113240,7 +111747,6 @@ SubClassOf( (Feliformia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:379583") @@ -113249,7 +111755,6 @@ SubClassOf( (Glaucocystophyceae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "glaucocystophytes") AnnotationAssertion( "ncbi_taxonomy") @@ -113262,7 +111767,6 @@ SubClassOf( (Murinae) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:109679") AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") @@ -113272,7 +111776,6 @@ SubClassOf( (Mammalia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "mammals") AnnotationAssertion( "ncbi_taxonomy") @@ -113283,7 +111786,6 @@ SubClassOf( (Neopterygii) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Neopterygi") @@ -113293,7 +111795,6 @@ SubClassOf( (Dinosauria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "dinosaur") AnnotationAssertion(Annotation( ) "dinosaurs") @@ -113304,7 +111805,6 @@ SubClassOf( (Saurischia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:436489") @@ -113313,7 +111813,6 @@ SubClassOf( (Theropoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:436491") @@ -113322,7 +111821,6 @@ SubClassOf( (Coelurosauria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:436492") @@ -113331,7 +111829,6 @@ SubClassOf( (Dikarya) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:15689432") AnnotationAssertion( "PMID:16151185") @@ -113345,7 +111842,6 @@ SubClassOf( (Taphrinomycotina) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:451866") @@ -113354,7 +111850,6 @@ SubClassOf( (Fungi) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:11062127") AnnotationAssertion( "PMID:12684019") @@ -113367,7 +111862,6 @@ SubClassOf( (Ascomycota) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:17572334") AnnotationAssertion(Annotation( ) "ascomycetes") @@ -113380,7 +111874,6 @@ SubClassOf( (Saccharomycetes) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Hemiascomycetes") @@ -113390,7 +111883,6 @@ SubClassOf( (Saccharomycetales) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Endomycetales") @@ -113401,7 +111893,6 @@ SubClassOf( (Saccharomycetaceae) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:221665") AnnotationAssertion( "NCBITaxon:44280") AnnotationAssertion( "GC_ID:1") @@ -113412,7 +111903,6 @@ SubClassOf( (Schizosaccharomycetaceae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "fission yeasts") AnnotationAssertion( "ncbi_taxonomy") @@ -113423,7 +111913,6 @@ SubClassOf( (Schizosaccharomyces) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:4895") @@ -113432,7 +111921,6 @@ SubClassOf( (Schizosaccharomyces pombe) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:45042") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "fission yeast") @@ -113444,7 +111932,6 @@ SubClassOf( (Saccharomyces) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:36915") AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") @@ -113455,7 +111942,6 @@ SubClassOf( (Saccharomyces cerevisiae) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:41870") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae 'var. diastaticus'") @@ -113475,7 +111961,6 @@ SubClassOf( (Insecta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "true insects") AnnotationAssertion( "ncbi_taxonomy") @@ -113486,7 +111971,6 @@ SubClassOf( (Amoebozoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:23020233") AnnotationAssertion( "PMID:30257078") @@ -113497,7 +111981,6 @@ SubClassOf( (Rhabditoidea) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:55879") @@ -113506,7 +111989,6 @@ SubClassOf( (Peloderinae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:55885") @@ -113515,7 +111997,6 @@ SubClassOf( (Dictyostelium) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:29367151") AnnotationAssertion( "ncbi_taxonomy") @@ -113526,7 +112007,6 @@ SubClassOf( (Tracheophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "vascular plants") AnnotationAssertion( "ncbi_taxonomy") @@ -113537,7 +112017,6 @@ SubClassOf( (Spermatophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "seed plants") AnnotationAssertion( "ncbi_taxonomy") @@ -113548,7 +112027,6 @@ SubClassOf( (Eumetazoa) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:6072") @@ -113557,7 +112035,6 @@ SubClassOf( (Cnidaria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "cnidarians") AnnotationAssertion(Annotation( ) "coelenterates") @@ -113570,7 +112047,6 @@ SubClassOf( (Platyhelminthes) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "flatworm") AnnotationAssertion(Annotation( ) "flatworms") @@ -113582,7 +112058,6 @@ SubClassOf( (Nematoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "nematode") AnnotationAssertion(Annotation( ) "nematodes") @@ -113597,7 +112072,6 @@ SubClassOf( (Rhabditida) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:33251") AnnotationAssertion( "NCBITaxon:6308") AnnotationAssertion( "GC_ID:1") @@ -113609,7 +112083,6 @@ SubClassOf( (Caenorhabditis) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:6237") @@ -113618,7 +112091,6 @@ SubClassOf( (Rhabditidae) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:54603") AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") @@ -113628,7 +112100,6 @@ SubClassOf( (Arthropoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "arthropods") AnnotationAssertion( "ncbi_taxonomy") @@ -113639,7 +112110,6 @@ SubClassOf( (Hexapoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "insects") AnnotationAssertion( "ncbi_taxonomy") @@ -113653,7 +112123,6 @@ SubClassOf( (saccharomyceta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:716545") @@ -113662,7 +112131,6 @@ SubClassOf( (Echinodermata) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "echinoderms") AnnotationAssertion( "ncbi_taxonomy") @@ -113673,7 +112141,6 @@ SubClassOf( (Chordata) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "chordates") AnnotationAssertion( "ncbi_taxonomy") @@ -113684,7 +112151,6 @@ SubClassOf( (Vertebrata ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Vertebrata") AnnotationAssertion(Annotation( ) "vertebrates") @@ -113696,7 +112162,6 @@ SubClassOf( (Gnathostomata ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Gnathostomata") AnnotationAssertion(Annotation( ) "jawed vertebrates") @@ -113707,7 +112172,6 @@ SubClassOf( (Euphyllophyta) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "euphyllophytes") AnnotationAssertion( "ncbi_taxonomy") @@ -113717,7 +112181,6 @@ SubClassOf( (Actinopterygii) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "fish") AnnotationAssertion(Annotation( ) "fishes") @@ -113732,7 +112195,6 @@ SubClassOf( (Sarcopterygii) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:8287") @@ -113741,7 +112203,6 @@ SubClassOf( (Sauropsida) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "sauropsids") AnnotationAssertion( "ncbi_taxonomy") @@ -113751,7 +112212,6 @@ SubClassOf( (Archosauria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:8492") @@ -113760,7 +112220,6 @@ SubClassOf( (Mus ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Mus") AnnotationAssertion( "ncbi_taxonomy") @@ -113770,7 +112229,6 @@ SubClassOf( (Aves) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "birds") AnnotationAssertion( "ncbi_taxonomy") @@ -113782,7 +112240,6 @@ SubClassOf( (Panarthropoda) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:88770") @@ -113791,7 +112248,6 @@ SubClassOf( (Craniata ) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Craniata") AnnotationAssertion( "ncbi_taxonomy") @@ -113801,7 +112257,6 @@ SubClassOf( (Eutheria) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "eutherian mammals") AnnotationAssertion(Annotation( ) "placental mammals") @@ -113815,7 +112270,6 @@ SubClassOf( (Primates) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "primate") AnnotationAssertion( "ncbi_taxonomy") @@ -113827,7 +112281,6 @@ SubClassOf( (Platyrrhini) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "New World monkeys") AnnotationAssertion(Annotation( ) "monkey") @@ -113839,7 +112292,6 @@ SubClassOf( (Callitrichinae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "marmosets and tamarins") AnnotationAssertion( "ncbi_taxonomy") @@ -113851,7 +112303,6 @@ SubClassOf( (Callithrix ) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:9492") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Callithrix") @@ -113862,7 +112313,6 @@ SubClassOf( (Callithrix jacchus) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:9484") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "common marmoset") @@ -113877,7 +112327,6 @@ SubClassOf( (Cebidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:9498") @@ -113886,7 +112335,6 @@ SubClassOf( (Catarrhini) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:9526") @@ -113895,7 +112343,6 @@ SubClassOf( (Hominidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "great apes") AnnotationAssertion( "ncbi_taxonomy") @@ -113906,7 +112353,6 @@ SubClassOf( (Homo) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "humans") AnnotationAssertion( "ncbi_taxonomy") @@ -113916,7 +112362,6 @@ SubClassOf( (Homo sapiens) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "human") AnnotationAssertion( "ncbi_taxonomy") @@ -113926,7 +112371,6 @@ SubClassOf( (Felidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "cat family") AnnotationAssertion( "ncbi_taxonomy") @@ -113936,7 +112380,6 @@ SubClassOf( (Felis) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:9682") @@ -113945,7 +112388,6 @@ SubClassOf( (Felis catus) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:36475") AnnotationAssertion( "GC_ID:1") AnnotationAssertion( "PMID:17600185") @@ -113963,7 +112405,6 @@ SubClassOf( (Perissodactyla) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "odd-toed ungulates") AnnotationAssertion( "ncbi_taxonomy") @@ -113974,7 +112415,6 @@ SubClassOf( (Equidae) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "horses") AnnotationAssertion( "ncbi_taxonomy") @@ -113984,7 +112424,6 @@ SubClassOf( (Equus) -AnnotationAssertion( ) AnnotationAssertion( "NCBITaxon:1225530") AnnotationAssertion( "NCBITaxon:35506") AnnotationAssertion( "NCBITaxon:35507") @@ -114013,7 +112452,6 @@ SubClassOf( (Rodentia) -AnnotationAssertion( ) AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "rodent") AnnotationAssertion( "ncbi_taxonomy") @@ -114156,7 +112594,6 @@ SubClassOf( (branched) AnnotationAssertion(Annotation( "WordNet:WordNet") "A branchiness quality inhering in a bearer by virtue of the bearer's having branches.") -AnnotationAssertion( ) AnnotationAssertion( "ramified") AnnotationAssertion( "ramiform") AnnotationAssertion( "quality") @@ -114170,7 +112607,6 @@ SubClassOf( (coiled) AnnotationAssertion(Annotation( "WordNet:WordNet") "A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals).") -AnnotationAssertion( ) AnnotationAssertion( "PATO:0001363") AnnotationAssertion( "spiral") AnnotationAssertion( "quality") @@ -114224,7 +112660,6 @@ SubClassOf( (abnormal) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "aberrant") AnnotationAssertion( "atypia") @@ -114240,7 +112675,6 @@ SubClassOf( (normal) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "average") AnnotationAssertion( "PATO:0000461") @@ -114253,7 +112687,6 @@ SubClassOf( (increased size) AnnotationAssertion(Annotation( "PATOC:GVG") "A size quality which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "PATO:0001202") AnnotationAssertion( "quality") AnnotationAssertion( "big") @@ -114271,7 +112704,6 @@ SubClassOf( (decreased size) AnnotationAssertion(Annotation( "PATOC:GVG") "A size quality which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "hypoplasia") AnnotationAssertion( "underdeveloped") AnnotationAssertion( "quality") @@ -114298,7 +112730,6 @@ SubClassOf( (closed) AnnotationAssertion(Annotation( "answers.com:answers.com") "A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "blocked") AnnotationAssertion( "PATO:0000608") @@ -114310,7 +112741,6 @@ DisjointClasses( (open) AnnotationAssertion(Annotation( "answers.com:answers.com") "A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0000610") AnnotationAssertion( ) @@ -114345,7 +112775,6 @@ SubClassOf( (opaque) AnnotationAssertion(Annotation( "PATOC:GVG") "A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.") -AnnotationAssertion( ) AnnotationAssertion( "non-transparent") AnnotationAssertion( "quality") AnnotationAssertion( "clouding") @@ -114359,7 +112788,6 @@ SubClassOf( (transparent) AnnotationAssertion(Annotation( "PATOC:GVG") "A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.") -AnnotationAssertion( ) AnnotationAssertion( "clear") AnnotationAssertion( "hyaline") AnnotationAssertion( "quality") @@ -114416,7 +112844,6 @@ SubClassOf( (elastic) AnnotationAssertion(Annotation( "merriam-webster:merriam-webster") "An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001171") AnnotationAssertion( ) @@ -114669,7 +113096,6 @@ SubClassOf( (immature) AnnotationAssertion(Annotation( "Merriam-Webster:Merriam-Webster") "A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "underdeveloped") AnnotationAssertion( "PATO:0001501") @@ -114690,7 +113116,6 @@ SubClassOf( (flexible) AnnotationAssertion(Annotation( "merriam-webster:merriam-webster") "A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking.") -AnnotationAssertion( ) AnnotationAssertion( "bendy") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001544") @@ -114743,7 +113168,6 @@ SubClassOf( (increased contractility) AnnotationAssertion(Annotation( "PATO:GVG") "A contractility which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "high contractility") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001580") @@ -114757,7 +113181,6 @@ SubClassOf( (decreased contractility) AnnotationAssertion(Annotation( "PATO:GVG") "A contractility which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "low contractility") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001581") @@ -114780,7 +113203,6 @@ SubClassOf( (increased life span) AnnotationAssertion(Annotation( "PATO:GVG") "A life span which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "high life span") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001603") @@ -114792,7 +113214,6 @@ SubClassOf( (decreased life span) AnnotationAssertion(Annotation( "PATO:GVG") "A life span which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "low life span") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001604") @@ -114804,7 +113225,6 @@ SubClassOf( (contractile) AnnotationAssertion(Annotation( "PATOC:GVG") "A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001690") AnnotationAssertion( ) @@ -114816,7 +113236,6 @@ SubClassOf( (increased viscosity) AnnotationAssertion(Annotation( "PATOC:GVG") "A viscosity which relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "high viscosity") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001693") @@ -114830,7 +113249,6 @@ SubClassOf( (decreased viscosity) AnnotationAssertion(Annotation( "PATOC:GVG") "A viscosity which relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "low viscosity") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001694") @@ -114874,7 +113292,6 @@ SubClassOf( (increased flexibility) AnnotationAssertion(Annotation( "PATOC:GVG") "A flexibility which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "high flexibility") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001776") @@ -114888,7 +113305,6 @@ SubClassOf( (decreased flexibility) AnnotationAssertion(Annotation( "PATOC:GVG") "A flexibility which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "low flexibility") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001777") @@ -114911,7 +113327,6 @@ SubClassOf( (increased coiling) AnnotationAssertion(Annotation( "PATOC:GVG") "A coiling which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( "high coiling") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001795") @@ -114925,7 +113340,6 @@ SubClassOf( (decreased coiling) AnnotationAssertion(Annotation( "PATOC:GVG") "A coiling which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( "low coiling") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001796") @@ -114939,7 +113353,6 @@ SubClassOf( (concave) AnnotationAssertion(Annotation( "WordNet:WordNet") "A shape quality in a bearer by virtue of the bearer's curving inward.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001857") AnnotationAssertion( ) @@ -115098,7 +113511,6 @@ SubClassOf( (convex 3-D shape) AnnotationAssertion(Annotation( "PATOC:CJM") "A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.") -AnnotationAssertion( ) AnnotationAssertion( "Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0002007") @@ -115111,7 +113523,6 @@ SubClassOf( ObjectSomeValuesFrom( (concave 3-D shape) AnnotationAssertion(Annotation( "PATOC:CJM") "A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave.") -AnnotationAssertion( ) AnnotationAssertion( "Image:http://en.wikipedia.org/wiki/Image:Convex_polygon_illustration2.png") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0002008") @@ -115154,7 +113565,6 @@ SubClassOf( (biconcave) AnnotationAssertion(Annotation( "PATOC:GVG") "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.") -AnnotationAssertion( ) AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0002039") AnnotationAssertion( ) @@ -115285,7 +113695,6 @@ SubClassOf( (increased elasticity) AnnotationAssertion(Annotation( "PATOC:GVG") "An elasticity which is relatively high.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-03-30T11:50:21Z") AnnotationAssertion( "quality") @@ -115299,7 +113708,6 @@ SubClassOf( (decreased elasticity) AnnotationAssertion(Annotation( "PATOC:GVG") "An elasticity which is relatively low.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-03-30T11:50:39Z") AnnotationAssertion( "quality") @@ -115327,7 +113735,6 @@ SubClassOf( (increased quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality that has a value that is increased compared to normal or average.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-06-16T06:39:43Z") AnnotationAssertion( "quality") @@ -115339,7 +113746,6 @@ SubClassOf( (decreased quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality that has a value that is decreased compared to normal or average.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-06-16T06:40:15Z") AnnotationAssertion( "quality") @@ -115351,7 +113757,6 @@ SubClassOf( (decreased object quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality of an object that has a value that is decreased compared to normal or average.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-06-16T06:51:54Z") AnnotationAssertion( "quality") @@ -115364,7 +113769,6 @@ SubClassOf( (increased object quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality of an object that has a value that is increased compared to normal or average.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-06-16T06:54:01Z") AnnotationAssertion( "quality") @@ -116143,7 +114547,6 @@ AnnotationAssertion(Annotation( "PR:000001006") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-2) @@ -116162,7 +114565,6 @@ AnnotationAssertion(Annotation( "PR:000001008") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-2") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-E) @@ -116179,7 +114581,6 @@ AnnotationAssertion( "PR:000001010") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-E") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-M) @@ -116199,7 +114600,6 @@ AnnotationAssertion(Annotation( "PR:000001012") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-M") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-X) @@ -116217,7 +114617,6 @@ AnnotationAssertion(Annotation( "PR:000001013") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-X") -AnnotationAssertion( ) SubClassOf( ) # Class: (receptor-type tyrosine-protein phosphatase C isoform CD45RABC) @@ -116231,7 +114630,6 @@ AnnotationAssertion( "PR:000001014") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exons 4(A), 5(B), and 6(C).") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45RABC") -AnnotationAssertion( ) SubClassOf( ) # Class: (receptor-type tyrosine-protein phosphatase C isoform CD45RA) @@ -116243,7 +114641,6 @@ AnnotationAssertion( "PR:000001015") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C).") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45RA") -AnnotationAssertion( ) SubClassOf( ) # Class: (receptor-type tyrosine-protein phosphatase C isoform CD45RO) @@ -116257,7 +114654,6 @@ AnnotationAssertion( "PR:000001017") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL. Note: This isoform lacks the region encoded by the variable exons 4(A), 5(B), and 6(C).") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45RO") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD3 subunit with immunoglobulin domain) @@ -116318,7 +114714,6 @@ AnnotationAssertion(Annotation( "PR:000001024") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "neural cell adhesion molecule 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-type lectin with multiple lectin domains) @@ -116345,7 +114740,6 @@ AnnotationAssertion( "PR:000001026") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL. Note: Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment.") AnnotationAssertion(rdfs:label "lymphocyte antigen 75") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD2 molecule) @@ -116384,7 +114778,6 @@ AnnotationAssertion(Annotation( "PR:000001084") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell surface glycoprotein CD8 beta chain) @@ -116403,7 +114796,6 @@ AnnotationAssertion(Annotation( "PR:000001085") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 beta chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (adhesion G-protein coupled receptor) @@ -116493,7 +114885,6 @@ AnnotationAssertion(Annotation( "PR:000001175") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "D(1A) dopamine receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (D(2) dopamine receptor) @@ -116506,7 +114897,6 @@ AnnotationAssertion( "PR:000001177") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "D(2) dopamine receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (chemokine receptor CCR1/3/1L) @@ -116538,7 +114928,6 @@ AnnotationAssertion(Annotation( "PR:000001199") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 4) @@ -116557,7 +114946,6 @@ AnnotationAssertion(Annotation( "PR:000001200") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 5) @@ -116578,7 +114966,6 @@ AnnotationAssertion(Annotation( "PR:000001201") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 6) @@ -116607,7 +114994,6 @@ AnnotationAssertion(Annotation( "PR:000001202") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 6") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 7) @@ -116633,7 +115019,6 @@ AnnotationAssertion(Annotation( "PR:000001203") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 7") -AnnotationAssertion( ) SubClassOf( ) # Class: (CX3C chemokine receptor 1) @@ -116656,7 +115041,6 @@ AnnotationAssertion(Annotation( "PR:000001206") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "CX3C chemokine receptor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-X-C chemokine receptor type 3) @@ -116679,7 +115063,6 @@ AnnotationAssertion(Annotation( "PR:000001207") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "C-X-C chemokine receptor type 3") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-X-C chemokine receptor type 4) @@ -116709,7 +115092,6 @@ AnnotationAssertion(Annotation( "PR:000001208") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-X-C chemokine receptor type 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-X-C chemokine receptor type 5) @@ -116732,7 +115114,6 @@ AnnotationAssertion(Annotation( "PR:000001209") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-X-C chemokine receptor type 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (medium-wave-sensitive opsin) @@ -116752,7 +115133,6 @@ AnnotationAssertion( "PR:000001224") AnnotationAssertion(rdfs:comment "Category=gene. Note: The human OPN1MW, OPN1MW2, and OPN1MW3 genes encode identical proteins.") AnnotationAssertion(rdfs:label "medium-wave-sensitive opsin") -AnnotationAssertion( ) SubClassOf( ) # Class: (high affinity interleukin-8 receptor) @@ -116777,7 +115157,6 @@ AnnotationAssertion(Annotation( "PR:000001243") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "melanopsin") -AnnotationAssertion( ) SubClassOf( ) # Class: (long-wave-sensitive opsin 1) @@ -116793,7 +115172,6 @@ AnnotationAssertion(Annotation( "PR:000001244") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "long-wave-sensitive opsin 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 1) @@ -116818,7 +115196,6 @@ AnnotationAssertion(Annotation( "PR:000001254") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C chemokine receptor type 3) @@ -116841,7 +115218,6 @@ AnnotationAssertion(Annotation( "PR:000001255") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-C chemokine receptor type 3") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-X-C chemokine receptor type 1) @@ -116862,7 +115238,6 @@ AnnotationAssertion(Annotation( "PR:000001256") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-X-C chemokine receptor type 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-X-C chemokine receptor type 2) @@ -116885,7 +115260,6 @@ AnnotationAssertion(Annotation( "PR:000001257") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-X-C chemokine receptor type 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (ADP-ribosyl cyclase) @@ -116914,7 +115288,6 @@ AnnotationAssertion(Annotation( "PR:000001288") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "B-cell receptor CD22") -AnnotationAssertion( ) SubClassOf( ) # Class: (membrane-spanning 4-domains subfamily A member 1) @@ -116967,7 +115340,6 @@ AnnotationAssertion(Annotation( "PR:000001292") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-type lectin domain family 4 member C") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-type lectin domain family 4 member K) @@ -116980,7 +115352,6 @@ AnnotationAssertion(Annotation( "PR:000001293") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-type lectin domain family 4 member K") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD209 molecule) @@ -117094,7 +115465,6 @@ AnnotationAssertion(Annotation( "PR:000001318") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "L-selectin") -AnnotationAssertion( ) SubClassOf( ) # Class: (SLAM family member 5) @@ -117110,7 +115480,6 @@ AnnotationAssertion(Annotation( "PR:000001319") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "SLAM family member 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (alpha-(1,3)-fucosyltransferase) @@ -117136,7 +115505,6 @@ AnnotationAssertion( "PR:000001326") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "bone marrow stromal antigen 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (cadherin) @@ -117162,7 +115530,6 @@ AnnotationAssertion(Annotation( "PR:000001332") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "carcinoembryonic antigen-related cell adhesion molecule 8") -AnnotationAssertion( ) SubClassOf( ) # Class: (complement receptor type 1) @@ -117176,7 +115543,6 @@ AnnotationAssertion(Annotation( "PR:000001337") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL. Note: There is no counterpart in mouse.") AnnotationAssertion(rdfs:label "complement receptor type 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (complement receptor type 2) @@ -117194,7 +115560,6 @@ AnnotationAssertion(Annotation( "PR:000001338") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "complement receptor type 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD69 molecule) @@ -117233,7 +115598,6 @@ AnnotationAssertion(Annotation( "PR:000001344") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "ectonucleotide pyrophosphatase/phosphodiesterase family member 3") -AnnotationAssertion( ) SubClassOf( ) # Class: (endoglin) @@ -117250,7 +115614,6 @@ AnnotationAssertion(Annotation( "PR:000001345") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "endoglin") -AnnotationAssertion( ) SubClassOf( ) # Class: (forkhead box protein P3) @@ -117264,7 +115627,6 @@ AnnotationAssertion(Annotation( "PR:000001350") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "forkhead box protein P3") -AnnotationAssertion( ) SubClassOf( ) # Class: (glycophorin) @@ -117316,7 +115678,6 @@ AnnotationAssertion(Annotation( "PR:000001380") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-2 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (interleukin-2 receptor subunit beta) @@ -117336,7 +115697,6 @@ AnnotationAssertion(Annotation( "PR:000001381") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-2 receptor subunit beta") -AnnotationAssertion( ) SubClassOf( ) # Class: (leukocyte immunoglobulin-like receptor subfamily A member 4) @@ -117353,7 +115713,6 @@ AnnotationAssertion(Annotation( "PR:000001398") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "leukocyte immunoglobulin-like receptor subfamily A member 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (killer cell lectin-like receptor subfamily D member 1) @@ -117399,7 +115758,6 @@ AnnotationAssertion( "PR:000001408") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD86 molecule) @@ -117466,7 +115824,6 @@ AnnotationAssertion( "PR:000001444") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cadherin-5") -AnnotationAssertion( ) SubClassOf( ) # Class: (cadherin-1) @@ -117485,7 +115842,6 @@ AnnotationAssertion(Annotation( "PR:000001447") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cadherin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (alpha-(1,3)-fucosyltransferase 4) @@ -117507,7 +115863,6 @@ AnnotationAssertion(Annotation( "PR:000001456") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "alpha-(1,3)-fucosyltransferase 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (glycophorin-A) @@ -117523,7 +115878,6 @@ AnnotationAssertion(Annotation( "PR:000001460") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glycophorin-A") -AnnotationAssertion( ) SubClassOf( ) # Class: (high affinity immunoglobulin gamma Fc receptor I) @@ -117541,7 +115895,6 @@ AnnotationAssertion(Annotation( "PR:000001465") AnnotationAssertion(rdfs:comment "Category=gene. The Fcgr1 gene in mouse is a 1:1 ortholog of FCGR1A, not FCGR1B. Requested by=CL.") AnnotationAssertion(rdfs:label "high affinity immunoglobulin gamma Fc receptor I") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin gamma Fc region receptor II) @@ -117579,7 +115932,6 @@ AnnotationAssertion(Annotation( "PR:000001481") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "low affinity immunoglobulin gamma Fc region receptor II-b") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin gamma Fc region receptor III) @@ -117663,7 +116015,6 @@ AnnotationAssertion( "PR:000001580") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "fMet-Leu-Phe receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (oxytocin receptor) @@ -117676,7 +116027,6 @@ AnnotationAssertion( "PR:000001635") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "oxytocin receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (relaxin receptor 1) @@ -117692,7 +116042,6 @@ AnnotationAssertion(Annotation( "PR:000001666") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "relaxin receptor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (transcription factor NF-kappa-B subunit) @@ -117732,7 +116081,6 @@ AnnotationAssertion(Annotation( "PR:000001786") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "prominin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-type lectin domain family 6 member A) @@ -117751,7 +116099,6 @@ AnnotationAssertion(Annotation( "PR:000001806") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-type lectin domain family 6 member A") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-type lectin domain family 7 member A) @@ -117773,7 +116120,6 @@ AnnotationAssertion(Annotation( "PR:000001807") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "C-type lectin domain family 7 member A") -AnnotationAssertion( ) SubClassOf( ) # Class: (C/C-C motif small inducible chemokine) @@ -117825,7 +116171,6 @@ AnnotationAssertion(Annotation( "PR:000001813") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "adhesion G protein-coupled receptor E1") -AnnotationAssertion( ) SubClassOf( ) # Class: (MHC class II histocompatibility antigen alpha chain) @@ -117875,7 +116220,6 @@ AnnotationAssertion(Annotation( "PR:000001835") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-box transcription factor TBX21") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD7 molecule) @@ -117918,7 +116262,6 @@ AnnotationAssertion(Annotation( "PR:000001839") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD5") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell-specific surface glycoprotein CD28) @@ -117931,7 +116274,6 @@ AnnotationAssertion( "PR:000001841") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell-specific surface glycoprotein CD28") -AnnotationAssertion( ) SubClassOf( ) # Class: (Thy-1 membrane glycoprotein) @@ -117947,7 +116289,6 @@ AnnotationAssertion(Annotation( "PR:000001843") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "Thy-1 membrane glycoprotein") -AnnotationAssertion( ) SubClassOf( ) # Class: (arginase-1) @@ -117961,7 +116302,6 @@ AnnotationAssertion( "PR:000001844") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "arginase-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (cathepsin K) @@ -117978,7 +116318,6 @@ AnnotationAssertion( "PR:000001850") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cathepsin K") -AnnotationAssertion( ) SubClassOf( ) # Class: (cytotoxic T-lymphocyte protein 4) @@ -117993,7 +116332,6 @@ AnnotationAssertion(Annotation( "PR:000001852") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "cytotoxic T-lymphocyte protein 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (immunoglobulin iota chain) @@ -118011,7 +116349,6 @@ AnnotationAssertion(Annotation( "PR:000001858") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "immunoglobulin iota chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (immunoglobulin lambda-like polypeptide 1) @@ -118029,7 +116366,6 @@ AnnotationAssertion( "PR:000001859") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "immunoglobulin lambda-like polypeptide 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (inducible T-cell costimulator) @@ -118048,7 +116384,6 @@ AnnotationAssertion( "PR:000001860") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "inducible T-cell costimulator") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin beta) @@ -118097,7 +116432,6 @@ AnnotationAssertion(Annotation( "PR:000001867") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-5 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (interleukin-7 receptor subunit alpha) @@ -118116,7 +116450,6 @@ AnnotationAssertion( "PR:000001869") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-7 receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (KLRB1-like protein) @@ -118146,7 +116479,6 @@ AnnotationAssertion(Annotation( "PR:000001879") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "leukosialin") -AnnotationAssertion( ) SubClassOf( ) # Class: (low affinity immunoglobulin epsilon Fc receptor) @@ -118170,7 +116502,6 @@ AnnotationAssertion(Annotation( "PR:000001880") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "low affinity immunoglobulin epsilon Fc receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (lysosome-associated membrane protein) @@ -118194,7 +116525,6 @@ AnnotationAssertion(Annotation( "PR:000001884") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrophage receptor MARCO") -AnnotationAssertion( ) SubClassOf( ) # Class: (macrophage scavenger receptor types I and II) @@ -118212,7 +116542,6 @@ AnnotationAssertion(Annotation( "PR:000001885") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrophage scavenger receptor types I and II") -AnnotationAssertion( ) SubClassOf( ) # Class: (membrane alanyl aminopeptidase-like metallopeptidase) @@ -118272,7 +116601,6 @@ AnnotationAssertion(Annotation( "PR:000001893") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "natural cytotoxicity triggering receptor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (natural cytotoxicity triggering receptor 2) @@ -118291,7 +116619,6 @@ AnnotationAssertion(Annotation( "PR:000001894") AnnotationAssertion(rdfs:comment "Category=gene. Not found in mouse.") AnnotationAssertion(rdfs:label "natural cytotoxicity triggering receptor 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (natural killer cell receptor 2B4) @@ -118312,7 +116639,6 @@ AnnotationAssertion(Annotation( "PR:000001896") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "natural killer cell receptor 2B4") -AnnotationAssertion( ) SubClassOf( ) # Class: (natural killer cell receptor NKG2) @@ -118346,7 +116672,6 @@ AnnotationAssertion(Annotation( "PR:000001898") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "neprilysin") -AnnotationAssertion( ) SubClassOf( ) # Class: (nuclear receptor ROR-gamma) @@ -118368,7 +116693,6 @@ AnnotationAssertion(Annotation( "PR:000001902") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "nuclear receptor ROR-gamma") -AnnotationAssertion( ) SubClassOf( ) # Class: (paired box protein PAX-5) @@ -118382,7 +116706,6 @@ AnnotationAssertion(Annotation( "PR:000001903") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "paired box protein PAX-5") -AnnotationAssertion( ) SubClassOf( ) # Class: (platelet glycoprotein 4) @@ -118406,7 +116729,6 @@ AnnotationAssertion(Annotation( "PR:000001905") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "platelet glycoprotein 4") -AnnotationAssertion( ) SubClassOf( ) # Class: (platelet glycoprotein Ib alpha chain) @@ -118424,7 +116746,6 @@ AnnotationAssertion( "PR:000001907") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "platelet glycoprotein Ib alpha chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (programmed cell death protein 1) @@ -118441,7 +116762,6 @@ AnnotationAssertion(Annotation( "PR:000001919") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "programmed cell death protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (scavenger receptor cysteine-rich type 1 protein M130) @@ -118454,7 +116774,6 @@ AnnotationAssertion(Annotation( "PR:000001925") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "scavenger receptor cysteine-rich type 1 protein M130") -AnnotationAssertion( ) SubClassOf( ) # Class: (sialic acid-binding Ig-like lectin 5) @@ -118476,7 +116795,6 @@ AnnotationAssertion( "PR:000001927") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "sialic acid-binding Ig-like lectin 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (sialic acid-binding Ig-like lectin 6) @@ -118496,7 +116814,6 @@ AnnotationAssertion(Annotation( "PR:000001928") AnnotationAssertion(rdfs:comment "Category=gene. There is no mouse ortholog.") AnnotationAssertion(rdfs:label "sialic acid-binding Ig-like lectin 6") -AnnotationAssertion( ) SubClassOf( ) # Class: (sialoadhesin) @@ -118514,7 +116831,6 @@ AnnotationAssertion(Annotation( "PR:000001931") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "sialoadhesin") -AnnotationAssertion( ) SubClassOf( ) # Class: (signal transducer CD24) @@ -118534,7 +116850,6 @@ AnnotationAssertion(Annotation( "PR:000001932") AnnotationAssertion(rdfs:comment "Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL.") AnnotationAssertion(rdfs:label "signal transducer CD24") -AnnotationAssertion( ) SubClassOf( ) # Class: (syndecan-1) @@ -118550,7 +116865,6 @@ AnnotationAssertion(Annotation( "PR:000001935") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "syndecan-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (tartrate-resistant acid phosphatase type 5) @@ -118568,7 +116882,6 @@ AnnotationAssertion(Annotation( "PR:000001937") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tartrate-resistant acid phosphatase type 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (thrombomodulin-like receptor) @@ -118591,7 +116904,6 @@ AnnotationAssertion(Annotation( "PR:000001941") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "trans-acting T-cell-specific transcription factor GATA-3") -AnnotationAssertion( ) SubClassOf( ) # Class: (transcription factor PU.1) @@ -118606,7 +116918,6 @@ AnnotationAssertion(Annotation( "PR:000001944") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "transcription factor PU.1") -AnnotationAssertion( ) SubClassOf( ) # Class: (transferrin receptor protein 1) @@ -118624,7 +116935,6 @@ AnnotationAssertion(Annotation( "PR:000001945") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "transferrin receptor protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (tumor necrosis factor ligand superfamily member 5) @@ -118660,7 +116970,6 @@ AnnotationAssertion(Annotation( "PR:000001954") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tumor necrosis factor receptor superfamily member 11A") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD27 molecule) @@ -118711,7 +117020,6 @@ AnnotationAssertion(Annotation( "PR:000001968") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tyrosine-protein phosphatase non-receptor type substrate 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (urokinase plasminogen activator surface receptor) @@ -118729,7 +117037,6 @@ AnnotationAssertion(Annotation( "PR:000001969") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "urokinase plasminogen activator surface receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (vascular endothelial growth factor receptor) @@ -118775,7 +117082,6 @@ AnnotationAssertion(Annotation( "PR:000002001") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein kinase FLT3") -AnnotationAssertion( ) SubClassOf( ) # Class: (MHC class II histocompatibility antigen alpha chain DRA) @@ -118807,7 +117113,6 @@ AnnotationAssertion(Annotation( "PR:000002023") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "NKG2-A/NKG2-B type II integral membrane protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell surface glycoprotein CD1a) @@ -118821,7 +117126,6 @@ AnnotationAssertion( "PR:000002025") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD1a") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell surface glycoprotein CD1c) @@ -118833,7 +117137,6 @@ AnnotationAssertion( "PR:000002027") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD1c") -AnnotationAssertion( ) SubClassOf( ) # Class: (antigen-presenting glycoprotein CD1d) @@ -118850,7 +117153,6 @@ AnnotationAssertion(Annotation( "PR:000002028") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "antigen-presenting glycoprotein CD1d") -AnnotationAssertion( ) SubClassOf( ) # Class: (alpha-type platelet-derived growth factor receptor) @@ -118896,7 +117198,6 @@ AnnotationAssertion(Annotation( "PR:000002031") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "aminopeptidase N") -AnnotationAssertion( ) SubClassOf( ) # Class: (complement component C1q receptor) @@ -118921,7 +117222,6 @@ AnnotationAssertion(Annotation( "PR:000002037") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "complement component C1q receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (glutamyl aminopeptidase) @@ -118939,7 +117239,6 @@ AnnotationAssertion( "PR:000002039") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glutamyl aminopeptidase") -AnnotationAssertion( ) SubClassOf( ) # Class: (macrophage colony-stimulating factor 1 receptor) @@ -118960,7 +117259,6 @@ AnnotationAssertion(Annotation( "PR:000002062") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrophage colony-stimulating factor 1 receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (macrosialin) @@ -118972,7 +117270,6 @@ AnnotationAssertion( "PR:000002064") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrosialin") -AnnotationAssertion( ) SubClassOf( ) # Class: (mast/stem cell growth factor receptor) @@ -119006,7 +117303,6 @@ AnnotationAssertion(Annotation( "PR:000002105") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "thrombomodulin") -AnnotationAssertion( ) SubClassOf( ) # Class: (vascular endothelial growth factor receptor 2) @@ -119027,7 +117323,6 @@ AnnotationAssertion(Annotation( "PR:000002112") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (C-C motif chemokine 3) @@ -119052,7 +117347,6 @@ AnnotationAssertion(Annotation( "PR:000002123") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "C-C motif chemokine 3") -AnnotationAssertion( ) SubClassOf( ) # Class: (macrophage mannose receptor 1) @@ -119071,7 +117365,6 @@ AnnotationAssertion( "PR:000002972") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "macrophage mannose receptor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (Ly-6-like protein) @@ -119186,7 +117479,6 @@ AnnotationAssertion(Annotation( "PR:000003264") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "collagen alpha-1(I) chain") -AnnotationAssertion( ) SubClassOf( ) # Class: (B-cell lymphoma 6 protein) @@ -119208,7 +117500,6 @@ AnnotationAssertion(Annotation( "PR:000003450") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "B-cell lymphoma 6 protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (nuclear receptor ROR-gamma isoform 2) @@ -119232,7 +117523,6 @@ AnnotationAssertion(Annotation( "PR:000003457") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "V(D)J recombination-activating protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (V(D)J recombination-activating protein 2) @@ -119244,7 +117534,6 @@ AnnotationAssertion( "PR:000003460") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "V(D)J recombination-activating protein 2") -AnnotationAssertion( ) SubClassOf( ) # Class: (eomesodermin) @@ -119273,7 +117562,6 @@ AnnotationAssertion(Annotation( "PR:000003466") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "perforin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (early growth response protein 2) @@ -119317,7 +117605,6 @@ AnnotationAssertion( "PR:000003499") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "granzyme B") -AnnotationAssertion( ) SubClassOf( ) # Class: (leukocyte granule-associated proteinase) @@ -119357,7 +117644,6 @@ AnnotationAssertion(Annotation( "PR:000003516") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "lactosylceramide 4-alpha-galactosyltransferase") -AnnotationAssertion( ) SubClassOf( ) # Class: (tyrosine-protein kinase receptor UFO) @@ -119373,7 +117659,6 @@ AnnotationAssertion(Annotation( "PR:000004528") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "tyrosine-protein kinase receptor UFO") -AnnotationAssertion( ) SubClassOf( ) # Class: (bestrophin-4) @@ -119386,7 +117671,6 @@ AnnotationAssertion(Annotation( "PR:000004724") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "bestrophin-4") -AnnotationAssertion( ) SubClassOf( ) # Class: (cholecystokinin) @@ -119397,7 +117681,6 @@ AnnotationAssertion( "PR:000005110") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "cholecystokinin") -AnnotationAssertion( ) SubClassOf( ) # Class: (CD9 molecule) @@ -119432,7 +117715,6 @@ AnnotationAssertion(Annotation( "PR:000005307") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "CCAAT/enhancer-binding protein alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (CCAAT/enhancer-binding protein epsilon) @@ -119445,7 +117727,6 @@ AnnotationAssertion(Annotation( "PR:000005310") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "CCAAT/enhancer-binding protein epsilon") -AnnotationAssertion( ) SubClassOf( ) # Class: (chondrolectin) @@ -119460,7 +117741,6 @@ AnnotationAssertion(Annotation( "PR:000005444") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "chondrolectin") -AnnotationAssertion( ) SubClassOf( ) # Class: (neuronal acetylcholine receptor subunit alpha-7) @@ -119474,7 +117754,6 @@ AnnotationAssertion(Annotation( "PR:000005460") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "neuronal acetylcholine receptor subunit alpha-7") -AnnotationAssertion( ) SubClassOf( ) # Class: (cell surface glycoprotein CD200 receptor 3) @@ -119517,7 +117796,6 @@ AnnotationAssertion(Annotation( "PR:000006611") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "DNA nucleotidylexotransferase") -AnnotationAssertion( ) SubClassOf( ) # Class: (eosinophil peroxidase) @@ -119531,7 +117809,6 @@ AnnotationAssertion(Annotation( "PR:000007152") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "eosinophil peroxidase") -AnnotationAssertion( ) SubClassOf( ) # Class: (estrogen receptor) @@ -119551,7 +117828,6 @@ AnnotationAssertion(Annotation( "PR:000007204") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "estrogen receptor") -AnnotationAssertion( ) SubClassOf( ) # Class: (high affinity immunoglobulin epsilon receptor subunit alpha) @@ -119567,7 +117843,6 @@ AnnotationAssertion( "PR:000007431") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "high affinity immunoglobulin epsilon receptor subunit alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (fibroblast growth factor 8) @@ -119583,7 +117858,6 @@ AnnotationAssertion( "PR:000007499") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "fibroblast growth factor 8") -AnnotationAssertion( ) SubClassOf( ) # Class: (protein c-Fos) @@ -119599,7 +117873,6 @@ AnnotationAssertion(Annotation( "PR:000007597") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "protein c-Fos") -AnnotationAssertion( ) SubClassOf( ) # Class: (forkhead box protein N1) @@ -119619,7 +117892,6 @@ AnnotationAssertion( "PR:000007636") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "forkhead box protein N1") -AnnotationAssertion( ) SubClassOf( ) # Class: (glutamate decarboxylase 1) @@ -119636,7 +117908,6 @@ AnnotationAssertion(Annotation( "PR:000007785") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "glutamate decarboxylase 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (erythroid transcription factor) @@ -119654,7 +117925,6 @@ AnnotationAssertion(Annotation( "PR:000007857") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "erythroid transcription factor") -AnnotationAssertion( ) SubClassOf( ) # Class: (endothelial transcription factor GATA-2) @@ -119666,7 +117936,6 @@ AnnotationAssertion( "PR:000007858") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "endothelial transcription factor GATA-2") -AnnotationAssertion( ) SubClassOf( ) # Class: (glial fibrillary acidic protein) @@ -119677,7 +117946,6 @@ AnnotationAssertion( "PR:000007939") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "glial fibrillary acidic protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (beta-globin) @@ -119705,7 +117973,6 @@ AnnotationAssertion(Annotation( "PR:000008467") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "hemoglobin subunit zeta") -AnnotationAssertion( ) SubClassOf( ) # Class: (hemoglobin subunit beta-1) @@ -119743,7 +118010,6 @@ AnnotationAssertion(Annotation( "PR:000008982") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-17 receptor B") -AnnotationAssertion( ) SubClassOf( ) # Class: (interleukin-1 receptor-like 1) @@ -119763,7 +118029,6 @@ AnnotationAssertion(Annotation( "PR:000008994") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "interleukin-1 receptor-like 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (insulin gene translation product) @@ -119775,7 +118040,6 @@ AnnotationAssertion( "PR:000009054") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "insulin gene translation product") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-IIb) @@ -119793,7 +118057,6 @@ AnnotationAssertion(Annotation( "PR:000009127") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-IIb") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha-4) @@ -119812,7 +118075,6 @@ AnnotationAssertion(Annotation( "PR:000009129") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin alpha-4") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin beta-7) @@ -119827,7 +118089,6 @@ AnnotationAssertion( "PR:000009143") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "integrin beta-7") -AnnotationAssertion( ) SubClassOf( ) # Class: (metastasis-suppressor KiSS-1) @@ -119840,7 +118101,6 @@ AnnotationAssertion(Annotation( "PR:000009344") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "metastasis-suppressor KiSS-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (killer cell lectin-like receptor subfamily G member 1) @@ -119859,7 +118119,6 @@ AnnotationAssertion(Annotation( "PR:000009426") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "killer cell lectin-like receptor subfamily G member 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell surface glycoprotein YE1/48) @@ -119938,7 +118197,6 @@ AnnotationAssertion(Annotation( "PR:000009725") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "neutrophil gelatinase-associated lipocalin") -AnnotationAssertion( ) SubClassOf( ) # Class: (galectin-1) @@ -119962,7 +118220,6 @@ AnnotationAssertion(Annotation( "PR:000009766") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "galectin-1") -AnnotationAssertion( ) SubClassOf( ) # Class: (LIM/homeobox protein Lhx3) @@ -119993,7 +118250,6 @@ AnnotationAssertion(Annotation( "PR:000009978") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "lactotransferrin") -AnnotationAssertion( ) SubClassOf( ) # Class: (lumican) @@ -120009,7 +118265,6 @@ AnnotationAssertion(Annotation( "PR:000009981") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "lumican") -AnnotationAssertion( ) SubClassOf( ) # Class: (homeobox protein Meis2) @@ -120023,7 +118278,6 @@ AnnotationAssertion(Annotation( "PR:000010317") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "homeobox protein Meis2") -AnnotationAssertion( ) SubClassOf( ) # Class: (tyrosine-protein kinase Mer) @@ -120039,7 +118293,6 @@ AnnotationAssertion(Annotation( "PR:000010329") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "tyrosine-protein kinase Mer") -AnnotationAssertion( ) SubClassOf( ) # Class: (myeloperoxidase) @@ -120051,7 +118304,6 @@ AnnotationAssertion( "PR:000010543") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "myeloperoxidase") -AnnotationAssertion( ) SubClassOf( ) # Class: (myb proto-oncogene protein) @@ -120075,7 +118327,6 @@ AnnotationAssertion(Annotation( "PR:000011143") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "neuropilin and tolloid-like protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (nuclear factor NF-kappa-B p100 subunit) @@ -120093,7 +118344,6 @@ AnnotationAssertion(Annotation( "PR:000011178") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "nuclear factor NF-kappa-B p100 subunit") -AnnotationAssertion( ) SubClassOf( ) # Class: (netrin-G1) @@ -120108,7 +118358,6 @@ AnnotationAssertion(Annotation( "PR:000011467") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "netrin-G1") -AnnotationAssertion( ) SubClassOf( ) # Class: (proenkephalin-B) @@ -120121,7 +118370,6 @@ AnnotationAssertion( "PR:000012526") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "proenkephalin-B") -AnnotationAssertion( ) SubClassOf( ) # Class: (bone marrow proteoglycan) @@ -120136,7 +118384,6 @@ AnnotationAssertion(Annotation( "PR:000013206") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "bone marrow proteoglycan") -AnnotationAssertion( ) SubClassOf( ) # Class: (prolactin) @@ -120147,7 +118394,6 @@ AnnotationAssertion( "PR:000013246") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "prolactin") -AnnotationAssertion( ) SubClassOf( ) # Class: (parvalbumin alpha) @@ -120159,7 +118405,6 @@ AnnotationAssertion(Annotation( "PR:000013502") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "parvalbumin alpha") -AnnotationAssertion( ) SubClassOf( ) # Class: (reelin) @@ -120172,7 +118417,6 @@ AnnotationAssertion(Annotation( "PR:000013879") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "reelin") -AnnotationAssertion( ) SubClassOf( ) # Class: (renin) @@ -120185,7 +118429,6 @@ AnnotationAssertion( "PR:000013883") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "renin") -AnnotationAssertion( ) SubClassOf( ) # Class: (non-secretory ribonuclease) @@ -120206,7 +118449,6 @@ AnnotationAssertion(Annotation( "PR:000014046") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "non-secretory ribonuclease") -AnnotationAssertion( ) SubClassOf( ) # Class: (eosinophil cationic protein) @@ -120221,7 +118463,6 @@ AnnotationAssertion( "PR:000014047") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "eosinophil cationic protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (runt-related transcription factor 1) @@ -120244,7 +118485,6 @@ AnnotationAssertion(Annotation( "PR:000014362") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "runt-related transcription factor 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (uteroglobin) @@ -120271,7 +118511,6 @@ AnnotationAssertion(Annotation( "PR:000014505") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "uteroglobin") -AnnotationAssertion( ) SubClassOf( ) # Class: (sonic hedgehog protein) @@ -120286,7 +118525,6 @@ AnnotationAssertion(Annotation( "PR:000014841") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "sonic hedgehog protein") -AnnotationAssertion( ) SubClassOf( ) # Class: (gamma-synuclein) @@ -120304,7 +118542,6 @@ AnnotationAssertion(Annotation( "PR:000015325") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "gamma-synuclein") -AnnotationAssertion( ) SubClassOf( ) # Class: (transcription factor SOX-2) @@ -120316,7 +118553,6 @@ AnnotationAssertion(Annotation( "PR:000015426") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "transcription factor SOX-2") -AnnotationAssertion( ) SubClassOf( ) # Class: (SCO-spondin) @@ -120329,7 +118565,6 @@ AnnotationAssertion(Annotation( "PR:000015658") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "SCO-spondin") -AnnotationAssertion( ) SubClassOf( ) # Class: (somatostatin) @@ -120342,7 +118577,6 @@ AnnotationAssertion(Annotation( "PR:000015665") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "somatostatin") -AnnotationAssertion( ) SubClassOf( ) # Class: (tachykinin-3) @@ -120360,7 +118594,6 @@ AnnotationAssertion(Annotation( "PR:000016004") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "tachykinin-3") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell acute lymphocytic leukemia protein 1) @@ -120379,7 +118612,6 @@ AnnotationAssertion(Annotation( "PR:000016043") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell acute lymphocytic leukemia protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (tyrosine 3-monooxygenase) @@ -120409,7 +118641,6 @@ AnnotationAssertion(Annotation( "PR:000016401") AnnotationAssertion(rdfs:comment "Category=gene. Requested by=CL.") AnnotationAssertion(rdfs:label "transmembrane emp24 domain-containing protein 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (vimentin) @@ -120420,7 +118651,6 @@ AnnotationAssertion( "PR:000017298") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "vimentin") -AnnotationAssertion( ) SubClassOf( ) # Class: (VIP peptides) @@ -120434,7 +118664,6 @@ AnnotationAssertion( "PR:000017299") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "VIP peptides") -AnnotationAssertion( ) SubClassOf( ) # Class: (amino acid chain) @@ -120886,7 +119115,6 @@ AnnotationAssertion( "PR:000025403") AnnotationAssertion(rdfs:comment "Category=sequence. Requested by=CL.") AnnotationAssertion(rdfs:label "T-cell surface glycoprotein CD8 alpha chain isoform 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (T-cell surface glycoprotein CD8 beta chain isoform 1) @@ -120984,7 +119212,6 @@ AnnotationAssertion(Annotation( "PR:000025670") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "killer cell lectin-like receptor subfamily B member 1") -AnnotationAssertion( ) SubClassOf( ) # Class: (integrin alpha) @@ -121102,7 +119329,6 @@ AnnotationAssertion(Annotation( "PR:000032148") AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "lysosome-associated membrane glycoprotein 5") -AnnotationAssertion( ) SubClassOf( ) # Class: (lymphocyte antigen 75 (human)) @@ -129596,8 +127822,6 @@ SubClassOf( ObjectSomeValuesFrom( "A material entity consisting of multiple components that are causally integrated.") AnnotationAssertion( "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43") -AnnotationAssertion( ) -AnnotationAssertion( "http://www.jbiomedsem.com/content/4/1/43") AnnotationAssertion(rdfs:label "system") SubClassOf( ) @@ -129619,9 +127843,6 @@ DisjointClasses( "Wikipedia:Cervix") Annotation( "http://orcid.org/0000-0002-6601-2165") "Lower, narrow portion of the uterus where it joins with the top end of the vagina.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001359") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/uterine+cervix") "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001359") Annotation( "VHOG") Annotation( "DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)") Annotation( "http://bgee.unil.ch/") "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]") -AnnotationAssertion( "cervical") AnnotationAssertion(Annotation( "EFO:0000979") "cervix") AnnotationAssertion( "BTO:0001421") AnnotationAssertion( "BTO:0002249") @@ -129657,15 +127878,15 @@ AnnotationAssertion( "uterine cervix") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (naris) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000311") Annotation( "AAO") Annotation( "AAO:EJS") "One of paired external openings of the nasal chamber.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000663") Annotation( "VHOG") Annotation( "DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)") Annotation( "http://bgee.unil.ch/") "Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]") -AnnotationAssertion( "in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity") -AnnotationAssertion(Annotation( "FMA") "we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure") AnnotationAssertion( "AAO:0000311") AnnotationAssertion( "EHDAA2:0001225") AnnotationAssertion( "EHDAA:9083") @@ -129680,16 +127901,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "naris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nose) AnnotationAssertion(Annotation( "UBERON:cjm") "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.") -AnnotationAssertion(Annotation( "ZFA:0000047") "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].") -AnnotationAssertion(Annotation( "Wikipedia:Nose") "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].") -AnnotationAssertion(Annotation( "MP:0002233") "the organ that is specialized for smell and is part of the respiratory system") -AnnotationAssertion( "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]") AnnotationAssertion( "BTO:0000840") AnnotationAssertion( "CALOHA:TS-2037") AnnotationAssertion( "EHDAA2:0001274") @@ -129725,7 +127945,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nose") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "ZFA-def") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -129736,7 +127958,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (chemosensory organ) -AnnotationAssertion(Annotation( ) "FBbt:00005157") AnnotationAssertion(Annotation( "FBbt:00005157") "chemosensory sensory organ") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000005") @@ -129744,17 +127965,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chemosensory organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (islet of Langerhans) AnnotationAssertion(Annotation( "MA:0000127") Annotation( "MESH:A03.734.414") Annotation( "MP:0005215") "The clusters of hormone-producing cells that are scattered throughout the pancreas.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010406") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000646") Annotation( "VHOG") Annotation( "PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)") Annotation( "http://bgee.unil.ch/") "Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]") -AnnotationAssertion(Annotation( "PMID:16417468") "A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)") -AnnotationAssertion( ) AnnotationAssertion( "AAO:0010406") AnnotationAssertion( "BTO:0000991") AnnotationAssertion( "CALOHA:TS-0741") @@ -129785,6 +128004,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "islet of Langerhans") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectSomeValuesFrom( )) @@ -129795,10 +128015,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pituitary gland) AnnotationAssertion(Annotation( "Wikipedia:Pituitary_gland") Annotation( "ZFIN:curator") "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010536") Annotation( "AAO") Annotation( "AAO:BJB") "An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000118") Annotation( "TAO") Annotation( "ZFIN:curator") "An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000143") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510") Annotation( "http://bgee.unil.ch/") "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]") -AnnotationAssertion( "The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]") AnnotationAssertion(Annotation( "BIRNLEX:1353") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "Hp") AnnotationAssertion( "AAO:0010536") AnnotationAssertion( "BAMS:PIT") @@ -129846,7 +128062,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "pituitary gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png"^^xsd:anyURI) SubClassOf(Annotation( "BTO") Annotation( "EFO") Annotation( "VHOG") ) -SubClassOf(Annotation( "MA") Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -129859,7 +128076,6 @@ SubClassOf(Annotation( "htt # Class: (submucosa) AnnotationAssertion(Annotation( "Wikipedia:Submucosa") "A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].") -AnnotationAssertion( "submucosal") AnnotationAssertion( "BTO:0002107") AnnotationAssertion( "FMA:85391") AnnotationAssertion( "FMA:85392") @@ -129890,10 +128106,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0007422") "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000142") Annotation( "TAO") Annotation( "ZFIN:curator") "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000429") Annotation( "AAO") Annotation( "AAO:BJB") "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]") -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Cumbo_terms") "The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000399") Annotation( "VHOG") Annotation( "DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)") Annotation( "http://bgee.unil.ch/") "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]") AnnotationAssertion(Annotation( ) "PNS") AnnotationAssertion( "AAO:0000429") AnnotationAssertion( "BAMS:PNS") @@ -129906,7 +128118,6 @@ AnnotationAssertion( "EHDAA:2893") AnnotationAssertion( "EMAPA:16665") AnnotationAssertion( "EV:0100335") -AnnotationAssertion(Annotation( ) "FBbt:00005098") AnnotationAssertion( "FMA:9903") AnnotationAssertion( "GAID:715") AnnotationAssertion( "MA:0000218") @@ -129941,8 +128152,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (parasympathetic nervous system) AnnotationAssertion(Annotation( "GO:0048486") "The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010488") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000755") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)") Annotation( "http://bgee.unil.ch/") "In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0010488") AnnotationAssertion( "BIRNLEX:2517") AnnotationAssertion( "BTO:0001833") @@ -129978,9 +128187,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "parasympathetic nervous system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf(Annotation( "FMA") Annotation( "MA") Annotation( "WP") Annotation( "ZFA-modified-from-isa") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatic nervous system) @@ -130009,10 +128218,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (sympathetic nervous system) AnnotationAssertion(Annotation( "GO:0048485") "The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010487") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000384") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000384") Annotation( "VHOG") Annotation( "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463") Annotation( "http://bgee.unil.ch/") "The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]") -AnnotationAssertion( "has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)") AnnotationAssertion( "AAO:0010487") AnnotationAssertion( "BIRNLEX:2516") AnnotationAssertion( "BTO:0001832") @@ -130053,12 +128258,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (zone of skin) AnnotationAssertion(Annotation( "Wikipedia:Skin") Annotation( "http://orcid.org/0000-0002-6601-2165") "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.") -AnnotationAssertion( "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000860") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)") Annotation( "http://bgee.unil.ch/") "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]") -AnnotationAssertion( "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive") -AnnotationAssertion( "EHDAA2:0001844") AnnotationAssertion( "EHDAA:6530") -AnnotationAssertion( "EMAPA:17525") AnnotationAssertion( "EV:0100152") AnnotationAssertion( "FMA:86166") AnnotationAssertion( "GAID:933") @@ -130080,6 +128280,8 @@ AnnotationAssertion( "zone of skin") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130108,10 +128310,6 @@ SubClassOf(Annotation( "CAR AnnotationAssertion(Annotation( "GO:GO") Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.") AnnotationAssertion( "create a separate class for distributed pancreas, eg cyclostomes?") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000049") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/Pancreas") "The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001260") Annotation( "TAO") Annotation( "ZFIN:curator") "The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000049") Annotation( "VHOG") Annotation( "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)") Annotation( "http://bgee.unil.ch/") "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]") -AnnotationAssertion(Annotation( "PMID:20959416") "endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys") AnnotationAssertion( "BTO:0000650") AnnotationAssertion( "CALOHA:TS-1302") AnnotationAssertion( "EFO:0002542") @@ -130119,7 +128317,6 @@ AnnotationAssertion( "EV:0100129") AnnotationAssertion( "FMA:16018") AnnotationAssertion( "MA:0001582") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D007515") AnnotationAssertion( "NCIT:C32509") AnnotationAssertion( "SCTID:361339003") AnnotationAssertion( "TAO:0001260") @@ -130140,6 +128337,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine pancreas") SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "AAO") Annotation( "FMA") Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130153,9 +128351,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GOC:GO") Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001249") Annotation( "TAO") Annotation( "ZFIN:curator") "The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000048") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/Pancreas") "The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000048") Annotation( "VHOG") Annotation( "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)") Annotation( "http://bgee.unil.ch/") "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]") AnnotationAssertion( "AAO:0010407") AnnotationAssertion( "BTO:0000434") AnnotationAssertion( "CALOHA:TS-1241") @@ -130163,7 +128358,6 @@ AnnotationAssertion( "EV:0100093") AnnotationAssertion( "FMA:16017") AnnotationAssertion( "MA:0002415") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D046790") AnnotationAssertion( "NCIT:C32546") AnnotationAssertion( "SCTID:248202004") AnnotationAssertion( "TAO:0001249") @@ -130185,8 +128379,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine pancreas") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130196,11 +128392,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (compound eye) AnnotationAssertion(Annotation( "FB:gg") Annotation( "Wikipedia:Compound_eye") "A light sensing organ composed of ommatidia.") -AnnotationAssertion(Annotation( "PMID:21062451") "The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures") AnnotationAssertion( "BTO:0001921") -AnnotationAssertion(Annotation( ) "FBbt:00004508") AnnotationAssertion( "HAO:0000217") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0002421") AnnotationAssertion( "TGMA:0000024") AnnotationAssertion( "Wikipedia:Compound_eye") AnnotationAssertion( "uberon") @@ -130216,14 +128409,13 @@ AnnotationAssertion( "compound eye") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/457"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "PMID:21062451") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (camera-type eye) AnnotationAssertion(Annotation( "GO:0043010") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000107") Annotation( "TAO") Annotation( "TAO:wd") "A cavitated compound organ that transduces light waves into neural signals.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000275") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)") Annotation( "http://bgee.unil.ch/") "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this") AnnotationAssertion(Annotation( "FMA:54448") "eye") AnnotationAssertion( "AAO:0010340") AnnotationAssertion( "BIRNLEX:1169") @@ -130254,12 +128446,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "camera-type eye") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sense organ) @@ -130272,7 +128466,6 @@ AnnotationAssertion( "EHDAA2:0001824") AnnotationAssertion( "EHDAA:500") AnnotationAssertion( "EMAPA:35955") -AnnotationAssertion(Annotation( ) "FBbt:00005155") AnnotationAssertion( "GAID:63") AnnotationAssertion( "HAO:0000930") AnnotationAssertion( "MA:0000017") @@ -130298,7 +128491,9 @@ AnnotationAssertion( "sense organ") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cutaneous appendage) @@ -130314,15 +128509,12 @@ AnnotationAssertion( "UBERON:0000021") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cutaneous appendage") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tube) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.") -AnnotationAssertion( "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)") -AnnotationAssertion( "tubular") AnnotationAssertion( "galen:Tube") AnnotationAssertion( "anatomical tube") AnnotationAssertion( "duct") @@ -130330,15 +128522,13 @@ AnnotationAssertion( "UBERON:0000025") AnnotationAssertion(rdfs:label "tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendage) AnnotationAssertion(Annotation( "CARO:DOS") "Major subdivision of an organism that protrudes from the body[DOS, CARO].") -AnnotationAssertion(Annotation( "BILA:0000018") "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].") -AnnotationAssertion(Annotation( "GO:0048736") "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].") -AnnotationAssertion( "appendicular") -AnnotationAssertion( "this is currently a subtype of organism subdivision - which would exclude feathers") AnnotationAssertion( "AEO:0000193") AnnotationAssertion( "BILA:0000018") AnnotationAssertion( "BTO:0001492") @@ -130347,7 +128537,6 @@ AnnotationAssertion( "EHDAA2:0003193") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37283") AnnotationAssertion( "EV:0100155") -AnnotationAssertion(Annotation( ) "FBbt:00007000") AnnotationAssertion( "HAO:0000144") AnnotationAssertion( "MAT:0000023") AnnotationAssertion( "MESH:D005121") @@ -130374,7 +128563,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0000784") "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001273") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630") Annotation( "http://bgee.unil.ch/") "Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]") AnnotationAssertion( "BTO:0000784") AnnotationAssertion( "CALOHA:TS-0579") AnnotationAssertion( "EFO:0000872") @@ -130407,13 +128595,17 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/650"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria) @@ -130461,16 +128653,12 @@ AnnotationAssertion( "UBERON:0000031") AnnotationAssertion(rdfs:label "lamina propria of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (head) AnnotationAssertion(Annotation( "GO:0060322") Annotation( "Wikipedia:Head") "The head is the anterior-most division of the body [GO].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010335") Annotation( "AAO") Annotation( "AAO:BJB") "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001114") Annotation( "TAO") Annotation( "ZFIN:curator") "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001644") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82") Annotation( "http://bgee.unil.ch/") "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]") AnnotationAssertion( "AAO:0010335") AnnotationAssertion( "AEO:0000106") AnnotationAssertion( "BILA:0000115") @@ -130510,7 +128698,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "head") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130537,6 +128724,7 @@ AnnotationAssertion( "primary ovarian follicle") EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary ovarian follicle) @@ -130563,7 +128751,9 @@ AnnotationAssertion( "secondary ovarian follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectMinCardinality(2 ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tertiary ovarian follicle) @@ -130594,14 +128784,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectMinCardinality(2 ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (follicular fluid) AnnotationAssertion(Annotation( "ISBN:145114847X") Annotation( "MESH:D015571") Annotation( "Wikipedia:Follicular_fluid") "The fluid surrounding the ovum and granulosa cells in the ovarian follicle.") AnnotationAssertion( ) -AnnotationAssertion( "Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]") -AnnotationAssertion( "The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.") AnnotationAssertion( "BTO:0004383") AnnotationAssertion( "CALOHA:TS-0728") AnnotationAssertion( "FMA:18665") @@ -130649,13 +128839,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "follicular antrum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serous membrane) AnnotationAssertion(Annotation( "Wikipedia:Serous_membrane") Annotation( "https://github.com/obophenotype/uberon/issues/86") "Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005425") Annotation( "TAO") Annotation( "Wikipedia:Serous_membrane") "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]") -AnnotationAssertion(Annotation( "Wikipedia:Serous_membrane") "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]") -AnnotationAssertion(Annotation( "FMA") "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.") AnnotationAssertion( "FMA:9581") AnnotationAssertion( "GAID:19") AnnotationAssertion( "MESH:D012704") @@ -130675,18 +128865,16 @@ AnnotationAssertion( "serous membrane") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (tendon) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000073") Annotation( "Wikipedia:Tendon") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Dense regular connective tissue that connects muscle to bone[VSAO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000073") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Dense regular connective tissue that connects muscle to bone.[VSAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001286") Annotation( "VHOG") Annotation( "DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)") Annotation( "http://bgee.unil.ch/") "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis") AnnotationAssertion( "AEO:0000091") AnnotationAssertion( "BTO:0001356") AnnotationAssertion( "CALOHA:TS-1021") @@ -130716,7 +128904,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg"^^xsd:anyURI) SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "OG") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130726,10 +128913,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:2596") "Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000200") Annotation( "TAO") Annotation( "ZFIN:curator") "Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000222") Annotation( "VHOG") Annotation( "DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)") Annotation( "http://bgee.unil.ch/") "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]") -AnnotationAssertion( "The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065]") -AnnotationAssertion(Annotation( "FMA") "MA and EMAPA introduce distinct classes for what appears to be the same thing") AnnotationAssertion( "UBERON:0026602") AnnotationAssertion( "AAO:0011032") AnnotationAssertion( "BIRNLEX:2596") @@ -130748,7 +128931,6 @@ AnnotationAssertion( "MA:0000231") AnnotationAssertion( "MA:0000232") AnnotationAssertion( "MAT:0000162") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005727") AnnotationAssertion( "MIAA:0000162") AnnotationAssertion( "NCIT:C12462") AnnotationAssertion( "SCTID:244455004") @@ -130780,19 +128962,16 @@ AnnotationAssertion(rdfs:seeAlso AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf(Annotation( "DOI:10.1101/gr.157586.113") Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ganglion) AnnotationAssertion(Annotation( "Wikipedia:Ganglion") Annotation( "https://github.com/obophenotype/uberon/issues/300") "A biological tissue mass, most commonly a mass of nerve cell bodies.") AnnotationAssertion( "TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "PMID:21062451") "A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010426") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000190") Annotation( "TAO") Annotation( "ZFIN:curator") "Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]") -AnnotationAssertion(Annotation( "NLXANAT:100302") "Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000156") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]") -AnnotationAssertion( "ganglionic") AnnotationAssertion( "AAO:0010426") AnnotationAssertion( "AEO:0000135") AnnotationAssertion( "BAMS:G") @@ -130837,7 +129016,6 @@ SubClassOf(Annotation( "htt SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) -DisjointClasses(Annotation( "BTO") ) # Class: (simple eye) @@ -130861,7 +129039,6 @@ AnnotationAssertion( "DHBA:10576") AnnotationAssertion( "DMBA:17767") AnnotationAssertion( "EMAPA:35352") -AnnotationAssertion(Annotation( "inferred") "FMA:61965") AnnotationAssertion( "FMA:83865") AnnotationAssertion( "HBA:9249") AnnotationAssertion( "MA:0002747") @@ -130889,7 +129066,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130922,15 +129099,13 @@ AnnotationAssertion( "macula lutea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (macula) AnnotationAssertion(Annotation( "MESH:A09.246.631.909.625.125") "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified].") -AnnotationAssertion( "this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000386") Annotation( "TAO") Annotation( "ZFIN:curator") "Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]") -AnnotationAssertion( "macular") AnnotationAssertion( "GAID:777") AnnotationAssertion( "MESH:D008267") AnnotationAssertion( "TAO:0000386") @@ -130947,6 +129122,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macula") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -130967,12 +129143,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0090189") Annotation( "Wikipedia:Ureter") "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010254") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000605") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000605") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543") Annotation( "http://bgee.unil.ch/") "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]") -AnnotationAssertion( "ureteral") -AnnotationAssertion( "ureteric") -AnnotationAssertion( "in humans, consists of adventitial, muscular and mucoa layers") AnnotationAssertion( "AAO:0010254") AnnotationAssertion( "BTO:0001409") AnnotationAssertion( "CALOHA:TS-1084") @@ -131005,10 +129175,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureter") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ) -SubClassOf(Annotation( "MA:0000378") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) @@ -131019,8 +129189,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (urethra) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0000537") "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.") -AnnotationAssertion( "urethral") -AnnotationAssertion( "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.") AnnotationAssertion( "BTO:0001426") AnnotationAssertion( "CALOHA:TS-1132") AnnotationAssertion( "EFO:0000931") @@ -131049,9 +129217,11 @@ AnnotationAssertion( "urethra") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131060,10 +129230,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (duct) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "http://www.siumed.edu/~dking2/intro/glands.htm#ducts") "A tubular structure that transports secreted or excreted substances.") -AnnotationAssertion(Annotation( "ZFA:0005171") "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].") -AnnotationAssertion( "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.") AnnotationAssertion( "AAO:0011123") -AnnotationAssertion(Annotation( ) "FBbt:00100314") AnnotationAssertion( "FMA:30320") AnnotationAssertion( "NCIT:C12948") AnnotationAssertion( "SCTID:91726008") @@ -131081,8 +129248,8 @@ AnnotationAssertion(Annotation( "UBERON:0000058") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131091,7 +129258,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Large_intestine_(anatomy)") "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000054") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566") Annotation( "http://bgee.unil.ch/") "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]") AnnotationAssertion( "AAO:0010396") AnnotationAssertion( "BTO:0000706") AnnotationAssertion( "CALOHA:TS-1306") @@ -131122,8 +129288,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb"^^xsd:anyURI) -SubClassOf( ) SubClassOf(Annotation( "cjm") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131132,10 +129298,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (anatomical wall) AnnotationAssertion(Annotation( "FMA:82482") "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.") -AnnotationAssertion(Annotation( "FMA") "in FMA, serosa is a wall") AnnotationAssertion( "UBERON:0009915") AnnotationAssertion( "wall") -AnnotationAssertion( "EMAPA:25036") AnnotationAssertion( "FMA:82482") AnnotationAssertion( "galen:Wall") AnnotationAssertion(Annotation( "FMA:82482") "wall of organ") @@ -131160,7 +129324,6 @@ AnnotationAssertion( "CARO:0000003") AnnotationAssertion( "EHDAA2:0003003") AnnotationAssertion( "EMAPA:0") -AnnotationAssertion(Annotation( ) "FBbt:00007001") AnnotationAssertion( "FMA:305751") AnnotationAssertion( "FMA:67135") AnnotationAssertion( "GAID:781") @@ -131191,8 +129354,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "GO:0048513") "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") -AnnotationAssertion( "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4") AnnotationAssertion( "BIRNLEX:4") AnnotationAssertion( "CARO:0020004") AnnotationAssertion( "EFO:0000634") @@ -131224,8 +129385,6 @@ DisjointClasses( "http://orcid.org/0000-0002-6601-2165") "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.") AnnotationAssertion( "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction") -AnnotationAssertion(Annotation( "FMA:86140") Annotation( "3") "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.") -AnnotationAssertion(Annotation( "FMA:86140") Annotation( "1") "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.") AnnotationAssertion( "FMA:86140") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FMA:86140") "organ region with fixed fiat boundary") @@ -131239,7 +129398,6 @@ SubClassOf( (organ part) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A multicellular structure that is a part of an organ.") -AnnotationAssertion( "currently defined in a very broad sense, may be replaced by more specific classes in the future") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -131277,7 +129435,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory tract") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK10107") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131298,6 +129456,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fully formed stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/566"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131324,8 +129483,8 @@ AnnotationAssertion( "embryogenesis") AnnotationAssertion( "UBERON:0000068") AnnotationAssertion(rdfs:label "embryo stage") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131334,13 +129493,10 @@ DisjointClasses( (larval stage) AnnotationAssertion(Annotation( "Wikipedia:Larva") "A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.") -AnnotationAssertion( "Uberon includes clade-specific subclasses, e.g. nematod larva") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "WP") "It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form") AnnotationAssertion( "BTO:0000915") AnnotationAssertion( "BTO:0000954") AnnotationAssertion( "EFO:0001303") -AnnotationAssertion( "FBdv:00005336") AnnotationAssertion( "MIAA:0000400") AnnotationAssertion( "OGES:000008") AnnotationAssertion( "Wikipedia:Larva") @@ -131383,6 +129539,7 @@ AnnotationAssertion( "UBERON:0000069") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "larval stage") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131394,7 +129551,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ncit") "ncit:Death is an outcome") AnnotationAssertion( "XAO:0000437") AnnotationAssertion( "XtroDO:0000085") AnnotationAssertion( "uberon") @@ -131402,15 +129558,13 @@ AnnotationAssertion( "UBERON:0000071") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "death stage") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximo-distal subdivision of respiratory tract) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An section of a respiratory tract.") -AnnotationAssertion(Annotation( "MA") "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole") -AnnotationAssertion( "EMAPA:16737") AnnotationAssertion( "FMA:45660") AnnotationAssertion( "MA:0000434") AnnotationAssertion( "uberon") @@ -131420,6 +129574,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximo-distal subdivision of respiratory tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regional part of nervous system) @@ -131437,12 +129594,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regional part of nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal glomerulus) AnnotationAssertion(Annotation( "MP:0005325") Annotation( "Wikipedia:Glomerulus") "A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ZFA") "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?") AnnotationAssertion( ) AnnotationAssertion( "2009-06-18T09:26:37Z") AnnotationAssertion( "glomerulus") @@ -131478,6 +129636,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131506,9 +129665,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0012532") "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.") AnnotationAssertion( "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)") -AnnotationAssertion( ) -AnnotationAssertion( "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006242") AnnotationAssertion( "EHDAA2:0001968") AnnotationAssertion( "EHDAA:1494") AnnotationAssertion( "EHDAA:350") @@ -131529,34 +129685,35 @@ AnnotationAssertion( "external ectoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png"^^xsd:anyURI) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (mixed endoderm/mesoderm-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops from the endoderm and the mesoderm.") -AnnotationAssertion( "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000077") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mixed endoderm/mesoderm-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mixed ectoderm/mesoderm/endoderm-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops from the ectoderm, mesoderm and endoderm.") -AnnotationAssertion( "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000078") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mixed ectoderm/mesoderm/endoderm-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (male reproductive system) AnnotationAssertion(Annotation( "MP:0001145") "The organs associated with producing offspring in the gender that produces spermatozoa.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000725") Annotation( "VHOG") Annotation( "ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43") Annotation( "http://bgee.unil.ch/") "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]") AnnotationAssertion( "BTO:0000082") AnnotationAssertion( "CALOHA:TS-1310") AnnotationAssertion( "EFO:0000970") @@ -131564,7 +129721,6 @@ AnnotationAssertion( "EHDAA:8136") AnnotationAssertion( "EMAPA:17968") AnnotationAssertion( "EV:0100101") -AnnotationAssertion(Annotation( ) "FBbt:00004927") AnnotationAssertion( "FMA:45664") AnnotationAssertion( "GAID:386") AnnotationAssertion( "HAO:0000505") @@ -131597,18 +129753,13 @@ AnnotationAssertion( "male reproductive system") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (mesonephros) AnnotationAssertion(Annotation( "GO:0001823") Annotation( "Wikipedia:Mesonephros") "The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000038") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010384") Annotation( "AAO") Annotation( "AAO:BJB") "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000038") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639") Annotation( "http://bgee.unil.ch/") "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]") -AnnotationAssertion( "mesonephric") -AnnotationAssertion( "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney") -AnnotationAssertion( "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]") AnnotationAssertion( "AAO:0010384") AnnotationAssertion( "BTO:0001542") AnnotationAssertion( "CALOHA:TS-0624") @@ -131646,16 +129797,13 @@ AnnotationAssertion( "mesonephros") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephros) AnnotationAssertion(Annotation( "GO:0001656") Annotation( "Wikipedia:Metanephros#Metanephros") "In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].") AnnotationAssertion( "TODO check developmental relationships") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000039") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000039") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543") Annotation( "http://bgee.unil.ch/") "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]") -AnnotationAssertion( "metanephric") -AnnotationAssertion( "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis") AnnotationAssertion( "BTO:0001543") AnnotationAssertion( "EHDAA2:0001137") AnnotationAssertion( "EHDAA:3089") @@ -131679,7 +129827,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metanephros") SubClassOf( ) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) @@ -131689,8 +129838,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Mesonephric_tubules") "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].") AnnotationAssertion( "TODO check") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000500") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/mesonephric+tubule") "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000500") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639") Annotation( "http://bgee.unil.ch/") "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]") AnnotationAssertion( "AAO:0010389") AnnotationAssertion( "EHDAA2:0001134") AnnotationAssertion( "EMAPA:16747") @@ -131703,13 +129850,13 @@ AnnotationAssertion(Annotation( "UBERON:0000083") AnnotationAssertion(rdfs:label "mesonephric tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (ureteric bud) AnnotationAssertion(Annotation( "MP:0010979") Annotation( "PMID:19828308") "An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000541") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]") -AnnotationAssertion(Annotation( "VHOG:0000541") "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000541") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543") Annotation( "http://bgee.unil.ch/") "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]") AnnotationAssertion( "BTO:0001646") AnnotationAssertion( "EHDAA2:0002140") AnnotationAssertion( "EHDAA:3091") @@ -131731,7 +129878,9 @@ AnnotationAssertion(Annotation( "UBERON:0000084") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureteric bud") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) @@ -131739,7 +129888,6 @@ SubClassOf(Annotation( "ISB # Class: (morula) AnnotationAssertion(Annotation( "MP:0012130") "A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 has embryo starting later") AnnotationAssertion( "BTO:0001508") AnnotationAssertion( "EHDAA2:0000005") AnnotationAssertion( "FMA:292334") @@ -131766,7 +129914,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Zona_pellucida") "A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000720") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159") Annotation( "http://bgee.unil.ch/") "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]") AnnotationAssertion(Annotation( "VHOG:0000720") "zona pellucida - vitelline membrane") AnnotationAssertion( "BTO:0003135") AnnotationAssertion( "EHDAA2:0002220") @@ -131780,7 +129927,6 @@ AnnotationAssertion( "NCIT:C33896") AnnotationAssertion( "TAO:0001111") AnnotationAssertion(Annotation( "ncithesaurus:Zona_Pellucida") "UMLS:C0043519") -AnnotationAssertion( "VHOG:0000720") AnnotationAssertion( "Wikipedia:Zona_pellucida") AnnotationAssertion( "ZFA:0001111") AnnotationAssertion( "uberon") @@ -131797,7 +129943,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "zona pellucida") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131805,9 +129951,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (inner cell mass) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:pvb") "A mass of cells that develop into the body of the embryo and some extraembryonic tissues.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000742") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000742") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144") Annotation( "http://bgee.unil.ch/") "A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]") -AnnotationAssertion( "This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]") AnnotationAssertion( "EFO:0000547") AnnotationAssertion( "EHDAA2:0000830") AnnotationAssertion( "EHDAA:40") @@ -131831,17 +129974,12 @@ AnnotationAssertion( "inner cell mass") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (trophoblast) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005031") "The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta.") -AnnotationAssertion(Annotation( "2012-08-23") Annotation( "MP:0005031") Annotation( "trophoblast layer") Annotation( "MP") Annotation( "ISBN:0-683-40008-8") "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]") -AnnotationAssertion( "trophoblastic") -AnnotationAssertion(Annotation( "PMID:19829370") "The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta") AnnotationAssertion( "BTO:0001079") AnnotationAssertion( "CALOHA:TS-1070") AnnotationAssertion( "EV:0100120") @@ -131894,7 +130032,6 @@ SubClassOf(Annotation( "Wik # Class: (post-embryonic stage) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Stage succeeding embryo, including mature structure.") -AnnotationAssertion( "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)") AnnotationAssertion( "BilaDO:0000003") AnnotationAssertion( "OGES:000010") AnnotationAssertion( "OGES:000014") @@ -131909,8 +130046,8 @@ AnnotationAssertion( "UBERON:0000092") AnnotationAssertion(rdfs:label "post-embryonic stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/344"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131938,14 +130075,13 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000094") AnnotationAssertion(rdfs:label "membrane organ") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA-def") ObjectSomeValuesFrom( )) # Class: (cardiac neural crest) AnnotationAssertion(Annotation( "Wikipedia:Cardiac_neural_crest") "Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].") -AnnotationAssertion(Annotation( "DOI:10.1242/dev.091751") "A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].") -AnnotationAssertion(Annotation( "ZFA") "ZFA treats this as a subtype of NC.") AnnotationAssertion( ) AnnotationAssertion( "2009-07-30T07:57:38Z") AnnotationAssertion( "TAO:0002173") @@ -131958,7 +130094,8 @@ AnnotationAssertion(Annotation( "UBERON:0000095") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac neural crest") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -131979,6 +130116,7 @@ AnnotationAssertion( "UBERON:0000101") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lobe of lung") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -131996,6 +130134,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (life cycle) @@ -132018,6 +130159,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "life cycle") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/532"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132029,8 +130171,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages") -AnnotationAssertion( "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage") AnnotationAssertion( "BILS:0000105") AnnotationAssertion( "EFO:0000399") AnnotationAssertion( "FBdv:00007012") @@ -132059,13 +130199,11 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (zygote stage) AnnotationAssertion(Annotation( "Wikipedia:Zygote") "A stage at which the organism is a single cell produced by means of sexual reproduction.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000745") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107") Annotation( "http://bgee.unil.ch/") "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]") AnnotationAssertion( "BILS:0000106") AnnotationAssertion( "BilaDO:0000005") AnnotationAssertion( "EFO:0001322") AnnotationAssertion( "EHDAA:27") AnnotationAssertion( "FBdv:00005288") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000302") AnnotationAssertion( "NCIT:C12601") AnnotationAssertion( "PdumDv:0000100") AnnotationAssertion( "VHOG:0000745") @@ -132084,6 +130222,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "zygote stage") AnnotationAssertion(rdfs:seeAlso ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132108,7 +130247,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cleavage stage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (blastula stage) @@ -132132,6 +130274,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blastula stage") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132160,6 +130303,7 @@ AnnotationAssertion(Annotation( "UBERON:0000109") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastrula stage") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BILS") ObjectSomeValuesFrom( )) @@ -132169,8 +130313,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neurula stage) AnnotationAssertion(Annotation( "GO:0001841") "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.") -AnnotationAssertion( ) -AnnotationAssertion( "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos.") AnnotationAssertion( "BILS:0000110") AnnotationAssertion( "BilaDO:0000009") AnnotationAssertion( "HsapDv:0000012") @@ -132181,6 +130323,7 @@ AnnotationAssertion( "neurula stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/343"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132203,6 +130346,7 @@ AnnotationAssertion( "organogenesis stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/533"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132210,8 +130354,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (sexually immature stage) -AnnotationAssertion(Annotation( "XAO:1000010") "The stage of being a sexually immature adult animal[XAO:1000010].") -AnnotationAssertion( "In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)") AnnotationAssertion( "BILS:0000112") AnnotationAssertion( "BTO:0002168") AnnotationAssertion( "EFO:0001300") @@ -132229,6 +130371,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sexually immature stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/427"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -132250,6 +130393,7 @@ AnnotationAssertion( "post-juvenile adult stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/345"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/499"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132258,7 +130402,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:anna") Annotation( "MP:0002276") Annotation( "PMID:14635660") "The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.") AnnotationAssertion( ) -AnnotationAssertion( "it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces") AnnotationAssertion( "EMAPA:35521") AnnotationAssertion( "FMA:27533") AnnotationAssertion( "MA:0001782") @@ -132275,13 +130418,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung epithelium) AnnotationAssertion(Annotation( "MP:0006382") "The epithelial layer of the lung.") -AnnotationAssertion( "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]") AnnotationAssertion( "BTO:0001653") AnnotationAssertion( "EMAPA:32860") AnnotationAssertion( "MA:0001783") @@ -132294,13 +130440,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory tube) AnnotationAssertion(Annotation( "GO:0030323") Annotation( "http://orcid.org/0000-0002-6601-2165") "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.") -AnnotationAssertion(Annotation( "GO") "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37946") AnnotationAssertion( "FMA:12224") AnnotationAssertion(Annotation( "FMA:12224") "segment of tracheobronchial tree") @@ -132312,6 +130459,10 @@ AnnotationAssertion( "UBERON:0000117") AnnotationAssertion(rdfs:label "respiratory tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung bud) @@ -132337,6 +130488,7 @@ AnnotationAssertion( "lung bud") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png"^^xsd:anyURI) SubClassOf(Annotation( "GO:0060441") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132354,13 +130506,11 @@ AnnotationAssertion( "UBERON:0000119") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell layer") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (blood brain barrier) AnnotationAssertion(Annotation( "DOI:10.1002/glia.20642") Annotation( "Wikipedia:Blood-brain_barrier") "Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001812") AnnotationAssertion( "NCIT:C13194") AnnotationAssertion(Annotation( "ncithesaurus:Blood-Brain_Barrier") "UMLS:C0005854") AnnotationAssertion( "Wikipedia:Blood-brain_barrier") @@ -132378,9 +130528,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (perineurium) AnnotationAssertion(Annotation( "NLXANAT:090205") Annotation( "PMID:18434767") Annotation( "PMID:25818566") "A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. The perineurium is a component of the blood–nerve barrier and is essential for protecting axons and their associated Schwann cells from ionic flux, toxins and infection.") -AnnotationAssertion(Annotation( "Wikipedia:Perineurium") "Connective tissue surrounding a fascicle[Wikipedia:Perineurium].") -AnnotationAssertion( "perineurial") -AnnotationAssertion(Annotation( "FBbt") "consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)") AnnotationAssertion( "BTO:0003153") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37849") AnnotationAssertion( "FMA:52585") @@ -132395,7 +130542,6 @@ AnnotationAssertion( "perineurium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132406,7 +130552,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "CARO:0001001") Annotation( "FBC:DOS") Annotation( "FBbt:00005099") "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.") AnnotationAssertion( "UBERON:0005163") AnnotationAssertion( "CARO:0001001") -AnnotationAssertion(Annotation( ) "FBbt:00005099") AnnotationAssertion( "NLX:147821") AnnotationAssertion( "funiculus") AnnotationAssertion(Annotation( "FBbt:00005099") "nerve fiber bundle") @@ -132421,7 +130566,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epineurium) AnnotationAssertion(Annotation( "NLXANAT:090203") "A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition.") -AnnotationAssertion(Annotation( "Wikipedia:Epineurium") "outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium].") AnnotationAssertion( "BTO:0003154") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37848") AnnotationAssertion( "FMA:12234") @@ -132441,8 +130585,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neural nucleus) AnnotationAssertion(Annotation( "NLX:28443") "A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).") -AnnotationAssertion(Annotation( "GO_REF:0000021") "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].") -AnnotationAssertion( "Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.") AnnotationAssertion( "nucleus") AnnotationAssertion( "AEO:0000136") AnnotationAssertion( "FMA:83686") @@ -132459,8 +130601,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural nucleus") SubClassOf( ) -SubClassOf(Annotation( "CUMBO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "we limit this structure by definition to chordate and vertebrate nervous systems") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial nerve nucleus) @@ -132479,11 +130620,12 @@ AnnotationAssertion( "cranial nerve nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial nucleus) AnnotationAssertion(Annotation( "ISBN:0838580343") Annotation( "MP:0000909") "The group of motor neurons residing in the pons that innervate the muscles of facial expression.") -AnnotationAssertion(Annotation( "FMA") "FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.") AnnotationAssertion( "BAMS:7") AnnotationAssertion( "BAMS:7N") AnnotationAssertion( "BAMS:VII") @@ -132508,9 +130650,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facial nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior region of body) @@ -132534,7 +130680,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A layer of the ovarian follicle that consists of theca cells.") AnnotationAssertion( ) -AnnotationAssertion( "The theca folliculi are responsible for the production of testosterone from androstenedione in females, and indirectly the production of estrogens by supplying the neighboring granulosa cells with androstenedione that can then be used as a substrate for aromatase. [Wikipedia:Theca_of_follicle]") AnnotationAssertion( "BTO:0002853") AnnotationAssertion( "EFO:0003629") AnnotationAssertion( "EMAPA:35636") @@ -132560,10 +130705,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "theca cell layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (membranous layer) -AnnotationAssertion(Annotation( "ncithesaurus:Membrane") "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.") AnnotationAssertion( "membrane") AnnotationAssertion( "FMA:30322") AnnotationAssertion( "FMA:82500") @@ -132586,7 +130735,6 @@ AnnotationAssertion( "EMAPA:18256") AnnotationAssertion( "FMA:15703") AnnotationAssertion( "MA:0000330") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001003") AnnotationAssertion( "NCIT:C12375") AnnotationAssertion( "SCTID:245438008") AnnotationAssertion(Annotation( "ncithesaurus:Anal_Canal") "UMLS:C0227411") @@ -132610,6 +130758,7 @@ AnnotationAssertion( "anal canal") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132621,10 +130770,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GOC:GO") Annotation( "Wikipedia:Intestine") "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.") AnnotationAssertion( "This class is probably too inclusive") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000246") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000056") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion( "intestinal") -AnnotationAssertion( "In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.") AnnotationAssertion( "AAO:0000246") AnnotationAssertion( "ANISEED:1235303") AnnotationAssertion( "BSA:0000093") @@ -132665,7 +130810,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (orifice) AnnotationAssertion(Annotation( "FMA:3724") "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].") -AnnotationAssertion(Annotation( "FMA") "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit") AnnotationAssertion(Annotation( "FMA:3724") "anatomical ostium") AnnotationAssertion( "ostium") AnnotationAssertion( "FMA:3724") @@ -132681,13 +130825,6 @@ SubClassOf( "ISBN:0073040584") Annotation( "Wikipedia:Cloaca") "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.") AnnotationAssertion( "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca") -AnnotationAssertion(Annotation( "most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.") ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001186") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/cloaca") "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000095") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001186") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572") Annotation( "http://bgee.unil.ch/") "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]") -AnnotationAssertion( "cloacal") -AnnotationAssertion( "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs") -AnnotationAssertion(Annotation( "WP") "hindgut endoderm and proctodeal ectoderm.") AnnotationAssertion( "AAO:0000095") AnnotationAssertion( "GAID:1206") AnnotationAssertion( "MESH:D002988") @@ -132712,7 +130849,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (embryonic cloaca) AnnotationAssertion(Annotation( "MP:0010115") Annotation( "Wikipedia:Cloaca_(embryology)") "Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].") -AnnotationAssertion( "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.") AnnotationAssertion( "EHDAA2:0000256") AnnotationAssertion( "EHDAA:4895") AnnotationAssertion( "EMAPA:27573") @@ -132731,9 +130867,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (primitive urogenital sinus) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010116") "The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000414") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/urogenital+sinus") "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000414") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300") Annotation( "http://bgee.unil.ch/") "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]") -AnnotationAssertion(Annotation( "MP") "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal") AnnotationAssertion(Annotation( "MP:0010116") "urogenital sinus") AnnotationAssertion( "EHDAA2:0004060") AnnotationAssertion( "EHDAA:5029") @@ -132752,9 +130885,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primitive urogenital sinus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MP-def") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -132762,11 +130894,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mouth) AnnotationAssertion(Annotation( "Wikipedia:Mouth") Annotation( "https://github.com/obophenotype/uberon/wiki/The-digestive-tract") "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010355") Annotation( "AAO") Annotation( "AAO:BJB") "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000812") Annotation( "VHOG") Annotation( "DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)") Annotation( "http://bgee.unil.ch/") "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]") -AnnotationAssertion( "oral") -AnnotationAssertion( "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives") -AnnotationAssertion(Annotation( "FMA") "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips") AnnotationAssertion( "AAO:0010355") AnnotationAssertion( "BTO:0001090") AnnotationAssertion( "BTO:0004698") @@ -132775,7 +130902,6 @@ AnnotationAssertion( "EHDAA2:0001326") AnnotationAssertion( "EHDAA:542") AnnotationAssertion( "EMAPA:16262") -AnnotationAssertion(Annotation( ) "FBbt:00003126") AnnotationAssertion( "FMA:49184") AnnotationAssertion( "GAID:75") AnnotationAssertion( "MA:0000341") @@ -132821,14 +130947,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/661"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (oral opening) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/The-digestive-tract") "The orifice that connects the mouth to the exterior of the body.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000280") Annotation( "VHOG") Annotation( "DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)") Annotation( "http://bgee.unil.ch/") "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]") AnnotationAssertion( "FMA:59806") AnnotationAssertion(Annotation( "FMA:59806") "oral fissure") AnnotationAssertion(Annotation( "FMA:59806") "oral orifice") @@ -132845,9 +130971,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (oral cavity) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "https://github.com/obophenotype/uberon/wiki/The-digestive-tract") Annotation( "https://orcid.org/0000-0002-6601-2165") "Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000960") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000188") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/oral+cavity") "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000188") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32") Annotation( "http://bgee.unil.ch/") "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]") AnnotationAssertion( "AAO:0000053") AnnotationAssertion( "AAO:0000960") AnnotationAssertion( "BSA:0000107") @@ -132860,7 +130983,6 @@ AnnotationAssertion( "EV:0100057") AnnotationAssertion( "FMA:20292") AnnotationAssertion( "HAO:0000669") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D009055") AnnotationAssertion( "NCIT:C12421") AnnotationAssertion( "SCTID:181220002") AnnotationAssertion( "TAO:0001027") @@ -132883,6 +131005,7 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal-distal subdivision of colon) @@ -132894,8 +131017,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal-distal subdivision of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "4") Annotation( "cjm") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pair of lungs) @@ -132912,15 +131036,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pair of lungs") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectExactCardinality(1 )) SubClassOf( ObjectExactCardinality(1 )) # Class: (respiration organ) AnnotationAssertion(Annotation( "GO:0007585") "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.") -AnnotationAssertion( "EMAPA:17607") AnnotationAssertion( "SCTID:272626006") AnnotationAssertion( "SPD:0000428") AnnotationAssertion( "TGMA:0001247") @@ -132937,7 +131063,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiration organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (amniotic fluid) @@ -132985,16 +131113,13 @@ AnnotationAssertion(Annotation( "UBERON:0000174") AnnotationAssertion(rdfs:label "excreta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood) AnnotationAssertion(Annotation( "FMA:9670") Annotation( "Wikipedia:Blood") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/9") "A fluid that is composed of blood plasma and erythrocytes.") -AnnotationAssertion( "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000007") Annotation( "TAO") Annotation( "ZFIN:curator") "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000046") Annotation( "AAO") Annotation( "AAO:LAP") "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000046") Annotation( "AAO") "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000224") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ") Annotation( "http://bgee.unil.ch/") "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]") AnnotationAssertion( "AAO:0000046") AnnotationAssertion( "BTO:0000089") AnnotationAssertion( "CALOHA:TS-0079") @@ -133028,6 +131153,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) @@ -133048,13 +131174,12 @@ AnnotationAssertion( "haemolymphatic fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gyrus) AnnotationAssertion(Annotation( "Wikipedia:Gyrus") Annotation( "https://github.com/obophenotype/uberon/issues/573") "A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "BTO:0002495") AnnotationAssertion( "FMA:83874") AnnotationAssertion( "NCIT:C32290") @@ -133077,9 +131202,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gyrus") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/573"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -133093,24 +131218,25 @@ AnnotationAssertion( "UBERON:0000201") AnnotationAssertion(rdfs:label "endothelial blood brain barrier") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (glial blood brain barrier) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A blood brain barrier composed of glial cells.") AnnotationAssertion( ) AnnotationAssertion( "2009-04-10T08:42:24Z") -AnnotationAssertion(Annotation( ) "FBbt:00007091") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000202") AnnotationAssertion(rdfs:label "glial blood brain barrier") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pallium) AnnotationAssertion(Annotation( "GO:0021543") Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Pallium_(neuroanatomy)") Annotation( "https://github.com/obophenotype/uberon/issues/287") "Dorsal part (roof region) of the telencephalon[GO].") AnnotationAssertion(Annotation( "PMID:8932866") ) -AnnotationAssertion(Annotation( "Wikipedia:Avian_pallium") Annotation( "NCBITaxon:8782") "In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume.") -AnnotationAssertion(Annotation( "WP") "In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus") AnnotationAssertion( ) AnnotationAssertion( "2009-04-18T12:03:09Z") AnnotationAssertion( "UBERON:0007333") @@ -133140,7 +131266,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (ventral part of telencephalon) AnnotationAssertion(Annotation( "GO:0021544") Annotation( "GO_REF:0000021") Annotation( "ISBN:0471888893") Annotation( "PMID:12626695") "Ventral part (base region) of the telencephalon.") -AnnotationAssertion(Annotation( "BTO") "BTO term refers specifically to the avian structure") AnnotationAssertion( ) AnnotationAssertion( "2009-04-18T12:12:27Z") AnnotationAssertion( "BTO:0003401") @@ -133159,14 +131284,12 @@ AnnotationAssertion( "ventral part of telencephalon") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "separated by cell-free region") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tetrapod frontal bone) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000107") Annotation( "PMID:7914451") Annotation( "Wikipedia:Frontal_bone") "The bone forming the forehead and roof of the eye orbit.") AnnotationAssertion( ) -AnnotationAssertion( "fused in humans, paired in other animals") -AnnotationAssertion( "In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).") AnnotationAssertion( "AAO:0000206") AnnotationAssertion( "EMAPA:19016") AnnotationAssertion( "FMA:52734") @@ -133176,7 +131299,6 @@ AnnotationAssertion( "NCIT:C32635") AnnotationAssertion( "SCTID:181793006") AnnotationAssertion(Annotation( "ncithesaurus:Frontal_Bone") "UMLS:C0016732") -AnnotationAssertion( "VHOG:0001324") AnnotationAssertion( "VSAO:0000208") AnnotationAssertion( "Wikipedia:Frontal_bone") AnnotationAssertion(Annotation( "AAO:0000206") "frontal") @@ -133191,18 +131313,15 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ligament) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000073") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.") -AnnotationAssertion(Annotation( "FMA:21496") "Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001682") Annotation( "TAO") Annotation( "TAO:wd") "Portion of connective tissue that connects bone or cartilage.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001272") Annotation( "VHOG") Annotation( "PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)") Annotation( "http://bgee.unil.ch/") "Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]") -AnnotationAssertion( "this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament") AnnotationAssertion( "CALOHA:TS-2145") AnnotationAssertion( "EFO:0001966") AnnotationAssertion( "EMAPA:35493") @@ -133241,6 +131360,8 @@ AnnotationAssertion( "UBERON:0000218") AnnotationAssertion(rdfs:label "vertebral arch of axis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebral foramen of atlas) @@ -133252,12 +131373,14 @@ AnnotationAssertion( "UBERON:0000219") AnnotationAssertion(rdfs:label "vertebral foramen of atlas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (atlanto-occipital joint) AnnotationAssertion(Annotation( "Wikipedia:Atlanto-occipital_joint") "The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital.") AnnotationAssertion( "FMA:24939") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001269") AnnotationAssertion( "NCIT:C32158") AnnotationAssertion( "SCTID:361831006") AnnotationAssertion(Annotation( "ncithesaurus:Atlanto-occipital_Joint") "UMLS:C0004169") @@ -133275,8 +131398,12 @@ AnnotationAssertion( "atlanto-occipital joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tendon sheath) @@ -133295,16 +131422,16 @@ AnnotationAssertion(Annotation( "UBERON:0000304") AnnotationAssertion(rdfs:label "tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (amnion) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0005029") "The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000721") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000721") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187") Annotation( "http://bgee.unil.ch/") "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]") -AnnotationAssertion( "amniotic") AnnotationAssertion( "BTO:0000065") AnnotationAssertion( "CALOHA:TS-0033") AnnotationAssertion( "EHDAA2:0000116") @@ -133327,6 +131454,8 @@ AnnotationAssertion( "amnion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -133357,12 +131486,11 @@ AnnotationAssertion( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (body wall) AnnotationAssertion(Annotation( "MP:0003385") "The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity.") -AnnotationAssertion( "defined generically to encompass both vertebrates and invertebrates") -AnnotationAssertion(Annotation( "BTO") "the BTO class refers to earthworms.") AnnotationAssertion( "BTO:0000139") AnnotationAssertion( "EMAPA:32761") AnnotationAssertion( "FMA:10427") @@ -133380,7 +131508,6 @@ SubClassOf( (breast) AnnotationAssertion(Annotation( "Wikipedia:Breast") "The upper ventral region of the torso of an organism.") -AnnotationAssertion(Annotation( "WP,unvetted") "The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.") AnnotationAssertion( "BTO:0000149") AnnotationAssertion( "CALOHA:TS-2083") AnnotationAssertion( "EV:0100124") @@ -133406,7 +131533,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (portion of cartilage tissue in tibia) AnnotationAssertion(Annotation( "Dorlands_Medical_Dictionary:MerckSource") "Cartilage pertaining to the tibia.") -AnnotationAssertion( "This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia") AnnotationAssertion( "BTO:0000207") AnnotationAssertion( "FMA:33923") AnnotationAssertion( "tibial cartilage") @@ -133415,6 +131541,9 @@ AnnotationAssertion(Annotation( "UBERON:0000313") AnnotationAssertion(rdfs:label "portion of cartilage tissue in tibia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cecum mucosa) @@ -133451,6 +131580,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cecum mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subarachnoid space) @@ -133477,9 +131608,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical mucus) @@ -133493,6 +131627,8 @@ AnnotationAssertion( "UBERON:0000316") AnnotationAssertion(rdfs:label "cervical mucus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colonic mucosa) @@ -133521,6 +131657,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "colonic mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duodenal mucosa) @@ -133543,16 +131681,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duodenal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (late embryo) AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-3308-6245") "An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.") AnnotationAssertion( "TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.") -AnnotationAssertion(Annotation( "FMA:63919") "Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].") AnnotationAssertion( "BTO:0000449") AnnotationAssertion( "CALOHA:TS-0360") AnnotationAssertion( "EFO:0001323") -AnnotationAssertion(Annotation( ) "FBbt:00005333") AnnotationAssertion( "FMA:63919") AnnotationAssertion( "GAID:552") AnnotationAssertion( "MESH:D005333") @@ -133568,6 +131706,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "late embryo") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastric gland) @@ -133581,6 +131721,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastric gland") SubClassOf(Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) # Class: (pancreatic juice) @@ -133598,11 +131739,12 @@ AnnotationAssertion(Annotation( "UBERON:0000326") AnnotationAssertion(rdfs:label "pancreatic juice") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gut wall) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).") -AnnotationAssertion( "We model the digestive tract as consisting of two parts: the wall and the lumen.") AnnotationAssertion( "BTO:0000547") AnnotationAssertion( "FMA:45653") AnnotationAssertion( "digestive tract wall") @@ -133613,6 +131755,8 @@ AnnotationAssertion( "UBERON:0000328") AnnotationAssertion(rdfs:label "gut wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ileal mucosa) @@ -133638,6 +131782,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ileal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (yellow bone marrow) @@ -133653,12 +131799,13 @@ AnnotationAssertion(Annotation( "UBERON:0000332") AnnotationAssertion(rdfs:label "yellow bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal gland) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].") -AnnotationAssertion( "Note that some sources treat 'intestinal gland' as synonymous with crypts") AnnotationAssertion( "BTO:0000640") AnnotationAssertion( "FMA:15052") AnnotationAssertion( "SCTID:266297002") @@ -133703,15 +131850,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intestinal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa) AnnotationAssertion(Annotation( "Wikipedia:Mucous_membrane") "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].") -AnnotationAssertion( ) -AnnotationAssertion( "mucosal") -AnnotationAssertion(Annotation( "FMA") "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately") AnnotationAssertion( "AEO:0000199") AnnotationAssertion( "BTO:0000886") AnnotationAssertion( "CALOHA:TS-2031") @@ -133739,6 +131883,7 @@ AnnotationAssertion( "mucosa") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -133748,8 +131893,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0009798") Annotation( "Wikipedia:Ophthalmic_nerve") "The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010648") Annotation( "AAO") Annotation( "AAO:EJS") "Sensory medial ramus of the trigeminal nerve.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001349") Annotation( "VHOG") Annotation( "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177") Annotation( "http://bgee.unil.ch/") "The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]") AnnotationAssertion( "AAO:0010648") AnnotationAssertion( "BTO:0000926") AnnotationAssertion( "EHDAA2:0002088") @@ -133796,10 +131939,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html]") AnnotationAssertion(rdfs:label "ophthalmic nerve") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "may be a distinct nerve in teleosts") Annotation( "multiple") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limbic system) @@ -133823,6 +131967,7 @@ AnnotationAssertion( "includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]") AnnotationAssertion(rdfs:label "limbic system") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -133834,8 +131979,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head") -AnnotationAssertion( "As it is required for running, not all animals have a nuchal ligament") AnnotationAssertion( "BTO:0000952") AnnotationAssertion( "EMAPA:19207") AnnotationAssertion( "FMA:13427") @@ -133848,19 +131991,15 @@ AnnotationAssertion( "paxwax") AnnotationAssertion( "UBERON:0000351") AnnotationAssertion(rdfs:label "nuchal ligament") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "C7 in humans") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parenchyma) AnnotationAssertion(Annotation( "Wikipedia:Parenchyma") "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.") -AnnotationAssertion( "parenchymal") -AnnotationAssertion(Annotation( "WP") "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin") -AnnotationAssertion(Annotation( "FMA") "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0000999") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0001539") AnnotationAssertion( "EHDAA:3015") AnnotationAssertion( "EHDAA:3905") AnnotationAssertion( "EHDAA:3999") @@ -133909,6 +132048,8 @@ AnnotationAssertion(Annotation( "UBERON:0000355") AnnotationAssertion(rdfs:label "pharyngeal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blastocyst) @@ -133956,13 +132097,14 @@ AnnotationAssertion(Annotation( "UBERON:0000361") AnnotationAssertion(rdfs:label "red bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal medulla) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:smb") Annotation( "MP:0003014") "The inner portion of the kidney consisting of the renal pyramids.") AnnotationAssertion( ) -AnnotationAssertion( "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water") AnnotationAssertion( "BTO:0001167") AnnotationAssertion( "CALOHA:TS-1157") AnnotationAssertion( "EMAPA:19279") @@ -133996,7 +132138,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134004,7 +132147,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (urothelium) AnnotationAssertion(Annotation( "Wikipedia:Urothelium") Annotation( "https://github.com/obophenotype/uberon/issues/92") "An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.") -AnnotationAssertion( "urothelial") AnnotationAssertion(Annotation( ) "transitional epithelium") AnnotationAssertion( "BTO:0003906") AnnotationAssertion( "CALOHA:TS-1096") @@ -134014,7 +132156,6 @@ AnnotationAssertion( "GAID:935") AnnotationAssertion( "MESH:D019459") AnnotationAssertion( "NCIT:C12884") -AnnotationAssertion( "NCIT:C13318") AnnotationAssertion( "SCTID:30117005") AnnotationAssertion( "SCTID:57789003") AnnotationAssertion(Annotation( "ncithesaurus:Transitional_Epithelium") "UMLS:C0225339") @@ -134036,8 +132177,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (corpus striatum) AnnotationAssertion(Annotation( "Wikipedia:Corpus_striatum") "The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001175") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10") Annotation( "http://bgee.unil.ch/") "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]") -AnnotationAssertion( "The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]") AnnotationAssertion( "UBERON:0010082") AnnotationAssertion( "BAMS:CSTR") AnnotationAssertion( "BTO:0001311") @@ -134088,7 +132227,6 @@ AnnotationAssertion( "syncytiotrophoblast") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134133,14 +132271,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mandibular nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb stylopod) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the hindlimb between pelvis and the knee, corresponding to the femur.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000349") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion(Annotation(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/61") "Naming conventions for pod terms under discussion within phenoscape group.") AnnotationAssertion( "BTO:0001376") AnnotationAssertion( "CALOHA:TS-2039") AnnotationAssertion( "EFO:0001943") @@ -134179,6 +132315,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134187,8 +132324,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0009799") Annotation( "Wikipedia:Maxillary_nerve") "The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010670") Annotation( "AAO") Annotation( "AAO:EJS") "Medial ramus (sensory) of the trigeminal nerve.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010670") Annotation( "AAO") "relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]") AnnotationAssertion( "AAO:0010670") AnnotationAssertion( "BTO:0001378") AnnotationAssertion( "EHDAA2:0002087") @@ -134222,13 +132357,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "maxillary nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tongue muscle) AnnotationAssertion(Annotation( "MP:0004136") Annotation( "Wikipedia:Muscles_of_tongue") "The muscular portion of the tongue.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001390") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)") Annotation( "http://bgee.unil.ch/") "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]") AnnotationAssertion( "BTO:0001386") AnnotationAssertion( "EHDAA2:0002065") AnnotationAssertion( "EHDAA:9146") @@ -134255,8 +132389,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf(Annotation( "FEED:rd") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FEED:rd") Annotation( "ISBN:1607950324") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134289,12 +132425,13 @@ AnnotationAssertion( "UBERON:0000379") AnnotationAssertion(rdfs:label "tracheal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (apocrine sweat gland) AnnotationAssertion(Annotation( "PMID:18489347") Annotation( "Wikipedia:Apocrine_sweat_gland") "Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP].") AnnotationAssertion(Annotation( "http://www.nal.usda.gov/awic/pubs/swine/swine.htm") ) -AnnotationAssertion( "In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region.") AnnotationAssertion( "BTO:0001458") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37426") AnnotationAssertion( "FMA:59155") @@ -134311,8 +132448,7 @@ AnnotationAssertion( "apocrine sweat gland") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2111") SubClassOf(Annotation( "FMA") ) -SubClassOf( ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) DisjointClasses( ) # Class: (musculature of body) @@ -134321,14 +132457,11 @@ AnnotationAssertion(Annotation( "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000033") Annotation( "VSAO") Annotation( "VSAO:curator") "Anatomical system that consists of the muscles of the body.[VSAO]") -AnnotationAssertion(Annotation( "MA") "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA") AnnotationAssertion( "AAO:0000307") AnnotationAssertion( "BILA:0000088") AnnotationAssertion( "BTO:0001369") AnnotationAssertion( "BTO:0001485") AnnotationAssertion( "EFO:0000801") -AnnotationAssertion( "EMAPA:35578") AnnotationAssertion( "FMA:72954") AnnotationAssertion( "MA:0002888") AnnotationAssertion( "MAT:0000025") @@ -134350,8 +132483,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens cortex) @@ -134368,8 +132503,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lens cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens nucleus) @@ -134385,14 +132523,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lens nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (leptomeninx) AnnotationAssertion(Annotation( "Wikipedia:Leptomeninges") Annotation( "https://github.com/obophenotype/uberon/issues/300") "Pia mater or arachnoid mater.") AnnotationAssertion( "check relationship to secondary meninx") -AnnotationAssertion(Annotation( "FMA") "in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular") AnnotationAssertion( "BTO:0001634") AnnotationAssertion( "CALOHA:TS-0546") AnnotationAssertion( "FMA:231515") @@ -134412,6 +132552,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "leptomeninx") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear ganglion) @@ -134446,15 +132587,17 @@ AnnotationAssertion( "cochlear ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "cell bodies") Annotation( "BTO-modified") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colonic epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a colon [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005128") Annotation( "TAO") Annotation( "ZFIN:curator") "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]") AnnotationAssertion( "BTO:0001709") AnnotationAssertion( "CALOHA:TS-0163") AnnotationAssertion( "EMAPA:18941") @@ -134478,7 +132621,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "colonic epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilage tissue of sternum) @@ -134490,6 +132634,9 @@ AnnotationAssertion( "Examples: cartilage of manubrium, cartilage of xiphoid process") AnnotationAssertion(rdfs:label "cartilage tissue of sternum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jejunal mucosa) @@ -134515,6 +132662,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "jejunal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jejunal epithelium) @@ -134532,7 +132681,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "jejunal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "BTO") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (nasal vestibule) @@ -134574,6 +132723,7 @@ AnnotationAssertion( "scalp") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134603,13 +132753,13 @@ AnnotationAssertion( "sympathetic trunk") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (serous gland) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "http://www.siumed.edu/~dking2/intro/glands.htm") "A gland in which the principal secretory cells are serous secreting cells.") -AnnotationAssertion(Annotation( "MP:0008052") "glands that secrete watery albuminous material that often contains enzymes[MP:0008052].") AnnotationAssertion( "BTO:0001837") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37950") AnnotationAssertion( "FMA:62889") @@ -134621,6 +132771,8 @@ AnnotationAssertion( "serous gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134659,14 +132811,14 @@ AnnotationAssertion( "UBERON:0000410") AnnotationAssertion(rdfs:label "bronchial mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermal papilla) AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2008.12.005") "A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen.") AnnotationAssertion( "consider adding grouping class for TAO:0001995 ! papilla") -AnnotationAssertion( "In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints)") -AnnotationAssertion( "Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells.") -AnnotationAssertion(Annotation( "ncit") "ncit has 'hair papilla' as part of hypodermis") AnnotationAssertion( "BTO:0001858") AnnotationAssertion( "CALOHA:TS-0431") AnnotationAssertion( "EMAPA:36484") @@ -134693,13 +132845,13 @@ AnnotationAssertion( "dermal papilla") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucous gland) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "http://www.siumed.edu/~dking2/intro/glands.htm") "A gland in which the principal secretory cells are mucus secreting cells.") -AnnotationAssertion(Annotation( "NCBITaxon:8292") Annotation( "ISBN:0073040584") "In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]") AnnotationAssertion( "AAO:0010601") AnnotationAssertion( "BTO:0001979") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37913") @@ -134716,6 +132868,7 @@ AnnotationAssertion( "mucous gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134732,6 +132885,8 @@ AnnotationAssertion( "UBERON:0000415") AnnotationAssertion(rdfs:label "artery wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myoepithelium) @@ -134745,13 +132900,14 @@ AnnotationAssertion(Annotation( "UBERON:0000420") AnnotationAssertion(rdfs:label "myoepithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eccrine sweat gland) AnnotationAssertion(Annotation( "Wikipedia:Eccrine_sweat_gland") Annotation( "http://orcid.org/0000-0002-6601-2165") "A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion.") AnnotationAssertion( ) -AnnotationAssertion( "in mice, found only on footpads; in humans, entire body including soles and palms") AnnotationAssertion( "BTO:0002323") AnnotationAssertion( "FMA:59154") AnnotationAssertion( "GAID:945") @@ -134773,7 +132929,6 @@ AnnotationAssertion( "eccrine sweat gland") SubClassOf( ) SubClassOf(Annotation( "MGI:anna") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (prostate epithelium) @@ -134805,8 +132960,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prostate epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enteric plexus) @@ -134828,6 +132987,8 @@ AnnotationAssertion( "enteric plexus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arachnoid barrier layer) @@ -134837,7 +132998,9 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000437") AnnotationAssertion(rdfs:label "arachnoid barrier layer") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -134854,12 +133017,15 @@ AnnotationAssertion(Annotation( "UBERON:0000439") AnnotationAssertion(rdfs:label "arachnoid trabecula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula) AnnotationAssertion(Annotation( "GO:0060343") Annotation( "Wikipedia:Trabecula") "A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].") -AnnotationAssertion( "trabecular") AnnotationAssertion( "BTO:0002501") AnnotationAssertion( "FMA:85273") AnnotationAssertion( "Wikipedia:Trabecula") @@ -134892,8 +133058,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right testicular vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left testicular vein) @@ -134913,8 +133081,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left testicular vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphoid follicle) @@ -134941,7 +133111,6 @@ SubClassOf(Annotation( "FMA # Class: (septum of telencephalon) AnnotationAssertion(Annotation( "BIRNLEX:963") "Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996).") -AnnotationAssertion(Annotation( "FMA:61842") "Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842].") AnnotationAssertion(Annotation( "PMID:23375746") Annotation( ) "Se") AnnotationAssertion(Annotation( "BIRNLEX:963") "septum") AnnotationAssertion( "BAMS:SA") @@ -134968,8 +133137,7 @@ AnnotationAssertion(Annotation( "UBERON:0000446") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "septum of telencephalon") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (cerebral subcortex) @@ -134985,12 +133153,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cerebral subcortex") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretion of exocrine gland) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A portion of organism substance that is produced by exocrine glands.") -AnnotationAssertion(Annotation( "BTO") "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions") AnnotationAssertion( "UBERON:0006540") AnnotationAssertion(Annotation( "FMA:9675") "secretion") AnnotationAssertion( "AEO:0001005") @@ -135014,6 +133182,8 @@ AnnotationAssertion(Annotation( "UBERON:0000456") AnnotationAssertion(rdfs:label "secretion of exocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cavernous artery) @@ -135026,6 +133196,9 @@ AnnotationAssertion( "UBERON:0000457") AnnotationAssertion(rdfs:label "cavernous artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocervix) @@ -135041,7 +133214,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocervix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (uterine wall) @@ -135057,6 +133234,8 @@ AnnotationAssertion( "UBERON:0000459") AnnotationAssertion(rdfs:label "uterine wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (organism substance) @@ -135072,7 +133251,6 @@ AnnotationAssertion( "CARO:0000004") AnnotationAssertion( "EHDAA2:0003004") AnnotationAssertion( "EMAPA:35178") -AnnotationAssertion(Annotation( ) "FBbt:00007019") AnnotationAssertion( "FMA:9669") AnnotationAssertion( "HAO:0000004") AnnotationAssertion( "MA:0002450") @@ -135096,7 +133274,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organism substance") SubClassOf( ) -SubClassOf(Annotation( "this relationship may be too strong and may be weakened in future") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical space) @@ -135112,7 +133290,6 @@ AnnotationAssertion( "BILA:0000005") AnnotationAssertion( "CARO:0000005") AnnotationAssertion( "EHDAA2:0003005") -AnnotationAssertion(Annotation( ) "FBbt:00007017") AnnotationAssertion( "FMA:5897") AnnotationAssertion( "HAO:0000005") AnnotationAssertion( "NCIT:C94478") @@ -135143,7 +133320,6 @@ AnnotationAssertion( "BILA:0000006") AnnotationAssertion( "CARO:0000006") AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion(Annotation( ) "FBbt:00007016") AnnotationAssertion( "FMA:67165") AnnotationAssertion( "HAO:0000006") AnnotationAssertion( "TAO:0001836") @@ -135169,7 +133345,6 @@ AnnotationAssertion( "BILA:0000007") AnnotationAssertion( "CARO:0000007") AnnotationAssertion( "EHDAA2:0003007") -AnnotationAssertion(Annotation( ) "FBbt:00007015") AnnotationAssertion( "FMA:67112") AnnotationAssertion( "HAO:0000007") AnnotationAssertion( "TAO:0001835") @@ -135203,10 +133378,8 @@ AnnotationAssertion( "EHDAA:392") AnnotationAssertion( "EMAPA:16103") AnnotationAssertion( "EV:0100000") -AnnotationAssertion(Annotation( ) "FBbt:00004856") AnnotationAssertion( "FMA:7149") AnnotationAssertion( "HAO:0000011") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0002460") AnnotationAssertion( "MA:0000003") AnnotationAssertion( "NCIT:C12919") AnnotationAssertion( "SCTID:278195005") @@ -135244,7 +133417,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "organismal") AnnotationAssertion(Annotation( "FBbt:00000001") Annotation( "VHOG:0000671") Annotation( "WBbt:0007833") "organism") AnnotationAssertion( "AAO:0010026") AnnotationAssertion( "AEO:0000191") @@ -135259,7 +133431,6 @@ AnnotationAssertion( "EHDAA:1") AnnotationAssertion( "EMAPA:25765") AnnotationAssertion( "EV:0100016") -AnnotationAssertion(Annotation( ) "FBbt:00000001") AnnotationAssertion( "FMA:256135") AnnotationAssertion( "HAO:0000012") AnnotationAssertion( "NCIT:C13041") @@ -135292,7 +133463,6 @@ SubClassOf( (compound organ component) AnnotationAssertion(Annotation( "CARO:0000019") Annotation( "http://orcid.org/0000-0001-9114-8737") "Multi-tissue structure that is part of a compound organ.") -AnnotationAssertion( "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future") AnnotationAssertion( "AAO:0010017") AnnotationAssertion( "AEO:0000019") AnnotationAssertion( "BILA:0000019") @@ -135314,10 +133484,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (testis) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A gonad of a male animal. A gonad produces and releases sperm.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000598") Annotation( "TAO") Annotation( "ZFIN:curator") "Male reproductive organ.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000252") Annotation( "VHOG") Annotation( "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)") Annotation( "http://bgee.unil.ch/") "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]") -AnnotationAssertion( "testicular") -AnnotationAssertion(Annotation( "ISBN:0123971756") Annotation( "NCBITaxon:40674") "The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally") AnnotationAssertion( "UBERON:0002117") AnnotationAssertion( "AAO:0000606") AnnotationAssertion( "BILA:0000124") @@ -135329,7 +133495,6 @@ AnnotationAssertion( "EHDAA:8146") AnnotationAssertion( "EMAPA:17972") AnnotationAssertion( "EV:0100102") -AnnotationAssertion(Annotation( ) "FBbt:00004928") AnnotationAssertion( "FMA:7210") AnnotationAssertion( "GAID:396") AnnotationAssertion( "HAO:0001007") @@ -135365,6 +133530,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -135373,7 +133539,6 @@ DisjointClasses( "MP:0001119") Annotation( "Wikipedia:Female_genitalia") Annotation( "http://orcid.org/0000-0002-6601-2165") "The organs and associated structures associated with bearing offspring in a female animal.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000726") Annotation( "VHOG") Annotation( "ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43") Annotation( "http://bgee.unil.ch/") "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]") AnnotationAssertion( "BTO:0000083") AnnotationAssertion( "CALOHA:TS-1303") AnnotationAssertion( "EFO:0000969") @@ -135381,7 +133546,6 @@ AnnotationAssertion( "EHDAA:8116") AnnotationAssertion( "EMAPA:17959") AnnotationAssertion( "EV:0100110") -AnnotationAssertion(Annotation( ) "FBbt:00004864") AnnotationAssertion( "FMA:45663") AnnotationAssertion( "GAID:364") AnnotationAssertion( "HAO:0000324") @@ -135435,7 +133599,6 @@ AnnotationAssertion( "EFO:0000808") AnnotationAssertion( "EHDAA2:0003032") AnnotationAssertion( "EMAPA:36031") -AnnotationAssertion(Annotation( ) "FBbt:00007009") AnnotationAssertion( "FMA:7153") AnnotationAssertion( "HAO:0000032") AnnotationAssertion( "MA:0002433") @@ -135477,7 +133640,6 @@ AnnotationAssertion( "BILA:0000040") AnnotationAssertion( "CARO:0000040") AnnotationAssertion( "EHDAA2:0003040") -AnnotationAssertion(Annotation( ) "FBbt:00007013") AnnotationAssertion( "FMA:63863") AnnotationAssertion( "HAO:0000040") AnnotationAssertion( "TAO:0000382") @@ -135499,7 +133661,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "FBbt:00007277") AnnotationAssertion( "VHOG:0001737") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000477") @@ -135518,7 +133679,6 @@ AnnotationAssertion( "CARO:0000042") AnnotationAssertion( "EHDAA2:0003042") AnnotationAssertion( "EHDAA:46") -AnnotationAssertion(Annotation( ) "FBbt:00005835") AnnotationAssertion( "FMA:85537") AnnotationAssertion( "HAO:0000042") AnnotationAssertion( "NCIT:C34055") @@ -135540,6 +133700,8 @@ AnnotationAssertion( "see also conceptus extraembryonic component in EHDAA2.") AnnotationAssertion(rdfs:label "extraembryonic structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tissue) @@ -135557,7 +133719,6 @@ AnnotationAssertion( "CARO:0000043") AnnotationAssertion( "EHDAA2:0003043") AnnotationAssertion( "EMAPA:35868") -AnnotationAssertion(Annotation( ) "FBbt:00007003") AnnotationAssertion( "FMA:9637") AnnotationAssertion( "HAO:0000043") AnnotationAssertion( "MA:0003002") @@ -135595,7 +133756,6 @@ AnnotationAssertion( "BILA:0000055") AnnotationAssertion( "CARO:0000055") AnnotationAssertion( "EHDAA2:0003055") -AnnotationAssertion(Annotation( ) "FBbt:00007010") AnnotationAssertion( "HAO:0000055") AnnotationAssertion( "TAO:0001488") AnnotationAssertion( "TGMA:0001847") @@ -135614,8 +133774,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epithelium) AnnotationAssertion(Annotation( "Wikipedia:Epithelium") Annotation( "http://orcid.org/0000-0001-9114-8737") "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000387") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59") Annotation( "http://bgee.unil.ch/") "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]") -AnnotationAssertion( "epithelial") AnnotationAssertion( "AAO:0000144") AnnotationAssertion( "AAO:0010055") AnnotationAssertion( "AEO:0000066") @@ -135625,7 +133783,6 @@ AnnotationAssertion( "CARO:0000066") AnnotationAssertion( "EHDAA2:0003066") AnnotationAssertion( "EMAPA:32738") -AnnotationAssertion(Annotation( ) "FBbt:00007005") AnnotationAssertion( "FMA:9639") AnnotationAssertion( "GAID:402") AnnotationAssertion( "HAO:0000066") @@ -135651,9 +133808,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://palaeos.com/metazoa/porifera/homoscleromorpha.html") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (simple cuboidal epithelium) @@ -135693,7 +133853,6 @@ AnnotationAssertion( "BILA:0000068") AnnotationAssertion( "CARO:0000068") AnnotationAssertion( "EHDAA2_RETIRED:0003068") -AnnotationAssertion(Annotation( ) "FBbt:00007027") AnnotationAssertion( "FMA:45567") AnnotationAssertion( "HAO:0000068") AnnotationAssertion( "NCIT:C33552") @@ -135718,7 +133877,6 @@ SubClassOf( (multilaminar epithelium) AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "Wikipedia:Stratified_epithelium") Annotation( "http://orcid.org/0000-0001-9114-8737") "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "CARO:0000069") Annotation( "CARO") Annotation( "FMA:45562") Annotation( "http://orcid.org/0000-0001-9114-8737") "Epithelium that consists of more than one layer of epithelial cells.[CARO]") AnnotationAssertion( "AAO:0010059") AnnotationAssertion( "AEO:0000069") AnnotationAssertion( "BILA:0000069") @@ -135746,7 +133904,6 @@ SubClassOf( (simple squamous epithelium) AnnotationAssertion(Annotation( "FMA:45565") Annotation( "Wikipedia:Simple_squamous_epithelium") Annotation( "http://orcid.org/0000-0001-9114-8737") "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "CARO:0000070") Annotation( "CARO") Annotation( "FMA:45565") Annotation( "http://orcid.org/0000-0001-9114-8737") "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]") AnnotationAssertion( "AAO:0010066") AnnotationAssertion( "AEO:0000070") AnnotationAssertion( "BILA:0000070") @@ -135770,6 +133927,8 @@ AnnotationAssertion( "simple squamous epithelium") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (atypical epithelium) @@ -135795,7 +133954,6 @@ SubClassOf( (cavitated compound organ) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Compound organ that contains one or more macroscopic anatomical spaces.") -AnnotationAssertion( "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future") AnnotationAssertion( "AAO:0010016") AnnotationAssertion( "AEO:0000072") AnnotationAssertion( "BILA:0000072") @@ -135816,12 +133974,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cavitated compound organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (unilaminar epithelium) AnnotationAssertion(Annotation( "FMA:45561") Annotation( "http://orcid.org/0000-0001-9114-8737") "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].") AnnotationAssertion( "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "CARO:0000073") Annotation( "CARO") Annotation( "FMA:45561") Annotation( "http://orcid.org/0000-0001-9114-8737") "Epithelium that consists of a single layer of epithelial cells.[CARO]") AnnotationAssertion( "AAO:0010062") AnnotationAssertion( "AEO:0000073") AnnotationAssertion( "BILA:0000073") @@ -135847,8 +134006,6 @@ SubClassOf( (mucus) AnnotationAssertion(Annotation( "Wikipedia:Mucus") "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.") -AnnotationAssertion( "mucoid") -AnnotationAssertion( "mucous") AnnotationAssertion( "CALOHA:TS-2144") AnnotationAssertion( "ENVO:02000040") AnnotationAssertion( "FMA:66938") @@ -135862,6 +134019,7 @@ AnnotationAssertion( "UBERON:0000912") AnnotationAssertion(rdfs:label "mucus") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -135869,7 +134027,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (interstitial fluid) AnnotationAssertion(Annotation( "Wikipedia:Interstitial_fluid") "Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.") -AnnotationAssertion( ) AnnotationAssertion( "ENVO:02000042") AnnotationAssertion( "FMA:9673") AnnotationAssertion( "NCIT:C120839") @@ -135888,10 +134045,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (thoracic segment of trunk) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Subdivision of trunk that lies between the head and the abdomen.") -AnnotationAssertion( "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "EMAPA:35862") AnnotationAssertion( "FMA:259209") AnnotationAssertion( "MA:0000022") @@ -135907,13 +134060,13 @@ AnnotationAssertion( "thoracic segment of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdomen) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.") AnnotationAssertion( "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class") -AnnotationAssertion( "abdominal") -AnnotationAssertion( "celiac") AnnotationAssertion( "BTO:0000020") AnnotationAssertion( "CALOHA:TS-0001") AnnotationAssertion( "EFO:0000968") @@ -135946,8 +134099,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (embryo) AnnotationAssertion(Annotation( "BTO:0000379") Annotation( "FB:FBrf0039741") Annotation( "FB:FBrf0041814") Annotation( "GO:0009790") Annotation( "Wikipedia:Embryo") "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.") -AnnotationAssertion( "embryonic") -AnnotationAssertion(Annotation( "ZFA") "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo") AnnotationAssertion( "AAO:0011035") AnnotationAssertion( "AEO:0000169") AnnotationAssertion( "BILA:0000056") @@ -135959,10 +134110,8 @@ AnnotationAssertion( "EHDAA2_RETIRED:0003236") AnnotationAssertion( "EHDAA:38") AnnotationAssertion( "EMAPA:16039") -AnnotationAssertion(Annotation( ) "FBbt:00000052") AnnotationAssertion( "FMA:69068") AnnotationAssertion( "GAID:963") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000646") AnnotationAssertion( "MAT:0000226") AnnotationAssertion( "MESH:D004622") AnnotationAssertion( "MIAA:0000019") @@ -135988,17 +134137,18 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/503"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (germ layer) AnnotationAssertion(Annotation( "Wikipedia:Germ_layer") Annotation( "https://github.com/obophenotype/uberon/issues/203") "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001223") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722") Annotation( "http://bgee.unil.ch/") "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]") AnnotationAssertion(Annotation( "FMA:69069") "embryonic tissue") AnnotationAssertion( "AAO:0000480") AnnotationAssertion( "BILA:0000035") AnnotationAssertion( "BTO:0000556") AnnotationAssertion( "EMAPA:36033") -AnnotationAssertion(Annotation( ) "FBbt:00000110") AnnotationAssertion( "FMA:69069") AnnotationAssertion( "GAID:1303") AnnotationAssertion( "MESH:D005855") @@ -136022,16 +134172,11 @@ AnnotationAssertion( "Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]") AnnotationAssertion(rdfs:label "germ layer") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectoderm) AnnotationAssertion(Annotation( "Wikipedia:Ectoderm") "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000137") Annotation( "AAO") Annotation( "AAO:EJS") "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000153") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722") Annotation( "http://bgee.unil.ch/") "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]") -AnnotationAssertion( "ectodermal") AnnotationAssertion( "AAO:0000137") AnnotationAssertion( "BILA:0000036") AnnotationAssertion( "BTO:0000315") @@ -136040,7 +134185,6 @@ AnnotationAssertion( "EHDAA2:0000428") AnnotationAssertion( "EMAPA:16069") AnnotationAssertion( "EV:0100003") -AnnotationAssertion(Annotation( ) "FBbt:00000111") AnnotationAssertion( "FMA:69070") AnnotationAssertion( "GAID:1304") AnnotationAssertion( "MAT:0000155") @@ -136071,8 +134215,6 @@ SubClassOf(Annotation( "Bge # Class: (endoderm) AnnotationAssertion(Annotation( "Wikipedia:Endoderm") "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000154") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722") Annotation( "http://bgee.unil.ch/") "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]") -AnnotationAssertion( "endodermal") AnnotationAssertion( "AAO:0000139") AnnotationAssertion( "BILA:0000038") AnnotationAssertion( "BTO:0000800") @@ -136081,7 +134223,6 @@ AnnotationAssertion( "EHDAA2:0000436") AnnotationAssertion( "EMAPA:16062") AnnotationAssertion( "EV:0100005") -AnnotationAssertion(Annotation( ) "FBbt:00000125") AnnotationAssertion( "FMA:69071") AnnotationAssertion( "GAID:1305") AnnotationAssertion( "MAT:0000175") @@ -136113,10 +134254,6 @@ SubClassOf(Annotation( "Bge AnnotationAssertion(Annotation( "Wikipedia:Mesoderm") "The middle germ layer of the embryo, between the endoderm and ectoderm.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000304") Annotation( "AAO") Annotation( "AAO:EJS") "Primary germ layer that is the middle of the embryonic germ layers.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000152") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722") Annotation( "http://bgee.unil.ch/") "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]") -AnnotationAssertion( "mesodermal") -AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates") AnnotationAssertion( "UBERON:0003263") AnnotationAssertion( "AAO:0000304") AnnotationAssertion( "BILA:0000037") @@ -136129,7 +134266,6 @@ AnnotationAssertion( "EHDAA:183") AnnotationAssertion( "EMAPA:16083") AnnotationAssertion( "EV:0100006") -AnnotationAssertion(Annotation( ) "FBbt:00000126") AnnotationAssertion( "FMA:69072") AnnotationAssertion( "GAID:522") AnnotationAssertion( "MAT:0000174") @@ -136154,24 +134290,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png"^^xsd:anyURI) -SubClassOf(Annotation( "sometimes not considered primary") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (stomodeum) AnnotationAssertion(Annotation( "Wikipedia:Stomodeum") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/326") "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.") AnnotationAssertion( "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001290") Annotation( "TAO") Annotation( "ZFIN:curator") "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]") -AnnotationAssertion(Annotation( "MP:0012522") Annotation( "NCBITaxon:40674") "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx") -AnnotationAssertion( "stomodeal") -AnnotationAssertion( "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.") AnnotationAssertion(Annotation( "XAO:0000269") "stomodeal-hypophyseal primordium") AnnotationAssertion( "BTO:0004224") AnnotationAssertion( "EHDAA2:0001929") AnnotationAssertion( "EMAPA:16263") -AnnotationAssertion(Annotation( ) "FBbt:00000439") AnnotationAssertion( "FMA:295846") AnnotationAssertion( "NCIT:C34306") AnnotationAssertion( "TAO:0001290") @@ -136204,13 +134334,9 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ZFA:0000066") Annotation( "https://github.com/obophenotype/uberon/issues/685") Annotation( "https://sourceforge.net/p/fbbtdv/tickets/52") "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.") AnnotationAssertion( "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000066") Annotation( "TAO") Annotation( "ZFIN:curator") "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011087") Annotation( "AAO") Annotation( "ZFA:0000066") "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]") -AnnotationAssertion( "proctodeal") AnnotationAssertion( "AAO:0011087") AnnotationAssertion( "EHDAA2:0000121") AnnotationAssertion( "EMAPA:25038") -AnnotationAssertion(Annotation( ) "FBbt:00000123") AnnotationAssertion( "NCIT:C34278") AnnotationAssertion( "TAO:0000066") AnnotationAssertion(Annotation( "ncithesaurus:Proctodeum") "UMLS:C0231054") @@ -136238,11 +134364,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (chordate pharyngeal muscle) AnnotationAssertion(Annotation( "Wikipedia:Pharyngeal_muscles") Annotation( "https://orcid.org/0000-0002-6601-2165") "A muscle that acts on the pharynx[WP, vetted].") -AnnotationAssertion(Annotation( "2012-06-30") Annotation( "GO:0043282") Annotation( "does not quite work for some muscles such as stylopharyngeus") Annotation( "GO") Annotation( "GOC:go_curators") "A pharyngeal muscle is any muscle that forms part of the pharynx[GO].") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0001048") AnnotationAssertion( "EFO:0003504") -AnnotationAssertion( "EMAPA:18963") AnnotationAssertion( "FMA:46619") AnnotationAssertion( "GAID:154") AnnotationAssertion( "MA:0001797") @@ -136271,15 +134394,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "chordate pharyngeal muscle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (imaginal disc) AnnotationAssertion(Annotation( "Wikipedia:Imaginal_disc") "One of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation.") AnnotationAssertion( "BTO:0004658") -AnnotationAssertion(Annotation( ) "FBbt:00001761") AnnotationAssertion( "MAT:0000064") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D060227") AnnotationAssertion( "MIAA:0000064") AnnotationAssertion( "Wikipedia:Imaginal_disc") AnnotationAssertion( "uberon") @@ -136296,10 +134419,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "ISBN:0471888893") "Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].") AnnotationAssertion( "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000435") Annotation( "TAO") Annotation( "ZFIN:curator") "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010345") Annotation( "AAO") Annotation( "AAO:EJS") "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000543") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon") AnnotationAssertion(Annotation( "BIRNLEX:1640") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "2n") AnnotationAssertion(Annotation( "FMA:50863") Annotation( "ZFA:0000435") Annotation( ) "optic nerve") AnnotationAssertion( "AAO:0010345") @@ -136347,9 +134466,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cranial nerve II") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach) @@ -136360,9 +134482,6 @@ AnnotationAssertion(Annotation( "ZFA") ) AnnotationAssertion(Annotation( "Wikipedia") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000579") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000408") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)") Annotation( "http://bgee.unil.ch/") "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP:Stomach#In_other_animals") "We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa") AnnotationAssertion( "AAO:0000579") AnnotationAssertion( "ANISEED:1235297") AnnotationAssertion( "BTO:0001307") @@ -136405,18 +134524,14 @@ AnnotationAssertion( "cjm") ) SubClassOf(Annotation( "cjm") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "absent in lampreys and hagfishes") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0486692132") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac valve) AnnotationAssertion(Annotation( "MESH:A07.541.510") Annotation( "MP:0000285") Annotation( "PMID:7926784") "A membranous fold of the heart that prevents reflux of fluid.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000818") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/heart+valve") "One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000818") Annotation( "VHOG") Annotation( "DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)") Annotation( "http://bgee.unil.ch/") "Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]") -AnnotationAssertion( "Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve") AnnotationAssertion( "BTO:0000564") AnnotationAssertion( "EMAPA:17869") AnnotationAssertion( "EV:0100024") @@ -136447,6 +134562,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac valve") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:15797462") ObjectSomeValuesFrom( )) @@ -136455,10 +134572,6 @@ SubClassOf(Annotation( "PMI AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MESH:A07.231.114.056") Annotation( "MP:0000272") Annotation( "Wikipedia:Aorta") Annotation( "http://orcid.org/0000-0002-6601-2165") "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.") AnnotationAssertion(Annotation( "WP") "This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010213") Annotation( "AAO") Annotation( "AAO:BJB") "The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001523") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]") -AnnotationAssertion( "aortic") -AnnotationAssertion( "All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches") AnnotationAssertion( "AAO:0010213") AnnotationAssertion( "BTO:0000135") AnnotationAssertion( "CALOHA:TS-0046") @@ -136494,9 +134607,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA-modified") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart) @@ -136505,11 +134618,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000114") Annotation( "TAO") Annotation( "ZFIN:curator") "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010210") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010210") Annotation( "AAO") "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000276") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481") Annotation( "http://bgee.unil.ch/") "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]") -AnnotationAssertion( "cardiac") AnnotationAssertion( "AAO:0010210") AnnotationAssertion( "BILA:0000020") AnnotationAssertion( "BTO:0000562") @@ -136553,25 +134661,25 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocrine system) AnnotationAssertion(Annotation( "NLM:endocrine+system") Annotation( "Wikipedia:Endocrine_system") "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010279") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000098") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)") Annotation( "http://bgee.unil.ch/") "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]") -AnnotationAssertion( "endocrine") AnnotationAssertion( "AAO:0010279") AnnotationAssertion( "CALOHA:TS-1301") AnnotationAssertion( "EFO:0002969") AnnotationAssertion( "EHDAA2:0002224") AnnotationAssertion( "EMAPA:35306") AnnotationAssertion( "EV:0100128") -AnnotationAssertion(Annotation( ) "FBbt:00005068") AnnotationAssertion( "FMA:9668") AnnotationAssertion( "GAID:439") AnnotationAssertion( "MA:0000012") @@ -136594,7 +134702,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine system") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -136625,16 +134733,16 @@ AnnotationAssertion( "UBERON:0000951") AnnotationAssertion(rdfs:label "rotator muscle of the vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain) AnnotationAssertion(Annotation( "Wikipedia:Brain") Annotation( "https://github.com/obophenotype/uberon/issues/300") "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].") AnnotationAssertion( "requires review for applicability to invertebrate structures, e.g. synganglion") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000008") Annotation( "TAO") Annotation( "ZFIN:curator") "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010478") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]") -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Cumbo_terms") "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000157") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0010478") AnnotationAssertion( "ABA:Brain") AnnotationAssertion( "BAMS:Br") @@ -136650,7 +134758,6 @@ AnnotationAssertion( "EHDAA:6485") AnnotationAssertion( "EMAPA:16894") AnnotationAssertion( "EV:0100164") -AnnotationAssertion(Annotation( ) "FBbt:00005095") AnnotationAssertion( "FMA:50801") AnnotationAssertion( "GAID:571") AnnotationAssertion( "HBA:4005") @@ -136690,6 +134797,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) SubClassOf(Annotation( "GO") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -136700,12 +134808,8 @@ SubClassOf(Annotation( "Bge # Class: (cerebral cortex) AnnotationAssertion(Annotation( "BIRNLEX:1494") "The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.") -AnnotationAssertion( "We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus).") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Cerebral_cortex") "The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000722") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)") Annotation( "http://bgee.unil.ch/") "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]") -AnnotationAssertion( "hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]") AnnotationAssertion( "BAMS:C") AnnotationAssertion( "BAMS:CTX") AnnotationAssertion( "BAMS:Cerebral_cortex") @@ -136751,6 +134855,7 @@ AnnotationAssertion( "cerebral cortex") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "GO") Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) @@ -136763,7 +134868,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Lamina_of_the_vertebral_arch") "Any thin layer or plate.") AnnotationAssertion( "TODO - merge with cell layer?") -AnnotationAssertion( "laminar") AnnotationAssertion( "Wikipedia:Lamina_of_the_vertebral_arch") AnnotationAssertion( "laminar tissue") AnnotationAssertion( "uberon") @@ -136774,12 +134878,12 @@ AnnotationAssertion( "lamina") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medulla of organ) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Middle part of an organ, surrounded by the cortex.") -AnnotationAssertion( "this class is used in a very general sense") -AnnotationAssertion( "medullary") AnnotationAssertion( "FMA:61108") AnnotationAssertion( "galen:Medulla") AnnotationAssertion(Annotation( "FMA:61108") "medulla") @@ -136794,8 +134898,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (optic chiasma) AnnotationAssertion(Annotation( "MGI:llw2") Annotation( "MP:0009770") Annotation( "Wikipedia:Optic_chiasm") Annotation( "http://orcid.org/0000-0002-6601-2165") "A decussation of the diencephalon where the fibers of the optic nerve cross.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010622") Annotation( "AAO") Annotation( "AAO:DSM") "The point at which fibers of the optic nerves cross.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000190") Annotation( "VHOG") Annotation( "DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)") Annotation( "http://bgee.unil.ch/") "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]") AnnotationAssertion( "AAO:0010622") AnnotationAssertion( "BAMS:DC") AnnotationAssertion( "BAMS:OC") @@ -136837,7 +134939,9 @@ AnnotationAssertion( "optic chiasma") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "cjm") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic ganglion) @@ -136867,6 +134971,8 @@ AnnotationAssertion( "thoracic ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of cervical vertebra) @@ -136891,24 +134997,25 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "nerve of cervical vertebra") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head sensillum) AnnotationAssertion( "this term should be ceded to the arthropod anatomy ontology") -AnnotationAssertion(Annotation( ) "FBbt:00004114") AnnotationAssertion( "MAT:0000204") AnnotationAssertion( "MIAA:0000204") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000963") AnnotationAssertion(rdfs:label "head sensillum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cornea) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MESH:A09.371.060.217") Annotation( "MP:0001312") "The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.") AnnotationAssertion( ) -AnnotationAssertion( "corneal") -AnnotationAssertion( "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water") AnnotationAssertion( "AAO:0010344") AnnotationAssertion( "BTO:0000286") AnnotationAssertion( "CALOHA:TS-0171") @@ -136941,7 +135048,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cornea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-isa") ObjectSomeValuesFrom( )) @@ -136949,7 +135058,7 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -136957,10 +135066,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (lens of camera-type eye) AnnotationAssertion(Annotation( "Wikipedia:Lens_(anatomy)") Annotation( "http://orcid.org/0000-0002-6601-2165") "A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina.") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000169") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)") Annotation( "http://bgee.unil.ch/") "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]") -AnnotationAssertion( "This class excludes compound eye corneal lenses.") AnnotationAssertion( "AAO:0010348") AnnotationAssertion( "BTO:0000723") AnnotationAssertion( "CALOHA:TS-0545") @@ -136996,9 +135102,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The lens is avascular and nourished by diffusion from the aqueous and vitreous humors.") AnnotationAssertion(rdfs:label "lens of camera-type eye") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137008,9 +135114,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Retina") Annotation( "ZFIN:curator") "The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000152") Annotation( "TAO") Annotation( "ZFIN:curator") "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000229") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)") Annotation( "http://bgee.unil.ch/") "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]") -AnnotationAssertion( "retinal") AnnotationAssertion( "AAO:0010352") AnnotationAssertion( "BAMS:R") AnnotationAssertion( "BIRNLEX:1153") @@ -137054,6 +135157,7 @@ AnnotationAssertion( "Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods") AnnotationAssertion(rdfs:label "retina") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137065,17 +135169,12 @@ SubClassOf(Annotation( "EHD # Class: (eye) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An organ that detects light.") -AnnotationAssertion( "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)") AnnotationAssertion( ) -AnnotationAssertion( "ocular") -AnnotationAssertion( "optic") -AnnotationAssertion( "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,") AnnotationAssertion( "BILA:0000017") AnnotationAssertion( "BTO:0000439") AnnotationAssertion( "CALOHA:TS-0309") AnnotationAssertion( "EFO:0000827") AnnotationAssertion( "EV:0100336") -AnnotationAssertion(Annotation( ) "FBbt:00005162") AnnotationAssertion( "GAID:69") AnnotationAssertion( "MAT:0000140") AnnotationAssertion( "MESH:D005123") @@ -137101,9 +135200,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (ommatidium) AnnotationAssertion(Annotation( "PMID:21062451") "The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.") -AnnotationAssertion( "ommatidial") AnnotationAssertion( "BTO:0001922") -AnnotationAssertion(Annotation( ) "FBbt:00004510") AnnotationAssertion( "HAO:0000666") AnnotationAssertion( "MAT:0000143") AnnotationAssertion( "MIAA:0000143") @@ -137121,9 +135218,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neck) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.") -AnnotationAssertion( "true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.") -AnnotationAssertion(Annotation( "ISBN:9780674021839") ) -AnnotationAssertion( "cervical") AnnotationAssertion( "AEO:0000108") AnnotationAssertion( "BTO:0000420") AnnotationAssertion( "CALOHA:TS-2045") @@ -137161,13 +135255,6 @@ AnnotationAssertion(Annotation( "in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum") AnnotationAssertion(Annotation( "Wikipedia") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000765") Annotation( "AAO") Annotation( "AAO:LAP") "Single element that constitutes the postzonal area of the pectoral girdle.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000765") Annotation( "AAO") "relationship loss: part_of postzonal element (AAO:0000938)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000856") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294") Annotation( "http://bgee.unil.ch/") "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]") -AnnotationAssertion( "sternal") -AnnotationAssertion( "It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life") -AnnotationAssertion( "in birds, either ratite (no keel or carina) or carinate (keel and carina present)") -AnnotationAssertion(Annotation( "WP") "While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad].") AnnotationAssertion( "AAO:0000765") AnnotationAssertion( "BTO:0001302") AnnotationAssertion( "CALOHA:TS-0972") @@ -137193,8 +135280,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sternum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0073040584") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137205,9 +135292,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "AAO:0000679") Annotation( "PHENOSCAPE:mah") Annotation( "https://github.com/obophenotype/uberon/issues/106") "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000679") Annotation( "AAO") Annotation( "AAO:LAP") "Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001158") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "humeral") AnnotationAssertion( "AAO:0000679") AnnotationAssertion( "CALOHA:TS-2202") AnnotationAssertion( "EFO:0001398") @@ -137237,24 +135321,21 @@ AnnotationAssertion( "humerus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pleura) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010820") Annotation( "UBERON:cjm") Annotation( "Wikipedia:Pulmonary_pleurae") Annotation( "https://github.com/obophenotype/uberon/issues/1231") "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).") AnnotationAssertion(Annotation( "ISBN:978-0030223693") Annotation( "https://orcid.org/0000-0003-3308-6245") ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000394") Annotation( "VHOG") Annotation( "ISBN:0124020607") Annotation( "http://bgee.unil.ch/") "The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]") -AnnotationAssertion( "pleural") -AnnotationAssertion( "In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86") AnnotationAssertion( "BTO:0001791") AnnotationAssertion( "CALOHA:TS-2081") AnnotationAssertion( "EFO:0001980") -AnnotationAssertion( "EMAPA:16775") AnnotationAssertion( "EV:0100044") AnnotationAssertion( "FMA:9583") AnnotationAssertion( "GAID:360") @@ -137276,8 +135357,11 @@ AnnotationAssertion( "pleura") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/86") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137286,8 +135370,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (leg) AnnotationAssertion(Annotation( "Wikipedia:Leg#Limb") "The portion of the hindlimb that contains both the stylopod and zeugopod.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000345") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion(Annotation( "3") "The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For") AnnotationAssertion( "BTO:0000721") AnnotationAssertion( "CALOHA:TS-2206") AnnotationAssertion( "EFO:0001411") @@ -137311,7 +135393,7 @@ AnnotationAssertion( "we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot") AnnotationAssertion(rdfs:label "leg") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137319,7 +135401,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "PHENOSCAPE:mah") "The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000890") Annotation( "AAO") Annotation( "AAO:LAP") "One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]") AnnotationAssertion( "AAO:0000890") AnnotationAssertion( "BTO:0001252") AnnotationAssertion( "CALOHA:TS-1048") @@ -137345,20 +135426,16 @@ AnnotationAssertion( "tibia") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (femur) AnnotationAssertion(Annotation( "VSAO:0000186") Annotation( "Wikipedia:Femur") "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000186") Annotation( "VSAO") Annotation( "VSAO:NI") "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000889") Annotation( "AAO") Annotation( "AAO:LAP") "Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001159") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "femoral") AnnotationAssertion( "AAO:0000887") AnnotationAssertion( "AAO:0000889") AnnotationAssertion( "BTO:0001284") @@ -137394,19 +135471,16 @@ AnnotationAssertion( "femur") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal joint) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000101") Annotation( "Wikipedia:Joint") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000101") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000367") Annotation( "TAO") Annotation( "TAO:pem") "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]") AnnotationAssertion(Annotation( "VSAO:0000101") "articulation") AnnotationAssertion(Annotation( "FMA:7490") Annotation( "VSAO:0000101") "joint") AnnotationAssertion( "AEO:0000182") @@ -137443,7 +135517,6 @@ AnnotationAssertion( "skeletal joint") EquivalentClasses( ObjectUnionOf( )) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -137451,7 +135524,6 @@ DisjointClasses( (metatarsus region) AnnotationAssertion(Annotation( "OBOL:automatic") "A metapodium region that is part of a pes.") -AnnotationAssertion( "mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton") AnnotationAssertion( "CALOHA:TS-2221") AnnotationAssertion( "FMA:24997") AnnotationAssertion( "MA:0000049") @@ -137469,6 +135541,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metatarsus region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137476,7 +135550,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Vein that drains the axilla.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "WP") "In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery") AnnotationAssertion( "EMAPA:18758") AnnotationAssertion( "FMA:13329") AnnotationAssertion( "GAID:527") @@ -137496,17 +135569,16 @@ AnnotationAssertion( "axillary vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pons) AnnotationAssertion(Annotation( "VHOG:0001176") "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.") AnnotationAssertion( "The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001176") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pons") "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001176") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474") Annotation( "http://bgee.unil.ch/") "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]") AnnotationAssertion( "BAMS:PONS") AnnotationAssertion( "BAMS:Pons") AnnotationAssertion( "BIRNLEX:733") @@ -137554,9 +135626,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (penis) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005187") Annotation( "Wikipedia:Penis") Annotation( "http://orcid.org/0000-0002-6601-2165") "An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.") -AnnotationAssertion( "penile") -AnnotationAssertion( "phallic") -AnnotationAssertion(Annotation( "WP") "Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca") AnnotationAssertion( "BTO:0000405") AnnotationAssertion( "CALOHA:TS-0758") AnnotationAssertion( "EFO:0000987") @@ -137587,6 +135656,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "penis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -137596,9 +135666,6 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "Wikipedia:Reproductive_system") "Anatomical system that has as its parts the organs concerned with reproduction.") AnnotationAssertion( "consider splitting genitalia from reproductive system") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010258") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000182") Annotation( "VHOG") Annotation( "PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)") Annotation( "http://bgee.unil.ch/") "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]") -AnnotationAssertion( ) AnnotationAssertion( "2022-06-10T18:22:34Z"^^xsd:dateTime) AnnotationAssertion( "AAO:0010258") AnnotationAssertion( "BILA:0000103") @@ -137609,13 +135676,11 @@ AnnotationAssertion( "EHDAA:5923") AnnotationAssertion( "EMAPA:17381") AnnotationAssertion( "EV:0100100") -AnnotationAssertion(Annotation( ) "FBbt:00004857") AnnotationAssertion( "FMA:7160") AnnotationAssertion( "GAID:363") AnnotationAssertion( "HAO:0000374") AnnotationAssertion( "HAO:0000895") AnnotationAssertion( "MA:0000326") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005835") AnnotationAssertion( "MIAA:0000305") AnnotationAssertion( "NCIT:C12841") AnnotationAssertion( "SCTID:278875001") @@ -137648,6 +135713,7 @@ AnnotationAssertion( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -137668,17 +135734,11 @@ DisjointClasses( (gonad) AnnotationAssertion(Annotation( "ISBN:0140512888") Annotation( "Wikipedia:Gonad") Annotation( "ZFA:0000413") Annotation( "ZFIN:curator") "Reproductive organ that produces and releases eggs (ovary) or sperm (testis).") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000213") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000413") Annotation( "TAO") Annotation( "ZFIN:curator") "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000397") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)") Annotation( "http://bgee.unil.ch/") "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]") -AnnotationAssertion( "gonadal") -AnnotationAssertion(Annotation( "FMA") "FMA xref is a 'general anatomical term'") AnnotationAssertion( "AAO:0000213") AnnotationAssertion( "BILA:0000123") AnnotationAssertion( "BSA:0000079") AnnotationAssertion( "BTO:0000534") AnnotationAssertion( "EMAPA:17383") -AnnotationAssertion(Annotation( ) "FBbt:00004858") AnnotationAssertion( "FMA:18250") AnnotationAssertion( "GAID:368") AnnotationAssertion( "HAO:0000379") @@ -137705,7 +135765,7 @@ AnnotationAssertion( "gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137713,11 +135773,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001126") Annotation( "Wikipedia:Ovary") "The gonad of a female organism which contains germ cells.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000371") Annotation( "AAO") Annotation( "AAO:BJB") "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000403") Annotation( "TAO") Annotation( "ZFIN:curator") "Female reproductive organ.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000251") Annotation( "VHOG") Annotation( "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)") Annotation( "http://bgee.unil.ch/") "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]") -AnnotationAssertion( "ovarian") -AnnotationAssertion(Annotation( "WP") "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo") AnnotationAssertion( "AAO:0000371") AnnotationAssertion( "BILA:0000125") AnnotationAssertion( "BSA:0000080") @@ -137728,7 +135783,6 @@ AnnotationAssertion( "EHDAA:8124") AnnotationAssertion( "EMAPA:17962") AnnotationAssertion( "EV:0100111") -AnnotationAssertion(Annotation( ) "FBbt:00004865") AnnotationAssertion( "FMA:7209") AnnotationAssertion( "GAID:367") AnnotationAssertion( "MA:0000384") @@ -137779,6 +135833,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -137786,11 +135842,6 @@ DisjointClasses( (oviduct) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A tube or collection of tubes in an animal from the ovaries to the outside of the body.") -AnnotationAssertion( "sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001136") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/oviduct") "A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001136") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688") Annotation( "http://bgee.unil.ch/") "In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]") -AnnotationAssertion( "The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]") -AnnotationAssertion( "in birds divided into infundibulum, magnum, isthmus, uterus, and vagina") AnnotationAssertion( "AAO:0010533") AnnotationAssertion( "BSA:0000083") AnnotationAssertion( "BTO:0000980") @@ -137822,6 +135873,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oviduct") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -137831,11 +135883,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0001120") "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001137") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/uterus") "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001137") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678") Annotation( "http://bgee.unil.ch/") "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]") -AnnotationAssertion( "uterine") -AnnotationAssertion( "Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.") -AnnotationAssertion( "Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]") AnnotationAssertion( "BTO:0001424") AnnotationAssertion( "CALOHA:TS-1102") AnnotationAssertion( "EFO:0000975") @@ -137872,11 +135919,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (vagina) AnnotationAssertion(Annotation( "Wikipedia:Vagina") Annotation( "http://orcid.org/0000-0002-6601-2165") "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].") -AnnotationAssertion(Annotation( "2012-11-29") Annotation( "FMA:19949") Annotation( "FMA") "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001138") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/vagina") "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001138") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688") Annotation( "http://bgee.unil.ch/") "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]") -AnnotationAssertion( "vaginal") -AnnotationAssertion( "'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688") AnnotationAssertion( "BTO:0000243") AnnotationAssertion( "CALOHA:TS-1103") AnnotationAssertion( "EFO:0000976") @@ -137905,6 +135947,7 @@ AnnotationAssertion( "vagina") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -137913,8 +135956,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mammalian vulva) AnnotationAssertion(Annotation( "Wikipedia:Vulva") "External genital organs of the female mammal[WP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001458") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/vulva") "The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]") -AnnotationAssertion( "vulval") AnnotationAssertion( "BTO:0003101") AnnotationAssertion( "CALOHA:TS-1168") AnnotationAssertion( "EFO:0000978") @@ -137948,15 +135989,13 @@ AnnotationAssertion( "mammalian vulva") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminal vesicle) AnnotationAssertion(Annotation( "BTO:0001234") Annotation( "Wikipedia:Seminal_vesicle") "Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001379") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/prominence") "Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001379") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556") Annotation( "http://bgee.unil.ch/") "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]") -AnnotationAssertion( "The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid.") AnnotationAssertion( "seminal gland") AnnotationAssertion( "AAO:0010788") AnnotationAssertion( "BTO:0001234") @@ -137994,6 +136033,7 @@ AnnotationAssertion( "seminal vesicle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138027,8 +136067,9 @@ AnnotationAssertion( "ejaculatory duct") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138041,8 +136082,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (vas deferens) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:pvb") Annotation( "MP:0002769") Annotation( "Wikipedia:Vas_deferens") Annotation( "http://orcid.org/0000-0002-6601-2165") "A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001135") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670") Annotation( "http://bgee.unil.ch/") "The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.") AnnotationAssertion( "BTO:0001427") AnnotationAssertion( "CALOHA:TS-1105") AnnotationAssertion( "EFO:0000981") @@ -138072,7 +136111,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vas deferens") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138085,12 +136125,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "http://orcid.org/0000-0002-6601-2165") "The outer epithelial layer of the skin that is superficial to the dermis.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000105") Annotation( "TAO") Annotation( "ZFIN:curator") "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000143") Annotation( "AAO") Annotation( "AAO:BJB") "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000143") Annotation( "AAO") "relationship loss: subclass external integument structures (AAO:0000961)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000077") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72") Annotation( "http://bgee.unil.ch/") "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]") -AnnotationAssertion( "epidermal") -AnnotationAssertion( "Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).") AnnotationAssertion( "epidermis") AnnotationAssertion( "skin") AnnotationAssertion( "AAO:0000143") @@ -138123,6 +136157,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138131,8 +136168,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Respiratory_system") Annotation( "http://orcid.org/0000-0002-6601-2165") "Functional system which consists of structures involved in respiration.") AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000541") Annotation( "AAO") Annotation( "AAO:BJB") "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000202") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23") Annotation( "http://bgee.unil.ch/") "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]") AnnotationAssertion( "AAO:0000541") AnnotationAssertion( "BTO:0000203") AnnotationAssertion( "CALOHA:TS-1319") @@ -138176,8 +136211,10 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -138197,10 +136234,8 @@ DisjointClasses( (respiratory airway) AnnotationAssertion(Annotation( "Wikipedia:Trachea") "An airway through which respiratory air passes in organisms.") -AnnotationAssertion( "This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "airway") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "airways") -AnnotationAssertion( "FMA:265130") AnnotationAssertion( "SCTID:361380005") AnnotationAssertion( "Wikipedia:Trachea") AnnotationAssertion( "uberon") @@ -138209,6 +136244,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory airway") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138216,16 +136252,11 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FB:gg") Annotation( "NLM:alimentary+system") Annotation( "Wikipedia:Digestive_system") "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000129") Annotation( "AAO") Annotation( "AAO:BJB") "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]") -AnnotationAssertion( "digestive") -AnnotationAssertion(Annotation( "MA") "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class") AnnotationAssertion( "AAO:0000129") AnnotationAssertion( "BILA:0000082") AnnotationAssertion( "BTO:0000058") AnnotationAssertion( "CALOHA:TS-1293") AnnotationAssertion( "EFO:0000793") -AnnotationAssertion( "EV:0100056") -AnnotationAssertion(Annotation( ) "FBbt:00005055") AnnotationAssertion( "FMA:7152") AnnotationAssertion( "GAID:278") AnnotationAssertion( "MA:0002431") @@ -138254,6 +136285,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "digestive system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -138275,10 +136308,6 @@ AnnotationAssertion(Annotation( "Wikipedia") ) AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010257") Annotation( "AAO") Annotation( "AAO:BJB") "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000723") Annotation( "VHOG") Annotation( "ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406") Annotation( "http://bgee.unil.ch/") "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]") -AnnotationAssertion(Annotation( "GO") "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels") -AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0099864") "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans") AnnotationAssertion( "excretory system") AnnotationAssertion( "AAO:0010257") AnnotationAssertion( "BILA:0000015") @@ -138290,7 +136319,6 @@ AnnotationAssertion( "EHDAA:5901") AnnotationAssertion( "EMAPA:17366") AnnotationAssertion( "EV:0100095") -AnnotationAssertion(Annotation( ) "FBbt:00005056") AnnotationAssertion( "FMA:7159") AnnotationAssertion( "GAID:391") AnnotationAssertion( "MA:0000325") @@ -138324,23 +136352,20 @@ AnnotationAssertion( "EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here") AnnotationAssertion(rdfs:label "renal system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (circulatory system) AnnotationAssertion(Annotation( "Wikipedia:Circulatory_system") "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].") -AnnotationAssertion( "the cardiovascular system and the lymphatic system are parts of the circulatory system") AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "WBbt coelomocyte currently classified as circulating cell") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000959") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001248") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493") Annotation( "http://bgee.unil.ch/") "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]") AnnotationAssertion( "AAO:0000959") AnnotationAssertion( "CALOHA:TS-2103") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D002319") AnnotationAssertion( "VHOG:0001248") AnnotationAssertion( "Wikipedia:Circulatory_system") AnnotationAssertion( "uberon") @@ -138371,13 +136396,6 @@ DisjointClasses( "MESH:A10.165.114") Annotation( "MGI:cwg") Annotation( "MP:0000003") Annotation( "Wikipedia:Adipose_tissue") Annotation( "http://orcid.org/0000-0002-6601-2165") "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002134") Annotation( "TAO") Annotation( "ZFIN:curator") "Connective tissue in which fat is stored.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000001") Annotation( "AAO") Annotation( "AAO:LAP") "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000001") Annotation( "AAO") "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001284") Annotation( "VHOG") Annotation( "DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)") Annotation( "http://bgee.unil.ch/") "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]") -AnnotationAssertion( "adipose") -AnnotationAssertion( "In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.") -AnnotationAssertion(Annotation( "FMA") "in FMA this is dense irregular connective tissue") AnnotationAssertion( "AAO:0000001") AnnotationAssertion( "AEO:000020") AnnotationAssertion( "BTO:0001487") @@ -138417,18 +136435,14 @@ AnnotationAssertion( "adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (musculature) AnnotationAssertion(Annotation( "Wikipedia:Muscular_system") Annotation( "https://orcid.org/0000-0002-6601-2165") "A subdivision of the muscular system corresponding to a subdisivision of an organism.") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.") -AnnotationAssertion( "AAO:0011066") AnnotationAssertion( "BTO:0000887") AnnotationAssertion( "EFO:0001949") -AnnotationAssertion( "EMAPA:32715") AnnotationAssertion( "EMAPA:35577") AnnotationAssertion( "FMA:32558") AnnotationAssertion( "MA:0000165") @@ -138465,11 +136479,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:844") Annotation( "ISBN:0-14-051288-8") Annotation( "ISBN:3110148986") Annotation( "NLM:nervous+system") Annotation( "WB:rynl") Annotation( "Wikipedia:Nervous_system") Annotation( "ZFIN:curator") "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000396") Annotation( "TAO") Annotation( "ZFIN:curator") "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000324") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000402") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117") Annotation( "http://bgee.unil.ch/") "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]") -AnnotationAssertion( "nervous") -AnnotationAssertion( "neural") AnnotationAssertion( "AAO:0000324") AnnotationAssertion( "BILA:0000079") AnnotationAssertion( "BIRNLEX:844") @@ -138480,7 +136489,6 @@ AnnotationAssertion( "EHDAA:826") AnnotationAssertion( "EMAPA:16469") AnnotationAssertion( "EV:0100162") -AnnotationAssertion(Annotation( ) "FBbt:00005093") AnnotationAssertion( "FMA:7157") AnnotationAssertion( "GAID:466") AnnotationAssertion( "MA:0000016") @@ -138535,10 +136543,6 @@ DisjointClasses( "GO:0021551") Annotation( "http://www.frontiersinzoology.com/content/7/1/29") Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/11422/") "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.") AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000090") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the nervous system which includes the brain and spinal cord.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000012") Annotation( "TAO") Annotation( "ZFIN:curator") "The brain and spinal cord. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "BIRNLEX:1099") "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000293") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]") AnnotationAssertion( "AAO:0000090") AnnotationAssertion( "BAMS:CNS") AnnotationAssertion( "BILA:0000080") @@ -138551,7 +136555,6 @@ AnnotationAssertion( "EMAPA:16470") AnnotationAssertion( "EMAPA:16754") AnnotationAssertion( "EV:0100163") -AnnotationAssertion(Annotation( ) "FBbt:00005094") AnnotationAssertion( "FMA:55675") AnnotationAssertion( "GAID:570") AnnotationAssertion( "MA:0000167") @@ -138579,6 +136582,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "central nervous system") +SubClassOf( ) SubClassOf(Annotation( "FBbt") Annotation( "cjm") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138587,10 +136591,8 @@ SubClassOf(Annotation( "Bge # Class: (axon tract) AnnotationAssertion(Annotation( "http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html") Annotation( "https://github.com/obophenotype/uberon/issues/286") "A group of axons linking two or more neuropils and having a common origin, termination[FBbt].") -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Cumbo_terms") "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)") AnnotationAssertion( "BIRNLEX:1649") AnnotationAssertion( "EV:0100304") -AnnotationAssertion(Annotation( ) "FBbt:00005100") AnnotationAssertion( "FMA:83847") AnnotationAssertion( "NLX:147822") AnnotationAssertion( "axonal tract") @@ -138606,7 +136608,7 @@ AnnotationAssertion( "WP says this is the analog of peripheral nerves in CNS.") AnnotationAssertion(rdfs:label "axon tract") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (nerve fasciculus) @@ -138636,8 +136638,6 @@ SubClassOf( "FBbt:00005105") Annotation( "http://orcid.org/0000-0002-6601-2165") "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0007009") Annotation( "TAO") Annotation( "ZFIN:curator") "A portion of tissue which is a fasiculated group of axons.[TAO]") -AnnotationAssertion( "nervous") AnnotationAssertion( "AAO:0011070") AnnotationAssertion( "AEO:0000137") AnnotationAssertion( "BAMS:n") @@ -138653,7 +136653,6 @@ AnnotationAssertion( "EMAPA:32808") AnnotationAssertion( "EMAPA:32815") AnnotationAssertion( "EV:0100371") -AnnotationAssertion(Annotation( ) "FBbt:00005105") AnnotationAssertion( "FMA:65132") AnnotationAssertion( "FMA:65239") AnnotationAssertion( "GAID:747") @@ -138694,7 +136693,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Sensory_nerve") "A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.") AnnotationAssertion( "AEO:0000201") AnnotationAssertion( "EHDAA2:0003200") -AnnotationAssertion(Annotation( ) "FBbt:00005136") AnnotationAssertion( "FMA:5868") AnnotationAssertion( "Wikipedia:Sensory_nerve") AnnotationAssertion(Annotation( "Wikipedia:Sensory_nerve") Annotation( ) "nervus sensorius") @@ -138710,15 +136708,12 @@ SubClassOf(Annotation( "AEO # Class: (sensory system) AnnotationAssertion(Annotation( "Wikipedia:Sensory_system") "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001674") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)") Annotation( "http://bgee.unil.ch/") "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]") -AnnotationAssertion( "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs") AnnotationAssertion( "AAO:0000555") AnnotationAssertion( "BAMS:SEN") AnnotationAssertion( "BILA:0000099") AnnotationAssertion( "EFO:0000805") AnnotationAssertion( "EHDAA2:0003094") AnnotationAssertion( "EMAPA:16192") -AnnotationAssertion(Annotation( ) "FBbt:00007692") AnnotationAssertion( "FMA:75259") AnnotationAssertion( "MA:0002442") AnnotationAssertion( "MAT:0000031") @@ -138753,10 +136748,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (gustatory system) AnnotationAssertion(Annotation( "NLXANAT:090803") "The sensory system for the sense of taste.") -AnnotationAssertion(Annotation( "NLXANAT:090803") "The sensory system for the sense of taste[NLXANAT:090803].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010577") Annotation( "AAO") Annotation( "AAO:EJS") "The sensory system used for the sense of taste.[AAO]") -AnnotationAssertion( "gustatory") -AnnotationAssertion(Annotation( "ZFA") "in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes") AnnotationAssertion( "AAO:0010577") AnnotationAssertion( "BILA:0000143") AnnotationAssertion( "EFO:0000830") @@ -138781,7 +136772,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gustatory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -138798,7 +136791,6 @@ DisjointClasses( "Wikipedia:Hair") "A filament, mostly protein, that grows from follicles found in the dermis[WP].") AnnotationAssertion( "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)") -AnnotationAssertion( "this class defines an individual hair") AnnotationAssertion( "BTO:0001501") AnnotationAssertion( "CALOHA:TS-0430") AnnotationAssertion( "EFO:0000958") @@ -138832,6 +136824,7 @@ AnnotationAssertion( "strand of hair") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -138842,7 +136835,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FB:FBrf0056378") Annotation( "Wikipedia:Chordotonal_organ") "Chordotonal organs are arthropod sensory structures consisting of special sensilla called the scolopidia, which are mechano-transducers and respond mainly to stretch or flexion. In insects, they consist of bundles of internal sensilla, each of which has a cap cell, an enveloping cell and one or more sense cells. The distal end of the organ is usually attached to the cuticle of the body wall, marked by a pit, a thickened disc or a nodule of chitin, and the base of the organ is connected with the hypodermis, often by a special ligament.") AnnotationAssertion( "EFO:0000940") -AnnotationAssertion(Annotation( ) "FBbt:00005215") AnnotationAssertion( "MAT:0000209") AnnotationAssertion( "MIAA:0000209") AnnotationAssertion( "Wikipedia:Chordotonal_organ") @@ -138862,10 +136854,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Yolk_sac") "A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].") AnnotationAssertion( "consider splitting class") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000830") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/yolk+sac") "One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]") -AnnotationAssertion(Annotation( "MP:0001718") "the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000830") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187") Annotation( "http://bgee.unil.ch/") "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]") -AnnotationAssertion( "In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]") AnnotationAssertion( "BTO:0001471") AnnotationAssertion( "CALOHA:TS-1130") AnnotationAssertion( "EFO:0003078") @@ -138889,6 +136877,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "yolk sac") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/635") ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) @@ -138898,15 +136887,12 @@ SubClassOf(Annotation( "ISB AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Anterior subdivision of a digestive tract.") AnnotationAssertion( "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure") -AnnotationAssertion(Annotation( "MP:0000474") "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000285") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0011042") AnnotationAssertion( "BILA:0000085") AnnotationAssertion( "BTO:0000507") AnnotationAssertion( "EHDAA2:0000557") AnnotationAssertion( "EHDAA:520") AnnotationAssertion( "EMAPA:16548") -AnnotationAssertion(Annotation( ) "FBbt:00005379") AnnotationAssertion( "FMA:45616") AnnotationAssertion( "MA:0001526") AnnotationAssertion( "NCIT:C34180") @@ -138930,15 +136916,6 @@ SubClassOf( (chordate pharynx) AnnotationAssertion(Annotation( "http://www.feedexp.org") "A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].") -AnnotationAssertion(Annotation( "MESH:A03.867") "A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000967") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000056") Annotation( "TAO") Annotation( "ZFIN:curator") "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-961014-576") "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000462") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000967") Annotation( "AAO") "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000967") Annotation( "AAO") "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000462") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503") Annotation( "http://bgee.unil.ch/") "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme") AnnotationAssertion(Annotation( "FMA:46688") Annotation( ) "pharynx") AnnotationAssertion( "AAO:0000967") AnnotationAssertion( "BTO:0001049") @@ -138978,10 +136955,6 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "Wikipedia:Esophagus") Annotation( "http://www.rivm.nl/interspeciesinfo/inter/oesophagus/") "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000145") Annotation( "AAO") Annotation( "AAO:EJS") "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000450") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)") Annotation( "http://bgee.unil.ch/") "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]") -AnnotationAssertion( "esophageal") -AnnotationAssertion(Annotation( "MA") "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)") AnnotationAssertion( "AAO:0000145") AnnotationAssertion( "ANISEED:1235301") AnnotationAssertion( "BTO:0000959") @@ -139019,20 +136992,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "esophagus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") Annotation( "MA") ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (saliva-secreting gland) AnnotationAssertion(Annotation( "GO:0007431") Annotation( "Wikipedia:Salivary_gland") "Saliva-secreting exocrine glands of the oral cavity[GO].") -AnnotationAssertion(Annotation( "3") "currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000376") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000376") Annotation( "VHOG") Annotation( "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211") Annotation( "http://bgee.unil.ch/") "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]") -AnnotationAssertion( "The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands") AnnotationAssertion( "BTO:0001203") AnnotationAssertion( "CALOHA:TS-0892") AnnotationAssertion( "EFO:0000859") @@ -139040,7 +137009,6 @@ AnnotationAssertion( "EHDAA:7987") AnnotationAssertion( "EMAPA:17751") AnnotationAssertion( "EV:0100059") -AnnotationAssertion(Annotation( ) "FBbt:00005382") AnnotationAssertion( "FMA:9597") AnnotationAssertion( "GAID:937") AnnotationAssertion( "MA:0000346") @@ -139066,26 +137034,22 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midgut) AnnotationAssertion(Annotation( "GO:0007494") Annotation( "Wikipedia:Midgut") "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].") AnnotationAssertion( "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000290") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon") -AnnotationAssertion(Annotation( "FMA") "in FMA this represents an embryonic region.") AnnotationAssertion( "BILA:0000086") AnnotationAssertion( "BTO:0000863") AnnotationAssertion( "EFO:0001950") AnnotationAssertion( "EHDAA2:0001185") AnnotationAssertion( "EHDAA:983") AnnotationAssertion( "EMAPA:16255") -AnnotationAssertion(Annotation( ) "FBbt:00005383") AnnotationAssertion( "FMA:45617") AnnotationAssertion( "MA:0001564") AnnotationAssertion( "NCIT:C34210") @@ -139111,16 +137075,12 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The caudalmost subdivision of a digestive tract.") AnnotationAssertion( "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class") -AnnotationAssertion(Annotation( "MP:0008786") "the caudal portion of the primitive digestive tube of the embryo") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000459") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "in FMA this class has no children. In MA it has a single child hindgut epithelium") AnnotationAssertion( "AAO:0011052") AnnotationAssertion( "BILA:0000087") AnnotationAssertion( "BTO:0000510") AnnotationAssertion( "EHDAA2:0000779") AnnotationAssertion( "EHDAA:975") AnnotationAssertion( "EMAPA:16715") -AnnotationAssertion(Annotation( ) "FBbt:00005384") AnnotationAssertion( "FMA:45618") AnnotationAssertion( "MA:0001527") AnnotationAssertion( "NCIT:C34188") @@ -139149,7 +137109,6 @@ AnnotationAssertion( "BTO:0001886") AnnotationAssertion( "EFO:0001652") AnnotationAssertion( "EHDAA2:0003171") -AnnotationAssertion(Annotation( ) "FBbt:00005495") AnnotationAssertion( "FMA:86589") AnnotationAssertion( "MAT:0000482") AnnotationAssertion( "NCIT:C34275") @@ -139173,10 +137132,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neural tube) AnnotationAssertion(Annotation( "Wikipedia:Neural_tube") "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010617") Annotation( "AAO") Annotation( "AAO:JOR") "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000307") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/neural+tube") "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000307") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") -AnnotationAssertion(Annotation( "GO:0021915") "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium") AnnotationAssertion( "AAO:0010617") AnnotationAssertion( "BTO:0001057") AnnotationAssertion( "CALOHA:TS-2371") @@ -139188,7 +137143,6 @@ AnnotationAssertion( "EMAPA:16757") AnnotationAssertion( "FMA:293882") AnnotationAssertion( "MAT:0000069") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054259") AnnotationAssertion( "MIAA:0000069") AnnotationAssertion( "NCIT:C34226") AnnotationAssertion( "SCTID:362852000") @@ -139210,6 +137164,8 @@ AnnotationAssertion( "neural tube") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -139217,9 +137173,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000492") Annotation( "http://orcid.org/0000-0002-6601-2165") "The terminal portion of the intestinal tube, terminating with the anus.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001751") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion( "rectal") -AnnotationAssertion( "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html") AnnotationAssertion( "AAO:0010401") AnnotationAssertion( "BTO:0001158") AnnotationAssertion( "CALOHA:TS-1180") @@ -139255,7 +137208,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb"^^xsd:anyURI) -SubClassOf(Annotation( "4") Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -139266,10 +137219,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (Malpighian tubule) AnnotationAssertion(Annotation( "Wikipedia:Malpighian_tubule_system") "A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified].") -AnnotationAssertion( "It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]") AnnotationAssertion( "BTO:0000810") AnnotationAssertion( "EFO:0000243") -AnnotationAssertion(Annotation( ) "FBbt:00005786") AnnotationAssertion( "GAID:1228") AnnotationAssertion( "MAT:0000123") AnnotationAssertion( "MESH:D008317") @@ -139296,10 +137247,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "PMID:20813265") "Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'") AnnotationAssertion( "BTO:0002675") AnnotationAssertion( "EFO:0000925") -AnnotationAssertion(Annotation( ) "FBbt:00005801") AnnotationAssertion( "GAID:1231") AnnotationAssertion( "MAT:0000336") AnnotationAssertion( "MESH:D024521") @@ -139314,7 +137263,7 @@ AnnotationAssertion( "mushroom body") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "annelids and arthropods") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -139331,7 +137280,6 @@ AnnotationAssertion( "BIRNLEX:6") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion(Annotation( ) "FBbt:10000000") AnnotationAssertion( "FMA:62955") AnnotationAssertion( "HAO:0000000") AnnotationAssertion( "MA:0000001") @@ -139352,8 +137300,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(Annotation( "Wikipedia:Pancreatic_duct") "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000256") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]") -AnnotationAssertion(Annotation( "WP") "Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.") AnnotationAssertion( "UBERON:0005627") AnnotationAssertion(Annotation( "MESH:A03.734.667") "pancreatic duct") AnnotationAssertion( "BTO:0002362") @@ -139383,8 +137329,8 @@ AnnotationAssertion( "EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue") AnnotationAssertion(rdfs:label "ventral pancreatic duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -139393,7 +137339,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intervertebral disk) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Intervertebral_disk") "A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core.") -AnnotationAssertion( "strictly speaking the term intervertebral disk [applies to intervertebral cartilage]") AnnotationAssertion( "BTO:0003625") AnnotationAssertion( "EFO:0001370") AnnotationAssertion( "EMAPA:32739") @@ -139419,6 +137364,9 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "intervertebral disk") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of back) @@ -139445,7 +137393,6 @@ SubClassOf(Annotation( "MA" AnnotationAssertion(Annotation( "MGI:anna") "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].") AnnotationAssertion( ) -AnnotationAssertion( "not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO") AnnotationAssertion( "AAO:0010218") AnnotationAssertion( "AAO:0010416") AnnotationAssertion( "BTO:0004696") @@ -139477,7 +137424,6 @@ AnnotationAssertion( "MA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (superficial cervical artery) @@ -139499,14 +137445,14 @@ AnnotationAssertion( "The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]") AnnotationAssertion(rdfs:label "superficial cervical artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior vena cava) AnnotationAssertion(Annotation( "Wikipedia:Inferior_vena_cava") Annotation( "http://orcid.org/0000-0002-6601-2165") "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:10951") "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001194") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455") Annotation( "http://bgee.unil.ch/") "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]") AnnotationAssertion( "AAO:0011083") AnnotationAssertion( "BTO:0002682") AnnotationAssertion( "EHDAA2:0000611") @@ -139536,7 +137482,9 @@ AnnotationAssertion( "posterior vena cava") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (ileocecal junction) @@ -139551,15 +137499,14 @@ AnnotationAssertion( "UBERON:0001073") AnnotationAssertion(rdfs:label "ileocecal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pericardial cavity) AnnotationAssertion(Annotation( "Wikipedia:Pericardium") "A potential space between the visceral and parietal layers of the pericardium.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002220") Annotation( "TAO") Annotation( "ZFIN:curator") "Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000556") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206") Annotation( "http://bgee.unil.ch/") "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)") AnnotationAssertion( "BSA:0000091") AnnotationAssertion( "EHDAA2:0001434") AnnotationAssertion( "EMAPA:16131") @@ -139585,19 +137532,16 @@ AnnotationAssertion( "pericardial cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bony vertebral centrum) AnnotationAssertion(Annotation( "VSAO:0000183") Annotation( "VSAO:curator") Annotation( "http://orcid.org/0000-0002-6601-2165") "Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000126") Annotation( "TAO") Annotation( "ZFIN:curator") "Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000697") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_2008") "Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia:Body_of_vertebra") "The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra].") -AnnotationAssertion(Annotation( "2012-09-06") Annotation( "VSAO:0000183") Annotation( "VSAO") Annotation( "Curator") "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]") -AnnotationAssertion(Annotation( "VSAO") "VSAO definition states it surrounds notochord but not applicable to post-natal.") AnnotationAssertion( "AAO:0000697") AnnotationAssertion( "EMAPA:36588") AnnotationAssertion( "FMA:11945") @@ -139628,16 +137572,13 @@ AnnotationAssertion( "bony vertebral centrum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural spine) AnnotationAssertion(Annotation( "TAO:0001336") Annotation( "http://orcid.org/0000-0002-6601-2165") "An extension of a neural arches dorsal to the neural canal[TAO,modified].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000705") Annotation( "AAO") Annotation( "AAO:Pugener_and_Maglia_2008") "Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001336") Annotation( "TAO") Annotation( "ZFIN:curator") "Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000739") Annotation( "AAO") Annotation( "AAO:Pugener_2002") "Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000705") Annotation( "AAO") "relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]") -AnnotationAssertion( "The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process]") AnnotationAssertion( "spinous process") AnnotationAssertion( "AAO:0000705") AnnotationAssertion( "EMAPA:25107") @@ -139668,7 +137609,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (transverse process of vertebra) AnnotationAssertion(Annotation( "Wikipedia:Transverse_process") "The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted].") -AnnotationAssertion(Annotation( "AAO:0000698") "Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.") AnnotationAssertion( "AAO:0000698") AnnotationAssertion( "FMA:11949") AnnotationAssertion( "MA:0001456") @@ -139716,14 +137656,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocardium of ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2-abduced") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicardium of ventricle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An epicardial layer that lines a cardiac ventricle.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005058") Annotation( "TAO") Annotation( "ZFIN:curator") "The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]") AnnotationAssertion( "FMA:12150") AnnotationAssertion( "TAO:0005058") AnnotationAssertion( "ZFA:0005058") @@ -139740,8 +137681,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (myocardium of ventricle) AnnotationAssertion(Annotation( "ZFIN:curator") "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005061") Annotation( "TAO") Annotation( "ZFIN:curator") "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000604") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481") Annotation( "http://bgee.unil.ch/") "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]") AnnotationAssertion( "EFO:0003088") AnnotationAssertion( "EMAPA:32748") AnnotationAssertion( "FMA:12151") @@ -139760,7 +137699,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myocardium of ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -139783,7 +137722,8 @@ AnnotationAssertion( "EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region") AnnotationAssertion(rdfs:label "skin of head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of trunk) @@ -139806,6 +137746,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "skin of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pleural fluid) @@ -139822,11 +137763,11 @@ AnnotationAssertion( "pleural fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urine) AnnotationAssertion(Annotation( "Wikipedia:Urine") Annotation( "https://github.com/geneontology/go-ontology/issues/11025") "Excretion that is the output of a kidney.") -AnnotationAssertion( "kidney excreta from some taxa (e.g. in aves) may not be liquid") AnnotationAssertion( "BTO:0001419") AnnotationAssertion( "CALOHA:TS-1092") AnnotationAssertion( "EFO:0001939") @@ -139849,6 +137790,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sweat) @@ -139869,14 +137812,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sweat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (synovial fluid) AnnotationAssertion(Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK274/") "Joint fluid is a transudate of plasma that is actively secreted by synovial cells.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005154") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]") -AnnotationAssertion( "It provides nutrients and lubrication for articular cartilage") -AnnotationAssertion( "The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma") AnnotationAssertion( "BTO:0001339") AnnotationAssertion( "CALOHA:TS-0996") AnnotationAssertion( "ENVO:02000039") @@ -139897,9 +137839,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "synovial fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (calcareous tooth) @@ -139908,9 +137852,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(Annotation( "PMID:10210685") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001733") Annotation( "VHOG") Annotation( "PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)") Annotation( "http://bgee.unil.ch/") "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]") -AnnotationAssertion( "dental") -AnnotationAssertion(Annotation( "PMID:10210685") "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni") AnnotationAssertion( "AEO:0000220") AnnotationAssertion( "BTO:0000397") AnnotationAssertion( "CALOHA:TS-1055") @@ -139931,7 +137872,6 @@ AnnotationAssertion(Annotation( "VHOG:0001733") AnnotationAssertion( "Wikipedia:Tooth") AnnotationAssertion( "XAO:0000431") -AnnotationAssertion( "ZFA:0000694") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "dental element") AnnotationAssertion( "dentine containing tooth") AnnotationAssertion( "tooth") @@ -139946,6 +137886,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "calcareous tooth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO-modified") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA-modified") ObjectSomeValuesFrom( )) @@ -139955,9 +137897,6 @@ SubClassOf(Annotation( "cjm AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The first vertebral bone in the vertebral column.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000709") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_1994") "First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001167") Annotation( "TAO") Annotation( "TAO:wd") "Vertebra that is posteriorly adjacent to the neurocranium.[TAO]") -AnnotationAssertion( "1"^^xsd:nonNegativeInteger) AnnotationAssertion( "C1") AnnotationAssertion( "AAO:0000709") AnnotationAssertion( "EHDAA:10606") @@ -139995,9 +137934,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The second vertebral bone in the vertebral column.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001168") Annotation( "TAO") Annotation( "TAO:wd") "Vertebra that is posteriorly adjacent to vertebra 1.[TAO]") -AnnotationAssertion( "not the same as ZFA term 'axis'") -AnnotationAssertion( "2"^^xsd:nonNegativeInteger) AnnotationAssertion( "EHDAA:10608") AnnotationAssertion( "EMAPA:19432") AnnotationAssertion( "FMA:12520") @@ -140034,8 +137970,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000326") Annotation( "TAO") Annotation( "ZFIN:curator") "Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]") -AnnotationAssertion(Annotation( "MA") "we deliberately merge the MA classes as we believe them equivalent") AnnotationAssertion( "UBERON:0006070") AnnotationAssertion(Annotation( "FMA:12527") Annotation( ) "caudal vertebra") AnnotationAssertion( "EMAPA:18374") @@ -140067,6 +138001,9 @@ AnnotationAssertion( "Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae") AnnotationAssertion(rdfs:label "caudal vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (wall of esophagus) @@ -140090,7 +138027,7 @@ AnnotationAssertion( "UBERON:0001096") AnnotationAssertion(rdfs:label "wall of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoralis minor) @@ -140120,21 +138057,13 @@ AnnotationAssertion( "pectoralis minor") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/5d/Pectoralis_minor.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "third to fifth ribs near their costal cartilages") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "medial border and superior surface of the coracoid process of the scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diaphragm) AnnotationAssertion(Annotation( "MP:0002279") "A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.") AnnotationAssertion(Annotation( "Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution") ) -AnnotationAssertion(Annotation( "GO:0060539") "The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000713") Annotation( "VHOG") Annotation( "ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278") Annotation( "http://bgee.unil.ch/") "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]") -AnnotationAssertion( "phrenic") -AnnotationAssertion( "The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]") -AnnotationAssertion( "The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)") -AnnotationAssertion( "barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus") -AnnotationAssertion( "breathing control") -AnnotationAssertion( "originate from the cervical somites, likely C3-C5[PMID:23586979]") AnnotationAssertion( "BTO:0000341") AnnotationAssertion( "CALOHA:TS-0198") AnnotationAssertion( "EFO:0000937") @@ -140163,25 +138092,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diaphragm") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (clavicle bone) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") Annotation( "https://github.com/obophenotype/uberon/issues/103") "A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000761") Annotation( "AAO") Annotation( "AAO:LAP") "Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000761") Annotation( "AAO") "relationship loss: part_of zonal element (AAO:0000936)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000849") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18") Annotation( "http://bgee.unil.ch/") "In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]") -AnnotationAssertion( "clavicular") -AnnotationAssertion( "The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X].") -AnnotationAssertion(Annotation( "ISBN:978-0-12-319060-4") "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.") -AnnotationAssertion(Annotation( "FMA") "FMA and MA differ in whether they consider this part of the shoulder") AnnotationAssertion( "AAO:0000761") AnnotationAssertion( "EMAPA:18721") AnnotationAssertion( "FMA:13321") @@ -140208,16 +138128,16 @@ AnnotationAssertion( "clavicle bone") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "mah") Annotation( "ISBN:978-0-12-319060-4") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "from secondary cartilage of fusion") Annotation( "ISBN:978-0-12-319060-4") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (latissimus dorsi muscle) AnnotationAssertion(Annotation( "Wikipedia:Latissimus_dorsi_muscle") "The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion( "In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192]") AnnotationAssertion( "EFO:0003067") AnnotationAssertion( "EHDAA2:0000932") AnnotationAssertion( "EHDAA:8307") @@ -140244,11 +138164,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "latissimus dorsi muscle") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "floor of intertubercular groove of the humerus") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) @@ -140269,13 +138191,13 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0001113") AnnotationAssertion(rdfs:label "lobe of liver") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lobe of liver) AnnotationAssertion(Annotation( "Wikipedia:Right_lobe_of_liver") "The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005173") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]") AnnotationAssertion( "EHDAA2:0001008") AnnotationAssertion( "EHDAA:4001") AnnotationAssertion( "EMAPA:18311") @@ -140309,7 +138231,6 @@ SubClassOf( (left lobe of liver) AnnotationAssertion(Annotation( "Wikipedia:Left_lobe_of_liver") "The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005172") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of the liver which develops on the fish's left side.[TAO]") AnnotationAssertion( "EHDAA2:0001000") AnnotationAssertion( "EHDAA:3995") AnnotationAssertion( "EMAPA:18307") @@ -140340,7 +138261,6 @@ SubClassOf( (lobe of thyroid gland) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A lobe of tissue that is part of a thyroid gland.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000732") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://www.thyroidmanager.org/Chapter1/chapter01.htm") "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0002032") AnnotationAssertion( "EMAPA:18196") AnnotationAssertion( "FMA:13367") @@ -140361,13 +138281,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "lobe of thyroid gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (right lobe of thyroid gland) AnnotationAssertion(Annotation( "OBOL:automatic") "A lobe of thyroid gland that is in the right side of a thyroid gland.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000733") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://www.thyroidmanager.org/Chapter1/chapter01.htm") "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0001759") AnnotationAssertion( "EMAPA:18198") AnnotationAssertion( "FMA:13368") @@ -140383,12 +138305,12 @@ AnnotationAssertion( "UBERON:0001119") AnnotationAssertion(rdfs:label "right lobe of thyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lobe of thyroid gland) AnnotationAssertion(Annotation( "OBOL:automatic") "A lobe of thyroid gland that is in the left side of a thyroid gland.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000734") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://www.thyroidmanager.org/Chapter1/chapter01.htm") "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0000965") AnnotationAssertion( "EMAPA:18197") AnnotationAssertion( "FMA:13369") @@ -140404,6 +138326,8 @@ AnnotationAssertion( "UBERON:0001120") AnnotationAssertion(rdfs:label "left lobe of thyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serratus ventralis) @@ -140433,10 +138357,11 @@ AnnotationAssertion( "serratus ventralis") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "long thoracic nerve") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "fleshy slips from the outer surface of upper 8 or 9 ribs") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "costal aspect of medial margin of the scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) # Class: (vertebral column) @@ -140445,9 +138370,6 @@ AnnotationAssertion(Annotation( "Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000185") Annotation( "VSAO") Annotation( "VSAO:curator") "Anatomical cluster that consists of all the vertebra in the body.[VSAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001142") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/vertebral+column") "The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001142") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53") Annotation( "http://bgee.unil.ch/") "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]") AnnotationAssertion(Annotation( "FMA:13478") "spine") AnnotationAssertion( "AAO:0000699") AnnotationAssertion( "AAO:0000734") @@ -140487,14 +138409,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebral foramen) AnnotationAssertion(Annotation( "Wikipedia:Vertebral_foramen") Annotation( "http://orcid.org/0000-0002-6601-2165") "A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000729") Annotation( "AAO") Annotation( "AAO:LAP") "Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]") AnnotationAssertion( "AAO:0000729") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37803") AnnotationAssertion( "FMA:13479") @@ -140509,18 +138432,15 @@ AnnotationAssertion( "vertebral foramen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parathyroid gland) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000678") Annotation( "Wikipedia:Parathyroid_gland") "The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001188") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/parathyroid+gland") "Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010545") Annotation( "AAO") Annotation( "AAO:BJB") "Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001188") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]") -AnnotationAssertion( "Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]") -AnnotationAssertion( "In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch") -AnnotationAssertion(Annotation( "PMID:16313389") "table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity.") AnnotationAssertion( "AAO:0010545") AnnotationAssertion( "BTO:0000997") AnnotationAssertion( "CALOHA:TS-0745") @@ -140548,8 +138468,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "parathyroid gland") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -140604,6 +138523,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -140611,9 +138531,6 @@ DisjointClasses( "https://github.com/obophenotype/uberon/issues/324") "Muscle tissue that consists primarily of skeletal muscle fibers.") AnnotationAssertion( "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005277") Annotation( "TAO") Annotation( "ZFIN:curator") "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]") -AnnotationAssertion(Annotation( "FMA:14069") Annotation( "FMA") "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000319") Annotation( "VHOG") Annotation( "PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)") Annotation( "http://bgee.unil.ch/") "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]") AnnotationAssertion( "skeletal muscle") AnnotationAssertion( "EMAPA:32716") AnnotationAssertion( "FMA:14069") @@ -140632,16 +138549,14 @@ AnnotationAssertion( "skeletal muscle tissue") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue) AnnotationAssertion(Annotation( "GO:0006939") Annotation( "Wikipedia:Smooth_muscle_tissue") "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005274") Annotation( "TAO") Annotation( "ZFIN:curator") "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010244") Annotation( "AAO") Annotation( "AAO:CAM") "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001246") Annotation( "VHOG") Annotation( "DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)") Annotation( "http://bgee.unil.ch/") "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]") -AnnotationAssertion( "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.") AnnotationAssertion( "AAO:0010244") AnnotationAssertion( "AEO:0000141") AnnotationAssertion( "BTO:0001260") @@ -140682,6 +138597,8 @@ AnnotationAssertion( "smooth muscle tissue") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -140712,13 +138629,14 @@ AnnotationAssertion( "mesothelium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (dorsum) AnnotationAssertion(Annotation( "BSPO:0000063") Annotation( "UBERONREF:0000006") Annotation( "Wikipedia:Dorsum_(anatomy)") "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..") -AnnotationAssertion( "dorsal") -AnnotationAssertion( "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body") AnnotationAssertion( "BTO:0001713") AnnotationAssertion( "CALOHA:TS-2223") AnnotationAssertion( "EFO:0001405") @@ -140766,15 +138684,16 @@ AnnotationAssertion( "superior mesenteric vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Vitelline_vein") ObjectSomeValuesFrom( )) # Class: (common iliac vein) AnnotationAssertion(Annotation( "MURDOCH:403") Annotation( "Wikipedia:Common_iliac_vein") "A vein that drains the pelvis and lower limbs into the inferior vena cava.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Common_iliac_vein") "In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.") AnnotationAssertion( "EMAPA:17874") AnnotationAssertion( "FMA:14333") AnnotationAssertion( "MA:0002143") @@ -140794,15 +138713,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal vein) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:csmith") Annotation( "MP:0011323") "Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Renal_vein") "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2, the renal vein is part of the kidney") AnnotationAssertion( "BTO:0002681") AnnotationAssertion( "EHDAA2:0001602") AnnotationAssertion( "EHDAA:8722") @@ -140831,13 +138748,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right renal vein) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A renal vein that drains the right kidney.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ncithesaurus:Right_Renal_Vein") "A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37381") AnnotationAssertion( "FMA:14335") AnnotationAssertion( "MA:0002212") @@ -140852,12 +138769,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left renal vein) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A renal vein that drains the left kidney.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ncithesaurus:Left_Renal_Vein") "A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37166") AnnotationAssertion( "FMA:14336") AnnotationAssertion( "MA:0002211") @@ -140873,6 +138791,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic vein) @@ -140905,8 +138825,10 @@ AnnotationAssertion( "hepatic vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -140914,7 +138836,6 @@ DisjointClasses( "Wikipedia:Testicular_vein") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://sourceforge.net/tracker/?func=detail&aid=3220553&group_id=76834&atid=1205376") "A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis.") AnnotationAssertion( "TODO - check testicular vs spermatic vein (MA:0002218)") -AnnotationAssertion( "In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel") AnnotationAssertion( "BTO:0002678") AnnotationAssertion( "EMAPA:18647") AnnotationAssertion( "FMA:14344") @@ -140940,9 +138861,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian vein) @@ -140973,7 +138896,10 @@ AnnotationAssertion( "ovarian vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (suprarenal vein) @@ -140994,12 +138920,12 @@ AnnotationAssertion( "suprarenal vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cystic duct) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0009493") "The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005166") Annotation( "TAO") Annotation( "ZFIN:Curator") "Duct that connects the gall bladder and the common bile duct.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000213") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") AnnotationAssertion( "EHDAA2:0000333") AnnotationAssertion( "EHDAA:3045") AnnotationAssertion( "EMAPA:16841") @@ -141026,9 +138952,9 @@ AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -141037,8 +138963,6 @@ DisjointClasses( "Wikipedia:Cecum") "A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.") AnnotationAssertion(Annotation( "Wikipedia") ) AnnotationAssertion( ) -AnnotationAssertion( "caecal") -AnnotationAssertion(Annotation( "WP") "A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.") AnnotationAssertion( "BTO:0000166") AnnotationAssertion( "CALOHA:TS-0122") AnnotationAssertion( "EFO:0000850") @@ -141078,7 +139002,6 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141090,9 +139013,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Vermiform_appendix") Annotation( "https://orcid.org/0000-0002-6826-8770") "A blind-ended tube connected to the cecum, from which it develops embryologically[WP].") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:14542") "Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001306") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)") Annotation( "http://bgee.unil.ch/") "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]") -AnnotationAssertion( "appendiceal") AnnotationAssertion( "vermix") AnnotationAssertion( "BTO:0000084") AnnotationAssertion( "CALOHA:TS-1267") @@ -141130,7 +139050,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://orcid.org/0000-0002-1572-1316") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -141140,13 +139060,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "Wikipedia:Colon_(anatomy)") Annotation( "ZFIN:curator") Annotation( "http://orcid.org/0000-0002-2825-0621") Annotation( "http://orcid.org/0000-0002-6601-2165") "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-1572-1316") "Some references do not consider the caecum to be part of the colon.") AnnotationAssertion( "TODO - abstract this such that it legitimately covers all vertebrates") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010400") Annotation( "AAO") Annotation( "UBERON:0001155") "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000706") Annotation( "TAO") Annotation( "ZFIN:curator") "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000648") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") -AnnotationAssertion( "colonic") -AnnotationAssertion( "In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]") -AnnotationAssertion( "In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]") -AnnotationAssertion( "it extracts water and salt from solid wastes before they are eliminated from the body[WP]") AnnotationAssertion( "AAO:0010400") AnnotationAssertion( "BTO:0000269") AnnotationAssertion( "CALOHA:TS-0158") @@ -141178,7 +139091,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "colon") -SubClassOf(Annotation( "3") Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141187,7 +139100,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FMA:14545") Annotation( "Wikipedia:Ascending_colon") "Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "in MA, this is a subclass of colon") AnnotationAssertion( "BTO:0000270") AnnotationAssertion( "CALOHA:TS-0057") AnnotationAssertion( "EFO:0000843") @@ -141195,7 +139107,6 @@ AnnotationAssertion( "FMA:14545") AnnotationAssertion( "MA:0001541") AnnotationAssertion( "MAT:0000311") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D044682") AnnotationAssertion( "MIAA:0000311") AnnotationAssertion( "NCIT:C12265") AnnotationAssertion( "SCTID:362162009") @@ -141228,7 +139139,6 @@ AnnotationAssertion( "FMA:14546") AnnotationAssertion( "MA:0001543") AnnotationAssertion( "MAT:0000312") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D044684") AnnotationAssertion( "MIAA:0000312") AnnotationAssertion( "NCIT:C12385") AnnotationAssertion( "SCTID:362163004") @@ -141260,7 +139170,6 @@ AnnotationAssertion( "FMA:14547") AnnotationAssertion( "MA:0001542") AnnotationAssertion( "MAT:0000313") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D044683") AnnotationAssertion( "MIAA:0000313") AnnotationAssertion( "NCIT:C12268") AnnotationAssertion( "SCTID:362165006") @@ -141320,8 +139229,6 @@ SubClassOf(Annotation( "Wik # Class: (fundus of stomach) AnnotationAssertion(Annotation( "GO:0014825") Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Fundus_(stomach)") "The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000421") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000421") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") AnnotationAssertion( "BTO:0000502") AnnotationAssertion( "EFO:0002554") AnnotationAssertion( "EHDAA2:0001919") @@ -141351,6 +139258,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fundus of stomach") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141414,6 +139322,9 @@ AnnotationAssertion( "cardia of stomach") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) @@ -141460,9 +139371,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0010785") "The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum.") AnnotationAssertion( "We follow Kardong in defining stomach regions by glands") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000420") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000420") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") -AnnotationAssertion( "pyloric") AnnotationAssertion( "BTO:0001146") AnnotationAssertion( "EHDAA2:0001580") AnnotationAssertion( "EHDAA:4860") @@ -141490,6 +139398,11 @@ AnnotationAssertion( "pylorus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of stomach) @@ -141513,7 +139426,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "wall of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141537,6 +139450,8 @@ AnnotationAssertion( "UBERON:0001168") AnnotationAssertion(rdfs:label "wall of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of large intestine) @@ -141552,6 +139467,8 @@ AnnotationAssertion( "UBERON:0001169") AnnotationAssertion(rdfs:label "wall of large intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of small intestine) @@ -141569,6 +139486,8 @@ AnnotationAssertion( "UBERON:0001170") AnnotationAssertion(rdfs:label "mesentery of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) # Class: (portal lobule) @@ -141582,6 +139501,7 @@ AnnotationAssertion( "UBERON:0001171") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "portal lobule") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "MA") Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141600,7 +139520,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0001172") AnnotationAssertion(rdfs:label "hepatic acinus") -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -141608,12 +139529,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (biliary tree) AnnotationAssertion(Annotation( "DOI:10.1002/ar.20664") "A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011020") Annotation( "AAO") Annotation( "UBERON:0001173") "Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]") AnnotationAssertion( "AAO:0011020") AnnotationAssertion( "EMAPA:35172") AnnotationAssertion( "FMA:14665") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001659") AnnotationAssertion( "SCTID:181267003") AnnotationAssertion(Annotation( "ncithesaurus:Biliary_Tract") "UMLS:C0005423") AnnotationAssertion( "Wikipedia:Biliary_tract") @@ -141627,18 +139545,21 @@ AnnotationAssertion( "The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]") AnnotationAssertion(rdfs:label "biliary tree") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (common bile duct) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0009495") "The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005165") Annotation( "TAO") Annotation( "ZFIN:Curator") "Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000214") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]") AnnotationAssertion( "EHDAA2:0000303") AnnotationAssertion( "EHDAA:3981") AnnotationAssertion( "EMAPA:17201") @@ -141665,17 +139586,14 @@ AnnotationAssertion( "common bile duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (common hepatic duct) AnnotationAssertion(Annotation( "Wikipedia:Common_hepatic_duct") Annotation( "ZFIN:curator") "Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP].") AnnotationAssertion( "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000220") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") AnnotationAssertion( "EMAPA:19101") AnnotationAssertion( "FMA:14668") AnnotationAssertion( "GAID:286") @@ -141698,14 +139616,12 @@ SubClassOf(Annotation( "FMA SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right hepatic duct) AnnotationAssertion(Annotation( "http://www.medterms.com/script/main/art.asp?articlekey=26034") "The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000217") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]") AnnotationAssertion( "EHDAA2:0001727") AnnotationAssertion( "EHDAA:3992") AnnotationAssertion( "EMAPA:32797") @@ -141720,12 +139636,13 @@ AnnotationAssertion(Annotation( "UBERON:0001176") AnnotationAssertion(rdfs:label "right hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left hepatic duct) AnnotationAssertion(Annotation( "http://www.medterms.com/script/main/art.asp?articlekey=26035") "The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000218") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]") AnnotationAssertion( "EHDAA2:0000941") AnnotationAssertion( "EHDAA:3990") AnnotationAssertion( "EMAPA:32795") @@ -141740,7 +139657,9 @@ AnnotationAssertion(Annotation( "UBERON:0001177") AnnotationAssertion(rdfs:label "left hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral peritoneum) @@ -141760,12 +139679,12 @@ AnnotationAssertion( "visceral peritoneum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peritoneal cavity) AnnotationAssertion(Annotation( "Wikipedia:Peritoneal_cavity") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/86") "Anatomical cavity bounded by visceral and parietal peritoneum.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000852") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/peritoneal+cavity") "The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000852") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206") Annotation( "http://bgee.unil.ch/") "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]") AnnotationAssertion( "BTO:0001782") AnnotationAssertion( "EHDAA2:0001446") AnnotationAssertion( "EMAPA:16138") @@ -141786,14 +139705,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peritoneal cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (superior mesenteric artery) AnnotationAssertion(Annotation( "MESH:A07.231.114.565.755") "Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO") "Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon") AnnotationAssertion( "BTO:0002303") AnnotationAssertion( "EHDAA2:0001949") AnnotationAssertion( "EHDAA:3358") @@ -141822,6 +139744,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inferior mesenteric artery) @@ -141854,14 +139779,16 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal artery) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Renal_artery") "One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates.") AnnotationAssertion( "renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010223") Annotation( "AAO") Annotation( "AAO:BJB") "Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia") Annotation( "Wikipedia:Renal_artery") "The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]") AnnotationAssertion( "AAO:0010223") AnnotationAssertion( "BTO:0001165") AnnotationAssertion( "EFO:0002552") @@ -141896,8 +139823,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "dorsal aorta in Kardong") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right renal artery) @@ -141921,6 +139848,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left renal artery) @@ -141942,6 +139871,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (testicular artery) @@ -141969,7 +139900,8 @@ AnnotationAssertion( "testicular artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right testicular artery) @@ -141987,7 +139919,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right testicular artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left testicular artery) @@ -142005,13 +139940,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left testicular artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian artery) AnnotationAssertion(Annotation( "OBOL:automatic") "An artery that supplies an ovary.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Ovarian_artery") "In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].") AnnotationAssertion( "EMAPA:18620") AnnotationAssertion( "FMA:14761") AnnotationAssertion( "MA:0002012") @@ -142028,7 +139965,9 @@ AnnotationAssertion( "ovarian artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (common iliac artery) @@ -142053,14 +139992,12 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "common iliac artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (hepatic artery) AnnotationAssertion(Annotation( "Wikipedia:Hepatic_artery_proper") Annotation( "https://orcid.org/0000-0002-6601-2165") "An artery that supplies the liver.") -AnnotationAssertion( "currently defined in a generic fashion.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005161") Annotation( "TAO") Annotation( "ZFIN:curator") "Artery that supplies blood to the liver.[TAO]") AnnotationAssertion( "BTO:0004307") AnnotationAssertion( "EMAPA:17859") AnnotationAssertion( "FMA:14769") @@ -142083,6 +140020,8 @@ AnnotationAssertion( "hepatic artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (splenic artery) @@ -142112,6 +140051,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -142137,6 +140078,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ileocolic artery) @@ -142160,11 +140104,15 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of stomach) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The mucosal layer that lines the stomach.") -AnnotationAssertion(Annotation( "Wikipedia:Gastric_mucosa") "The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].") AnnotationAssertion( "BTO:0001308") AnnotationAssertion( "CALOHA:TS-0404") AnnotationAssertion( "EMAPA:35817") @@ -142205,6 +140153,7 @@ AnnotationAssertion( "mucosa of stomach") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -142232,7 +140181,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -142293,7 +140242,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serosa of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -142301,7 +140250,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001466") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1525-142x.2000.00076.x") Annotation( "http://bgee.unil.ch/") "(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]") AnnotationAssertion( "AAO:0011093") AnnotationAssertion( "EMAPA:19251") AnnotationAssertion( "FMA:14916") @@ -142318,6 +140266,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pyloric sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -142381,13 +140331,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of small intestine) AnnotationAssertion(Annotation( "OBOL:automatic") "A serous membrane that is part of a small intestine [Automatically generated definition].") -AnnotationAssertion( "duodenum, 1st part serosa, 2nd - 4th adventitia") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37561") AnnotationAssertion( "FMA:14938") AnnotationAssertion( "MA:0001558") @@ -142455,7 +140404,7 @@ AnnotationAssertion(Annotation( "UBERON:0001208") AnnotationAssertion(rdfs:label "submucosa of large intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of large intestine) @@ -142486,9 +140435,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MESH:A10.549.600") Annotation( "MP:0000696") Annotation( "PMID:15841100") Annotation( "http://orcid.org/0000-0002-6601-2165") "The protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles.") AnnotationAssertion(Annotation( "PMID:PMID:20181529") ) -AnnotationAssertion( "Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas).") -AnnotationAssertion(Annotation( "FMA") "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]") -AnnotationAssertion(Annotation( "MA") "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs") AnnotationAssertion( "BTO:0001784") AnnotationAssertion( "CALOHA:TS-0780") AnnotationAssertion( "EFO:0001381") @@ -142519,7 +140465,6 @@ SubClassOf(Annotation( "PMI AnnotationAssertion(Annotation( "Wikipedia:Brunner's_glands") "A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP].") AnnotationAssertion( "currently defined as equivalent to any submucosal gland in the duodenum.") -AnnotationAssertion(Annotation( "ISBN:9780521617147") "Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds") AnnotationAssertion( "BTO:0002376") AnnotationAssertion( "EMAPA:36522") AnnotationAssertion( "FMA:15060") @@ -142542,19 +140487,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duodenal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MP") ) -SubClassOf(Annotation( "compound tubular") ) -SubClassOf(Annotation( "MA-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA, modified") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "unclear for Aves") Annotation( "ISBN:9780521617147") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal villus) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MGI:rbabiuk") Annotation( "MP:0008108") "The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold.") AnnotationAssertion( "in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005125") Annotation( "TAO") Annotation( "ZFIN:curator") "The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]") -AnnotationAssertion(Annotation( "BTO") "the BTO class refers to a generic villous") AnnotationAssertion( "UBERON:0007607") AnnotationAssertion( "BTO:0003121") AnnotationAssertion( "EMAPA:35784") @@ -142583,9 +140525,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intestinal villus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -142614,6 +140556,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA/obol") ObjectSomeValuesFrom( )) # Class: (jejunal vein) @@ -142632,6 +140576,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA/obol") ObjectSomeValuesFrom( )) # Class: (ileal vein) @@ -142651,6 +140596,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (middle colic vein) @@ -142673,6 +140619,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ileocolic vein) @@ -142695,11 +140644,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right ureter) AnnotationAssertion(Annotation( "OBOL:automatic") "An ureter that is part of a right side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37373") AnnotationAssertion( "FMA:15571") AnnotationAssertion( "MA:0001685") @@ -142712,11 +140663,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left ureter) AnnotationAssertion(Annotation( "OBOL:automatic") "An ureter that is part of a left side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37372") AnnotationAssertion( "FMA:15572") AnnotationAssertion( "MA:0001684") @@ -142729,6 +140681,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal pelvis) @@ -142758,6 +140712,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "renal pelvis") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -142771,7 +140726,6 @@ DisjointClasses( "Wikipedia:Renal_cortex") "Outer cortical portion of the kidney, between the renal capsule and the renal medulla.") AnnotationAssertion( ) -AnnotationAssertion( "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]") AnnotationAssertion( "BTO:0001166") AnnotationAssertion( "CALOHA:TS-0503") AnnotationAssertion( "EMAPA:17952") @@ -142838,9 +140792,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0002827") "The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-11-28") Annotation( "BTO:0000333") Annotation( "BTO") Annotation( "BTO:curator") "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]") -AnnotationAssertion(Annotation( "2012-11-28") Annotation( "XAO:0000146") Annotation( "XAO") Annotation( "XAO:curator") "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005281") Annotation( "TAO") Annotation( "ZFIN:curator") "The part of the nephron that filters blood.[TAO]") AnnotationAssertion( "BTO:0000333") AnnotationAssertion( "CALOHA:TS-1317") AnnotationAssertion( "EMAPA:28236") @@ -142873,16 +140824,12 @@ AnnotationAssertion( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular capsule) AnnotationAssertion(Annotation( "MGI:pvb") Annotation( "MP:0002828") Annotation( "Wikipedia:Bowman%27s_capsule") "A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010526") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]") -AnnotationAssertion( "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP].") -AnnotationAssertion( "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]") AnnotationAssertion( "AAO:0010526") AnnotationAssertion( "BTO:0002297") AnnotationAssertion( "EMAPA:27973") @@ -142927,7 +140874,6 @@ DisjointClasses( "GO:0072078") Annotation( "Wikipedia:Renal_tubule") "An epithelial tube that is part of the nephron, the functional part of the kidney.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA") AnnotationAssertion( "UBERON:0004210") AnnotationAssertion( "renal tubule") AnnotationAssertion( "BTO:0000343") @@ -142957,17 +140903,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nephron tubule") EquivalentClasses(Annotation( "GO") Annotation( "MA") Annotation( "ZFA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "GO") ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "checkme") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (collecting duct of renal tubule) AnnotationAssertion(Annotation( "GO:0072044") Annotation( "Wikipedia:Collecting_tubule") "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005294") Annotation( "TAO") Annotation( "ZFIN:curator") "Renal duct that collects the output from renal tubules.[TAO]") -AnnotationAssertion(Annotation( "FMA") "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron") AnnotationAssertion( "BTO:0000761") AnnotationAssertion( "CALOHA:TS-0860") AnnotationAssertion( "EMAPA:28407") @@ -142998,17 +140943,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "collecting duct of renal tubule") -SubClassOf( ) -SubClassOf(Annotation( "checkme") Annotation( "GO") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right adrenal gland) AnnotationAssertion(Annotation( "OBOL:automatic") "An adrenal gland that is in the right side of the abdomen.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion(Annotation( "WP") "In humans, the right adrenal gland is triangular shaped") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37357") AnnotationAssertion( "FMA:15629") AnnotationAssertion( "MA:0000719") @@ -143021,12 +140963,12 @@ AnnotationAssertion( "UBERON:0001233") AnnotationAssertion(rdfs:label "right adrenal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left adrenal gland) AnnotationAssertion(Annotation( "OBOL:automatic") "An adrenal gland that is in the left side of the abdomen.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion(Annotation( "WP") "In humans, the left adrenal gland is semilunar shaped") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37356") AnnotationAssertion( "FMA:15630") AnnotationAssertion( "MA:0000718") @@ -143039,12 +140981,12 @@ AnnotationAssertion( "UBERON:0001234") AnnotationAssertion(rdfs:label "left adrenal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adrenal cortex) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:llw2") Annotation( "MP:0008288") "The thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001481") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9") Annotation( "http://bgee.unil.ch/") "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]") -AnnotationAssertion( "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO") AnnotationAssertion( "AAO:0011009") AnnotationAssertion( "BTO:0000045") AnnotationAssertion( "CALOHA:TS-0015") @@ -143078,8 +141020,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143088,7 +141031,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (adrenal medulla) AnnotationAssertion(Annotation( "MESH:A06.407.071.265") Annotation( "MGI:llw2") Annotation( "MP:0008289") "The inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001378") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9") Annotation( "http://bgee.unil.ch/") "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]") AnnotationAssertion( "AAO:0011010") AnnotationAssertion( "BTO:0000049") AnnotationAssertion( "CALOHA:TS-0018") @@ -143124,10 +141066,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0073040584") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143181,8 +141124,7 @@ AnnotationAssertion( "UBERON:0001238") AnnotationAssertion(rdfs:label "lamina propria of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of small intestine) @@ -143251,6 +141193,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intestinal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of intestine) @@ -143303,19 +141246,16 @@ AnnotationAssertion( "UBERON:0001243") AnnotationAssertion(rdfs:label "serosa of intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anus) AnnotationAssertion(Annotation( "Wikipedia:Anus") Annotation( "ZFIN:curator") "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.") AnnotationAssertion( ) -AnnotationAssertion( "anal") -AnnotationAssertion( "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html") AnnotationAssertion( "BTO:0001680") AnnotationAssertion( "CALOHA:TS-2005") AnnotationAssertion( "EV:0100082") -AnnotationAssertion(Annotation( ) "FBbt:00047153") AnnotationAssertion( "FMA:15711") AnnotationAssertion( "GAID:312") AnnotationAssertion( "MA:0000331") @@ -143340,7 +141280,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (interlobular bile duct) @@ -143366,7 +141309,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (falciform ligament) AnnotationAssertion(Annotation( "Wikipedia:Falciform_ligament") "A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP].") -AnnotationAssertion(Annotation( "FMA") "in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament") AnnotationAssertion( "EHDAA2:0000499") AnnotationAssertion( "EHDAA:4856") AnnotationAssertion( "EMAPA:18288") @@ -143387,9 +141329,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "FMA-modified") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spleen lymphoid follicle) @@ -143415,9 +141359,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen lymphoid follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "CL:tm") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143446,6 +141391,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "red pulp of spleen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143454,7 +141400,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0002362") "The zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line.") AnnotationAssertion(Annotation( "Wikipedia:Marginal_zone") "marginal zone") AnnotationAssertion( "CALOHA:TS-2395") AnnotationAssertion( "EMAPA:36650") @@ -143472,6 +141417,7 @@ AnnotationAssertion( "marginal zone of spleen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143493,6 +141439,8 @@ AnnotationAssertion( "UBERON:0001252") AnnotationAssertion(rdfs:label "adventitia of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (lamina propria of ureter) @@ -143514,15 +141462,13 @@ AnnotationAssertion( "lamina propria of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (urothelium of ureter) AnnotationAssertion(Annotation( "MP:0000535") "The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MP") "MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium") AnnotationAssertion( "EMAPA:28089") AnnotationAssertion( "FMA:15897") AnnotationAssertion( "MA:0002655") @@ -143536,18 +141482,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urothelium of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "Wikipedia:Urinary_bladder") "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-3308-6245") Annotation( "GOTAX:0010073") Annotation( "https://github.com/obophenotype/uberon/issues/454") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000740") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000623") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000740") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78") Annotation( "http://bgee.unil.ch/") "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]") -AnnotationAssertion( "vesical") -AnnotationAssertion( "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]") AnnotationAssertion(Annotation( "EHDAA2:0000174") "bladder") AnnotationAssertion( "AAO:0000623") AnnotationAssertion( "BTO:0001418") @@ -143585,10 +141529,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "upper part of UG sinus") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of urinary bladder) @@ -143615,14 +141560,13 @@ AnnotationAssertion( "wall of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigone of urinary bladder) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0011768") "The smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa.") AnnotationAssertion( ) -AnnotationAssertion( "The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill.") -AnnotationAssertion(Annotation( "WP") "Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present") AnnotationAssertion( "EMAPA:35174") AnnotationAssertion( "FMA:15910") AnnotationAssertion( "MA:0002492") @@ -143651,6 +141595,7 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143679,6 +141624,9 @@ AnnotationAssertion( "neck of urinary bladder") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of urinary bladder) @@ -143711,6 +141659,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143745,7 +141695,6 @@ SubClassOf(Annotation( "htt AnnotationAssertion(Annotation( "OBOL:automatic") "A lamina propria that is part of a urinary bladder [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion( "Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue") AnnotationAssertion( "EMAPA:30088") AnnotationAssertion( "FMA:15935") AnnotationAssertion( "MA:0001695") @@ -143768,7 +141717,7 @@ AnnotationAssertion( "lamina propria of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of intestine) @@ -143795,12 +141744,13 @@ AnnotationAssertion(Annotation( "UBERON:0001262") AnnotationAssertion(rdfs:label "wall of intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreatic acinus) AnnotationAssertion(Annotation( "MP:0009145") "The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0000028") AnnotationAssertion( "EMAPA:35651") AnnotationAssertion( "FMA:16011") AnnotationAssertion( "MA:0002417") @@ -143817,6 +141767,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pancreatic acinus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -143825,12 +141777,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0031016") "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010112") Annotation( "AAO") Annotation( "AAO:BJB") "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000050") Annotation( "VHOG") Annotation( "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)") Annotation( "http://bgee.unil.ch/") "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]") -AnnotationAssertion( "pancreatic") -AnnotationAssertion(Annotation( "PMID:20959416") "As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)") -AnnotationAssertion( "The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm") -AnnotationAssertion(Annotation( "PMID:16417468") "The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans") AnnotationAssertion( "AAO:0010112") AnnotationAssertion( "BTO:0000988") AnnotationAssertion( "CALOHA:TS-0736") @@ -143867,11 +141813,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -143894,6 +141838,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trabecula of spleen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (splenic cord) @@ -143913,6 +141859,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "splenic cord") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (peritoneal fluid) @@ -143922,7 +141869,6 @@ AnnotationAssertion( "EMAPA:35683") AnnotationAssertion( "FMA:16515") AnnotationAssertion( "MA:0002531") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001202") AnnotationAssertion( "Wikipedia:Peritoneal_fluid") AnnotationAssertion( "ncithesaurus:Peritoneal_Fluid") AnnotationAssertion( "uberon") @@ -143931,13 +141877,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peritoneal fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic girdle region) AnnotationAssertion(Annotation( "DOI:10.1002/dvdy.22617") Annotation( "FMA:16581") Annotation( "FMA:23217") Annotation( "UBERONREF:0000003") Annotation( "https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion") Annotation( "https://orcid.org/0000-0002-6601-2165") "The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions.") -AnnotationAssertion( "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000304") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37862") AnnotationAssertion( "FMA:16581") AnnotationAssertion( "NCIT:C33291") @@ -143952,7 +141899,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic girdle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -143962,8 +141912,6 @@ DisjointClasses( "Wikipedia:Hip_bone") Annotation( "https://github.com/obophenotype/uberon/issues/290") Annotation( "https://orcid.org/0000-0002-6601-2165") "A fused bone consisting of the ilium, ischium and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified].") AnnotationAssertion( "currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "WP") "The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column") -AnnotationAssertion(Annotation( "FMA") "in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra.") AnnotationAssertion(Annotation( "FMA:16585") "bone of pelvic girdle") AnnotationAssertion( "innominate") AnnotationAssertion( "FMA:16585") @@ -143984,20 +141932,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "innominate bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ilium) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") Annotation( "https://github.com/obophenotype/uberon/issues/105") Annotation( "https://github.com/obophenotype/uberon/issues/60") "Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad].") AnnotationAssertion(Annotation( "Wikipedia") ) -AnnotationAssertion(Annotation( "Wikipedia") ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000772") Annotation( "AAO") Annotation( "AAO:LAP") "Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO]") -AnnotationAssertion( "iliac") -AnnotationAssertion(Annotation( "WP") "All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium") -AnnotationAssertion(Annotation( "MA") "this is_a hip bone in MA.") AnnotationAssertion( "AAO:0000772") AnnotationAssertion( "CALOHA:TS-2200") AnnotationAssertion( "EFO:0003049") @@ -144026,8 +141970,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144035,9 +141982,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (ischium) AnnotationAssertion(Annotation( "VSAO:0005006") Annotation( "VSAO:NI") Annotation( "Wikipedia:Ischium") "Endochondral bone that is paired, forming the posterior part of the pelvis, articulating with the pubis and ilium.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000860") Annotation( "AAO") Annotation( "AAO:LAP") "Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO]") -AnnotationAssertion( "ischial") -AnnotationAssertion(Annotation( "MA") "this is_a hip bone in MA; in FMA it is a zone of bone organ.") AnnotationAssertion( "AAO:0000860") AnnotationAssertion( "EMAPA:18727") AnnotationAssertion( "FMA:16592") @@ -144065,8 +142009,9 @@ EquivalentClasses( ObjectIntersec SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "MA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144074,7 +142019,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epithelium of stomach) AnnotationAssertion(Annotation( "MP:0000471") "The epithelial layer of the stomach .") -AnnotationAssertion(Annotation( "FMA") "in FMA this is classified as simple columnar, MA divides this into squamous and glandular") AnnotationAssertion( "BTO:0000500") AnnotationAssertion( "CALOHA:TS-2068") AnnotationAssertion( "EHDAA2:0001918") @@ -144097,13 +142041,15 @@ AnnotationAssertion( "epithelium of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal epithelium) AnnotationAssertion(Annotation( "UBERON:cjm") "Epithelial layer that lines the intestine.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005124") Annotation( "TAO") Annotation( "ZFIN:curator") "Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]") AnnotationAssertion( "BTO:0000781") AnnotationAssertion( "EMAPA:32873") AnnotationAssertion( "FMA:17229") @@ -144131,6 +142077,9 @@ AnnotationAssertion( "intestinal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144156,7 +142105,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:csmith") Annotation( "MP:0008993") Annotation( "http://orcid.org/0000-0002-6601-2165") "A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.") AnnotationAssertion( ) -AnnotationAssertion( "The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver.") AnnotationAssertion( "FMA:17523") AnnotationAssertion( "MA:0002499") AnnotationAssertion( "NCIT:C33342") @@ -144172,6 +142120,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "portal triad") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144182,7 +142132,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (liver parenchyma) AnnotationAssertion(Annotation( "MP:0008986") "The functional units of the liver including the lobules.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000539") Annotation( "VHOG") Annotation( "DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)") Annotation( "http://bgee.unil.ch/") "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]") AnnotationAssertion( "UBERON:0003223") AnnotationAssertion( "AAO:0010405") AnnotationAssertion( "EHDAA2:0001004") @@ -144204,6 +142153,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "liver parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144211,7 +142163,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Hepatic_sinusoid") Annotation( "ZFIN:curator") "Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000708") Annotation( "VHOG") Annotation( "DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)") Annotation( "http://bgee.unil.ch/") "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]") AnnotationAssertion( "UBERON:0003275") AnnotationAssertion( "EHDAA2:0000999") AnnotationAssertion( "EMAPA:17365") @@ -144241,6 +142192,8 @@ AnnotationAssertion( "hepatic sinusoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144285,8 +142238,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "PMID:9268568") Annotation( "Wikipedia:Nephron") "The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP].") AnnotationAssertion( "kidney terms require review for cross-vertebrate compatibility and developmental relationships.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002153") Annotation( "TAO") Annotation( "ZFIN:curator") "Functional unit of the kidney that filters waste.[TAO]") -AnnotationAssertion(Annotation( "GO") "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)") AnnotationAssertion( "BTO:0000924") AnnotationAssertion( "CALOHA:TS-1312") AnnotationAssertion( "EMAPA:28491") @@ -144315,7 +142266,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) @@ -144323,7 +142274,6 @@ SubClassOf(Annotation( "Bge AnnotationAssertion(Annotation( "MP:0011499") Annotation( "Wikipedia:Bowman's_space") Annotation( "http://medical-dictionary.thefreedictionary.com/bowman's+space") "A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP].") AnnotationAssertion( "TODO - fix ZFA") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005283") Annotation( "TAO:0005312") Annotation( "TAO") Annotation( "ZFIN:curator") "Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO]") AnnotationAssertion( "EMAPA:27985") AnnotationAssertion( "EMAPA:28263") AnnotationAssertion( "FMA:17676") @@ -144359,7 +142309,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (proximal convoluted tubule) AnnotationAssertion(Annotation( "GO:0072019") "The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005290") Annotation( "TAO") Annotation( "ZFIN:curator") "Renal tubule that connects to the renal corpuscle.[TAO]") AnnotationAssertion( "CALOHA:TS-2198") AnnotationAssertion( "EMAPA:28287") AnnotationAssertion( "EV:0100388") @@ -144388,8 +142337,9 @@ AnnotationAssertion( "proximal convoluted tubule") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "checkme") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA uses subclass") Annotation( "GOC:mtg_kidney_jan10") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -144399,11 +142349,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0004755") "The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine.") AnnotationAssertion( "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review.") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001270") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]") -AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0099864") "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva .") -AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0099864") "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids.") AnnotationAssertion( "BTO:0004608") AnnotationAssertion( "EMAPA:19280") AnnotationAssertion( "EV:0100390") @@ -144426,6 +142372,9 @@ AnnotationAssertion( "loop of Henle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (descending limb of loop of Henle) @@ -144458,7 +142407,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0072020") "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule.") AnnotationAssertion( "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005291") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]") AnnotationAssertion( "UBERON:0005166") AnnotationAssertion( "BTO:0000055") AnnotationAssertion( "EMAPA:29661") @@ -144481,9 +142429,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal straight tubule") +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA uses subclass") Annotation( "GOC:mtg_kidney_jan10") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144518,7 +142467,6 @@ AnnotationAssertion( "thick ascending limb of loop of Henle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "GOC:dph") Annotation( "MA-modified-from-isa") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144526,8 +142474,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0072025") "The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Distal_convoluted_tubule") "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule].") -AnnotationAssertion( "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.") AnnotationAssertion( "EMAPA:28393") AnnotationAssertion( "EV:0100389") AnnotationAssertion( "FMA:17721") @@ -144549,7 +142495,8 @@ AnnotationAssertion( "distal convoluted tubule") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") Annotation( "GO") Annotation( "MA-modified-from-isa") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144576,14 +142523,12 @@ AnnotationAssertion( "outer medulla of kidney") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner medulla of kidney) AnnotationAssertion(Annotation( "GO:0072053") "Innermost region of the mammalian kidney.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "GO:0072053") "unique to mammals") AnnotationAssertion( "BTO:0001745") AnnotationAssertion( "CALOHA:TS-0506") AnnotationAssertion( "EMAPA:28349") @@ -144604,7 +142549,6 @@ AnnotationAssertion( "inner medulla of kidney") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO:0072053") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144612,11 +142556,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MESH:A05.360.319.679.490") Annotation( "MGI:smb") Annotation( "MP:0004896") "The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001285") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/Endometrium") "The mucous membrane lining the uterus. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001285") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144") Annotation( "http://bgee.unil.ch/") "The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]") -AnnotationAssertion( "endometrial") -AnnotationAssertion( "Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead") -AnnotationAssertion(Annotation( "FMA") "in FMA this is subdivided into basal and outer") AnnotationAssertion( "BTO:0001422") AnnotationAssertion( "CALOHA:TS-0276") AnnotationAssertion( "EFO:0000980") @@ -144647,6 +142586,7 @@ AnnotationAssertion( "endometrium") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144654,10 +142594,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (myometrium) AnnotationAssertion(Annotation( "MESH:A02.633.570.500") Annotation( "MGI:brs") Annotation( "MP:0008256") "The smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001281") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/myometrium") "The muscular wall of the uterus. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001281") Annotation( "VHOG") Annotation( "PMID:15471813 Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004)") Annotation( "http://bgee.unil.ch/") "In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG]") -AnnotationAssertion( "myometrial") -AnnotationAssertion( "The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss.") AnnotationAssertion( "BTO:0000907") AnnotationAssertion( "CALOHA:TS-0652") AnnotationAssertion( "EFO:0001970") @@ -144683,12 +142619,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myometrium") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of uterus) @@ -144715,6 +142651,8 @@ AnnotationAssertion( "serosa of uterus") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (glans penis) @@ -144742,6 +142680,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144750,9 +142690,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:pvb") Annotation( "MP:0002631") "The elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens.") AnnotationAssertion( "Kardong has epididymis in elasmobranch") -AnnotationAssertion( "epididymal") -AnnotationAssertion(Annotation( "WP") "A similar, but probably non-homologous, structure is found in cartilaginous fishes") -AnnotationAssertion( "Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.") AnnotationAssertion( "BTO:0000408") AnnotationAssertion( "CALOHA:TS-0285") AnnotationAssertion( "EFO:0000982") @@ -144777,7 +142714,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epididymis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -144789,8 +142728,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (right uterine tube) AnnotationAssertion(Annotation( "OBOL:automatic") "A fallopian tube that is part of a right side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "non-functional in monotremes[ISBN:978-0226870137]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37369") AnnotationAssertion( "FMA:18483") AnnotationAssertion( "MA:0001717") @@ -144804,11 +142741,12 @@ AnnotationAssertion( "right uterine tube") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left uterine tube) AnnotationAssertion(Annotation( "OBOL:automatic") "A fallopian tube that is part of a left side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37368") AnnotationAssertion( "FMA:18484") AnnotationAssertion( "MA:0001716") @@ -144822,6 +142760,8 @@ AnnotationAssertion( "left uterine tube") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (germinal epithelium of ovary) @@ -144849,16 +142789,15 @@ AnnotationAssertion( "Controversial - see article. Requires expert input. Also check BTO placement") AnnotationAssertion(rdfs:label "germinal epithelium of ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian follicle) AnnotationAssertion(Annotation( "Wikipedia:Ovarian_follicle") Annotation( "http://www.repropedia.org/ovarian-follicle") "A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified].") AnnotationAssertion( "TODO - align subtypes based on staging, which is taxon-specific") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001110") Annotation( "TAO") Annotation( "ZFIN:curator") "Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001536") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)") Annotation( "http://bgee.unil.ch/") "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]") -AnnotationAssertion( "These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)") -AnnotationAssertion( "The somatic cell component of the follicle produces hormones important for oocyte development and proper endocrine function") AnnotationAssertion( "BTO:0000475") AnnotationAssertion( "CALOHA:TS-0726") AnnotationAssertion( "EMAPA:35627") @@ -144889,6 +142828,7 @@ AnnotationAssertion( "ovarian follicle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -144912,6 +142852,8 @@ AnnotationAssertion( "capsule of ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (external iliac artery) @@ -144993,7 +142935,7 @@ AnnotationAssertion(rdfs:seeAlso AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (inferior vesical artery) @@ -145016,13 +142958,14 @@ AnnotationAssertion( "inferior vesical artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (superior vesical artery) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An artery that supplies blood to the upper urinary bladder.") AnnotationAssertion( ) -AnnotationAssertion( "The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37123") AnnotationAssertion( "FMA:18839") AnnotationAssertion( "MA:0002080") @@ -145040,7 +142983,8 @@ AnnotationAssertion( "superior vesical artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (external iliac vein) @@ -145111,6 +143055,7 @@ AnnotationAssertion( "inferior vesical vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") Annotation( "MA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vaginal vein) @@ -145130,13 +143075,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA/obol") ObjectSomeValuesFrom( )) # Class: (sciatic nerve) AnnotationAssertion(Annotation( "Wikipedia:Sciatic_nerve") "A large nerve that supplies nearly the whole of the skin of the leg, the muscles of the back of the thigh, and those of the leg and foot. It begins in the lower back and runs through the buttock and down the lower limb.") AnnotationAssertion( ) -AnnotationAssertion( "mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/") AnnotationAssertion( "BIRNLEX:1133") AnnotationAssertion( "BTO:0001221") AnnotationAssertion( "CALOHA:TS-0899") @@ -145189,14 +143135,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tibial nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "WP") ObjectSomeValuesFrom( )) # Class: (muscle of pelvis) AnnotationAssertion(Annotation( "FMA:19086") "Muscle (organ) which is a part of the pelvis. Examples: levator ani,.") -AnnotationAssertion( "EMAPA:18184") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37481") AnnotationAssertion( "FMA:19086") AnnotationAssertion( "MA:0000534") @@ -145211,11 +143155,11 @@ AnnotationAssertion( "muscle of pelvis") EquivalentClasses(Annotation( "FMAdef") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) # Class: (lobe of prostate) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/665") "A portion of a prostate that forms a lobe.") -AnnotationAssertion(Annotation( "PMID:15163300") Annotation( "https://github.com/obophenotype/uberon/issues/665") "Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue") AnnotationAssertion( "BTO:0000548") AnnotationAssertion( "EMAPA:35712") AnnotationAssertion( "FMA:19570") @@ -145230,6 +143174,10 @@ AnnotationAssertion( "UBERON:0001328") AnnotationAssertion(rdfs:label "lobe of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pampiniform plexus) @@ -145270,6 +143218,10 @@ AnnotationAssertion( "UBERON:0001331") AnnotationAssertion(rdfs:label "skin of penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (prepuce of penis) @@ -145281,7 +143233,6 @@ AnnotationAssertion( "CALOHA:TS-0383") AnnotationAssertion( "EFO:0001664") AnnotationAssertion( "EMAPA:18989") -AnnotationAssertion( "EV:0100109") AnnotationAssertion( "FMA:19639") AnnotationAssertion( "MA:0000407") AnnotationAssertion( "NCIT:C33049") @@ -145303,6 +143254,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -145325,6 +143278,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female urethra) @@ -145346,6 +143301,8 @@ AnnotationAssertion( "female urethra") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostatic urethra) @@ -145372,6 +143329,7 @@ AnnotationAssertion( "prostatic urethra") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -145380,7 +143338,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (urethral gland) AnnotationAssertion(Annotation( "MP:anna") "Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine.") -AnnotationAssertion(Annotation( "NCIT") "NCIT:C12339 paraurethral gland belongs here") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37784") AnnotationAssertion( "FMA:19683") AnnotationAssertion( "MA:0001688") @@ -145397,16 +143354,14 @@ AnnotationAssertion( "urethral gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MP") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminiferous tubule of testis) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:csmith") Annotation( "MP:0002216") Annotation( "https://github.com/obophenotype/uberon/issues/1381") "The tubules in the testes where spermatogenesis occurs.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010399") Annotation( "AAO") Annotation( "AAO:BJB") "Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001363") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/SEMINIFEROUS+TUBULE") "One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001363") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28") Annotation( "http://bgee.unil.ch/") "Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]") AnnotationAssertion( "AAO:0010399") AnnotationAssertion( "BTO:0001235") AnnotationAssertion( "CALOHA:TS-1239") @@ -145440,7 +143395,9 @@ AnnotationAssertion( "seminiferous tubule of testis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -145449,7 +143406,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epithelium of vagina) AnnotationAssertion(Annotation( "MP:0001140") "The epithelial layer of the vagina.") -AnnotationAssertion(Annotation( "FMA") "FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)") AnnotationAssertion( "BTO:0000422") AnnotationAssertion( "CALOHA:TS-1325") AnnotationAssertion( "EMAPA:30991") @@ -145468,13 +143424,13 @@ AnnotationAssertion( "epithelium of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (white adipose tissue) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005670") "Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified].") -AnnotationAssertion(Annotation( "FMA") "Adipose tissue, cells of which contain a single large lipid droplet.") AnnotationAssertion( "BTO:0001456") AnnotationAssertion( "CALOHA:TS-1119") AnnotationAssertion( "EFO:0000813") @@ -145482,7 +143438,6 @@ AnnotationAssertion( "FMA:20117") AnnotationAssertion( "MA:0000058") AnnotationAssertion( "MAT:0000199") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D052436") AnnotationAssertion( "MIAA:0000199") AnnotationAssertion( "NCIT:C33889") AnnotationAssertion(Annotation( "ncithesaurus:White_Adipose_Tissue") "UMLS:C1704223") @@ -145499,13 +143454,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brown adipose tissue) AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0011698") "A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified].") -AnnotationAssertion(Annotation( "FMA") "Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]") -AnnotationAssertion( "especially abundant in newborns and in hibernating mammals") -AnnotationAssertion( "thermogenesis") AnnotationAssertion( "BTO:0000156") AnnotationAssertion( "CALOHA:TS-0099") AnnotationAssertion( "EFO:0000812") @@ -145534,7 +143488,9 @@ AnnotationAssertion( "brown adipose tissue") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal sac) @@ -145554,6 +143510,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lacrimal sac") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -145561,8 +143518,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:External_acoustic_meatus") "A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter.") AnnotationAssertion( "consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct.") -AnnotationAssertion( "tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]") -AnnotationAssertion(Annotation( "FMA") "subdivision of head in FMA.") AnnotationAssertion( "EHDAA2:0000460") AnnotationAssertion( "EHDAA:8975") AnnotationAssertion( "EMAPA:17588") @@ -145590,6 +143545,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "external acoustic meatus") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:11237469") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -145598,7 +143555,6 @@ SubClassOf(Annotation( "EHD # Class: (anal region) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The anus and surrounding regions. Encompasses both internal and external regions, where present.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000395") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") AnnotationAssertion( "EFO:0000847") AnnotationAssertion( "EHDAA2:0000122") AnnotationAssertion( "EHDAA:2931") @@ -145623,7 +143579,7 @@ AnnotationAssertion(rdfs:seeAlso AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png"^^xsd:anyURI) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deep femoral artery) @@ -145645,6 +143601,9 @@ AnnotationAssertion( "deep femoral artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medial circumflex femoral artery) @@ -145664,16 +143623,14 @@ AnnotationAssertion( "medial circumflex femoral artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (cerebrospinal fluid) AnnotationAssertion(Annotation( "Wikipedia:Cerebrospinal_fluid") "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.") AnnotationAssertion( "many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002184") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001278") Annotation( "VHOG") Annotation( "DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)") Annotation( "http://bgee.unil.ch/") "In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 models this as developing from CP, which is wrong") -AnnotationAssertion(Annotation( "FMA") "the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.") AnnotationAssertion( "BIRNLEX:1798") AnnotationAssertion( "BTO:0000237") AnnotationAssertion( "CALOHA:TS-0130") @@ -145705,14 +143662,13 @@ AnnotationAssertion( "cerebrospinal fluid") SubClassOf(Annotation( "Wikipedia") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "see notes") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (femoral vein) AnnotationAssertion(Annotation( "Wikipedia:Femoral_vein") "In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010237") Annotation( "AAO") Annotation( "AAO:BJB") "Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO]") AnnotationAssertion( "AAO:0010237") AnnotationAssertion( "EMAPA:17876") AnnotationAssertion( "FMA:21185") @@ -145731,7 +143687,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "femoral vein") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (great saphenous vein) @@ -145764,7 +143720,6 @@ SubClassOf(Annotation( "FMA # Class: (parietal peritoneum) AnnotationAssertion(Annotation( "Wikipedia:Peritoneum#Types") Annotation( "http://orcid.org/0000-0002-6601-2165") "The outer layer of peritoneum that is attached to the abdominal and pelvic walls.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010816") Annotation( "AAO") Annotation( "AAO:JMG") "Peritoneum attached to the abdominal wall.[AAO]") AnnotationAssertion( "UBERON:0004459") AnnotationAssertion( "AAO:0010816") AnnotationAssertion( "EMAPA:16591") @@ -145783,18 +143738,17 @@ AnnotationAssertion( "parietal peritoneum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of leg) AnnotationAssertion(Annotation( "Wikipedia:Leg_muscle") Annotation( "https://orcid.org/0000-0002-6601-2165") "A muscle that is part of the region of the hindlimb between the pelvis and ankle.") AnnotationAssertion( ) -AnnotationAssertion( "see notes on UBERON:0000978 for possible confusion over the term 'leg'.") AnnotationAssertion( "UBERON:0003270") AnnotationAssertion( "BTO:0000722") AnnotationAssertion( "EHDAA:8291") -AnnotationAssertion( "EMAPA:19144") -AnnotationAssertion( "EMAPA:19318") AnnotationAssertion( "MA:0000672") AnnotationAssertion( "RETIRED_EHDAA2:0000974") AnnotationAssertion( "Wikipedia:Leg_muscle") @@ -145815,6 +143769,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of leg") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (primary motor cortex) @@ -145822,8 +143777,6 @@ SubClassOf(Annotation( "pro AnnotationAssertion(Annotation( "NLX:143555") "The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html.") AnnotationAssertion( "TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "NLX:143555") "The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html") -AnnotationAssertion(Annotation( "2012-08-31") Annotation( "MP:0000800") Annotation( "MP") Annotation( "MGI:csmith") "the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP]") AnnotationAssertion( "BAMS:M1") AnnotationAssertion( "BAMS:MO") AnnotationAssertion( "BAMS:MOp") @@ -145860,9 +143813,7 @@ AnnotationAssertion( "primary motor cortex") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -145870,7 +143821,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Artery that supplies the axilla.") AnnotationAssertion( ) -AnnotationAssertion( "In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery.") AnnotationAssertion( "EMAPA:18749") AnnotationAssertion( "FMA:22654") AnnotationAssertion( "GAID:473") @@ -145891,8 +143841,10 @@ AnnotationAssertion( "axillary artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (subscapular artery) @@ -145931,6 +143883,8 @@ AnnotationAssertion( "UBERON:0001415") AnnotationAssertion(rdfs:label "skin of pelvis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of abdomen) @@ -145953,6 +143907,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of abdomen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of neck) @@ -145973,6 +143929,8 @@ AnnotationAssertion( "UBERON:0001417") AnnotationAssertion(rdfs:label "skin of neck") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of thorax) @@ -145991,6 +143949,8 @@ AnnotationAssertion( "UBERON:0001418") AnnotationAssertion(rdfs:label "skin of thorax") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of limb) @@ -146009,14 +143969,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral girdle region) AnnotationAssertion(Annotation( "FMA:23217") Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.") -AnnotationAssertion( "this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000305") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]") -AnnotationAssertion(Annotation( "2012-09-06") Annotation( "VSAO:0000305") Annotation( "VSAO") Annotation( "Curator") "Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37856") AnnotationAssertion( "FMA:23217") AnnotationAssertion( "SCTID:229759004") @@ -146036,6 +143994,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral girdle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -146057,6 +144018,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facial lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral lymphatic vessel) @@ -146070,17 +144033,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal system) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000027") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000434") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000027") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000566") Annotation( "AAO") Annotation( "AAO:LAP") "System that provides physical support to the organism.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001254") Annotation( "VHOG") Annotation( "DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)") Annotation( "http://bgee.unil.ch/") "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]") -AnnotationAssertion( "skeletal") -AnnotationAssertion(Annotation( "GO") "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates") AnnotationAssertion( "AAO:0000566") AnnotationAssertion( "BTO:0001486") AnnotationAssertion( "CALOHA:TS-1320") @@ -146108,7 +144066,10 @@ AnnotationAssertion( "skeletal system") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -146124,7 +144085,6 @@ DisjointClasses( (carpal bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm].") -AnnotationAssertion(Annotation( "Wikipedia:Carpus") "In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist.") AnnotationAssertion( "EMAPA:25056") AnnotationAssertion( "FMA:23889") AnnotationAssertion( "GAID:179") @@ -146147,14 +144107,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (phalanx of manus) AnnotationAssertion(Annotation( "Wikipedia:Phalanges_of_the_hand") Annotation( "https://orcid.org/0000-0002-6601-2165") "A phalanx that is part of a forelimb autopod[Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000947") Annotation( "AAO") Annotation( "AAO:LAP") "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO]") AnnotationAssertion( "AAO:0000947") AnnotationAssertion( "EMAPA:32650") AnnotationAssertion( "FMA:23914") @@ -146185,17 +144145,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis) AnnotationAssertion(Annotation( "MESH:A02.835.232.251") Annotation( "http://orcid.org/0000-0002-6601-2165") "The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000742") Annotation( "AAO") Annotation( "AAO:Pugener_2002") "Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]") -AnnotationAssertion(Annotation( "FMA:24012") "Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur.") -AnnotationAssertion( "epiphyseal") -AnnotationAssertion( "epiphysial") AnnotationAssertion( "AAO:0000742") AnnotationAssertion( "BTO:0000413") AnnotationAssertion( "EMAPA:35508") @@ -146225,7 +144183,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FMA:24014") Annotation( "Wikipedia:Metaphysis") "Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA].") AnnotationAssertion( "todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA.") -AnnotationAssertion(Annotation( "FMA:24014") "Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]") AnnotationAssertion( "EMAPA:35509") AnnotationAssertion( "FMA:24014") AnnotationAssertion( "MA:0001363") @@ -146252,7 +144209,6 @@ AnnotationAssertion(Annotation( "EMAPA:35250") AnnotationAssertion( "FMA:24018") AnnotationAssertion( "MA:0001461") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000071538") AnnotationAssertion( "NCIT:C52714") AnnotationAssertion( "SCTID:361728003") AnnotationAssertion(Annotation( "ncithesaurus:Cortical_Bone") "UMLS:C0222661") @@ -146282,10 +144238,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle.") AnnotationAssertion( "TODO - find a home for: FMA:24139 ! skeleton of upper limb") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000202") Annotation( "AAO") Annotation( "AAO:LAP") "Skeletal structure of the paired, anterior appendages.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000202") Annotation( "AAO") "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001256") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") AnnotationAssertion( "AAO:0000202") AnnotationAssertion( "EHDAA2:0002222") AnnotationAssertion( "EMAPA:32623") @@ -146310,16 +144262,16 @@ AnnotationAssertion( "UBERON:0001440") AnnotationAssertion(rdfs:label "forelimb skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000217") Annotation( "AAO") Annotation( "AAO:LAP") "Skeletal structure of the paired, posterior appendages.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000217") Annotation( "AAO") "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001255") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") AnnotationAssertion( "AAO:0000217") AnnotationAssertion( "EHDAA2:0002226") AnnotationAssertion( "EMAPA:32633") @@ -146343,14 +144295,16 @@ AnnotationAssertion( "TOOD - find a home for: FMA:24140") AnnotationAssertion(rdfs:label "hindlimb skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of manus) AnnotationAssertion(Annotation( "PHENOSCAPE:MAH") Annotation( "https://github.com/obophenotype/uberon/issues/74") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0002227") AnnotationAssertion( "EMAPA:32643") AnnotationAssertion( "FMA:24159") @@ -146374,17 +144328,16 @@ AnnotationAssertion( "here 'manus' includes both the wrist region, metatarsal region and acropodial region") AnnotationAssertion(rdfs:label "skeleton of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (chest) AnnotationAssertion(Annotation( "FMA:9576") Annotation( "Wikipedia:Chest") "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].") AnnotationAssertion( "FMA:24216 present in FMA1, but gone in subsequent versions") -AnnotationAssertion( ) -AnnotationAssertion( "pectoral") -AnnotationAssertion( "thoracic") AnnotationAssertion( "BTO:0001368") AnnotationAssertion( "CALOHA:TS-1039") AnnotationAssertion( "EFO:0000965") @@ -146437,7 +144390,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (skeleton of pes) AnnotationAssertion(Annotation( "PHENOSCAPE:MAH") Annotation( "https://github.com/obophenotype/uberon/issues/75") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0002228") AnnotationAssertion( "FMA:24222") AnnotationAssertion( "VSAO:0005021") @@ -146456,15 +144408,15 @@ AnnotationAssertion( "here 'pes' includes both the ankle region, metatarsals and acropodial region") AnnotationAssertion(rdfs:label "skeleton of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibula) AnnotationAssertion(Annotation( "PHENOSCAPE:mah") "The major postaxial endochondral bone in the posterior zeugopod[Phenoscape].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000891") Annotation( "AAO") Annotation( "AAO:LAP") "One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]") -AnnotationAssertion( "fibular") AnnotationAssertion( "AAO:0000891") AnnotationAssertion( "BTO:0002346") AnnotationAssertion( "CALOHA:TS-2203") @@ -146488,15 +144440,15 @@ AnnotationAssertion( "fibula") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsal bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia.") -AnnotationAssertion(Annotation( "Wikipedia:Tarsus_(skeleton)") "In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment") AnnotationAssertion( "BTO:0002343") AnnotationAssertion( "EMAPA:25072") AnnotationAssertion( "FMA:24491") @@ -146525,7 +144477,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -146554,7 +144507,10 @@ AnnotationAssertion( "metatarsal bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -146562,7 +144518,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (phalanx of pes) AnnotationAssertion(Annotation( "Wikipedia:Phalanges_of_the_foot") Annotation( "https://orcid.org/0000-0002-6601-2165") "A phalanx that is part of a hindlimb autopod[Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000930") Annotation( "AAO") Annotation( "AAO:LAP") "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]") AnnotationAssertion( "UBERON:0004272") AnnotationAssertion(Annotation( "OBOL:automatic") "digital bone of pes") AnnotationAssertion( "AAO:0000930") @@ -146592,18 +144547,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (face) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).") -AnnotationAssertion(Annotation( "FMA:24728") "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.") -AnnotationAssertion(Annotation( "HAO:0000316") Annotation( "http://api.hymao.org/api/ref/67791") Annotation( "NCBITaxon:7399") "The area that extends from the median ocellus to the oral foramen[HAO].") -AnnotationAssertion( "facial") -AnnotationAssertion(Annotation( "vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf") "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)") AnnotationAssertion( "BTO:0003369") AnnotationAssertion( "CALOHA:TS-2216") AnnotationAssertion( "EMAPA:32763") @@ -146648,6 +144600,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of eyelid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of lip) @@ -146667,6 +144621,7 @@ AnnotationAssertion( "skin of lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of external ear) @@ -146692,15 +144647,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arm) AnnotationAssertion(Annotation( "Wikipedia:Arm") "The part of the forelimb extending from the shoulder to the autopod[cjm].") AnnotationAssertion( "currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand") -AnnotationAssertion( "this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000339") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") AnnotationAssertion( "BTO:0001435") AnnotationAssertion( "CALOHA:TS-2204") AnnotationAssertion( "EFO:0001410") @@ -146724,15 +144677,13 @@ AnnotationAssertion( "arm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (elbow) AnnotationAssertion(Annotation( "Wikipedia:Elbow") "The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].") -AnnotationAssertion( "cubital") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group") AnnotationAssertion( "CALOHA:TS-2222") AnnotationAssertion( "EFO:0003069") AnnotationAssertion( "EHDAA2:0000429") @@ -146758,15 +144709,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "elbow") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (hip) AnnotationAssertion(Annotation( "Wikipedia:Hip") "The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000346") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333") Annotation( "http://bgee.unil.ch/") "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]") -AnnotationAssertion( "coxal") -AnnotationAssertion(Annotation( "BTO") "See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint") AnnotationAssertion( "BTO:0001457") AnnotationAssertion( "CALOHA:TS-2226") AnnotationAssertion( "EFO:0001929") @@ -146824,7 +144772,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "knee") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit) @@ -146863,14 +144811,13 @@ AnnotationAssertion( "pedal digit") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000342") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332") Annotation( "http://bgee.unil.ch/") "(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone") AnnotationAssertion( "CALOHA:TS-2229") AnnotationAssertion( "EFO:0003068") AnnotationAssertion( "EHDAA2:0001834") @@ -146905,7 +144852,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intervertebral joint) AnnotationAssertion(Annotation( "http://www.medilexicon.com/medicaldictionary.php?t=87401") "The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments.") -AnnotationAssertion(Annotation( "FMA") "FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra") AnnotationAssertion( "vertebral joint") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37622") AnnotationAssertion( "FMA:25511") @@ -146923,7 +144869,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "connects successive pairs of centra") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sternoclavicular joint) @@ -146948,14 +144894,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "clavicular notch of the manubrium sterni") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "sternal end of the clavicle and first rib") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glenohumeral joint) AnnotationAssertion(Annotation( "Wikipedia:Glenohumeral_joint") "The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted].") AnnotationAssertion( "note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship") -AnnotationAssertion(Annotation( "FMA") "in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle") AnnotationAssertion(Annotation( "OBOL:automatic") "joint of shoulder") AnnotationAssertion(Annotation( "MA:0000459") "shoulder joint") AnnotationAssertion( "EMAPA:19105") @@ -146978,15 +144923,17 @@ AnnotationAssertion( "glenohumeral joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of prepuce of penis) AnnotationAssertion(Annotation( "MP:0003553") Annotation( "NCBI:matt") "The loose fold of skin that covers the penis.") -AnnotationAssertion( "EV:0100109") AnnotationAssertion( "FMA:27648") AnnotationAssertion( "MA:0001744") AnnotationAssertion( "SCTID:39059001") @@ -146999,7 +144946,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of prepuce of penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vaginal venous plexus) @@ -147018,15 +144966,14 @@ AnnotationAssertion( "vaginal venous plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic vessel) AnnotationAssertion(Annotation( "BTO:0000752") Annotation( "Wikipedia:Lymphatic_vessel") "A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO].") -AnnotationAssertion(Annotation( "DOI:10.1152/japplphysiol.00201.2013") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005105") Annotation( "TAO") Annotation( "ZFIN:curator") "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011005") Annotation( "AAO") Annotation( "AAO:EJS") "A vessel that contains or conveys lymph.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001249") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627") Annotation( "http://bgee.unil.ch/") "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]") AnnotationAssertion( "AAO:0011005") AnnotationAssertion( "BTO:0000752") AnnotationAssertion( "CALOHA:TS-2102") @@ -147035,10 +144982,8 @@ AnnotationAssertion( "FMA:30315") AnnotationAssertion( "MA:0000138") AnnotationAssertion( "MAT:0000443") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D042601") AnnotationAssertion( "NCIT:C33038") AnnotationAssertion( "SCTID:279089004") -AnnotationAssertion( "TAO:0005105") AnnotationAssertion(Annotation( "ncithesaurus:Lymphatic_Vessel") "UMLS:C0229889") AnnotationAssertion( "VHOG:0001249") AnnotationAssertion( "Wikipedia:Lymphatic_vessel") @@ -147055,7 +145000,8 @@ AnnotationAssertion( "lymphatic vessel") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -147063,14 +145009,6 @@ DisjointClasses( (bone element) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000057") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/277") "Skeletal element that is composed of bone tissue.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000047") Annotation( "AAO") Annotation( "AAO:LAP") "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001514") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000057") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Skeletal element that is composed of bone tissue.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000047") Annotation( "AAO") "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001190") Annotation( "VHOG") Annotation( "DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)") Annotation( "http://bgee.unil.ch/") "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]") AnnotationAssertion( "AAO:0000047") AnnotationAssertion( "AEO:0000082") AnnotationAssertion( "BTO:0000140") @@ -147110,7 +145048,6 @@ AnnotationAssertion( "bone element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO-modified") ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -147121,7 +145058,6 @@ DisjointClasses( "FMA:32521") Annotation( "http://orcid.org/0000-0002-6601-2165") "A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010716") Annotation( "AAO") Annotation( "AAO:MEJ") "Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO]") AnnotationAssertion( "AAO:0010716") AnnotationAssertion( "EFO:0001412") AnnotationAssertion( "EHDAA2:0000339") @@ -147151,15 +145087,18 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "deltoid tuberosity of humerus") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) # Class: (sesamoid bone) @@ -147187,6 +145126,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "UBERON:cjm") ) +SubClassOf( ) # Class: (proximal carpal bone) @@ -147199,7 +145139,9 @@ AnnotationAssertion( "UBERON:0001480") AnnotationAssertion(rdfs:label "proximal carpal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of shoulder) @@ -147217,13 +145159,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of shoulder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of shoulder) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "A zone of skin that is part of a shoulder region.") -AnnotationAssertion(Annotation( "MA") "in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon") AnnotationAssertion( "EMAPA:18059") AnnotationAssertion( "FMA:34830") AnnotationAssertion( "MA:0000635") @@ -147235,11 +145178,12 @@ AnnotationAssertion( "UBERON:0001483") AnnotationAssertion(rdfs:label "skin of shoulder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (articular capsule) AnnotationAssertion(Annotation( "Wikipedia:Articular_capsule") "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].") -AnnotationAssertion(Annotation( "ncit") "check ncita") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37621") AnnotationAssertion( "FMA:34836") AnnotationAssertion( "GAID:263") @@ -147264,6 +145208,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (knee joint) @@ -147292,15 +145239,18 @@ AnnotationAssertion( "knee joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes joint) AnnotationAssertion(Annotation( "OBOL:automatic") "A skeletal joint that is part of a pes [Automatically generated definition].") AnnotationAssertion( "TODO check FMA - use the set class for now") -AnnotationAssertion( ) AnnotationAssertion( "EMAPA:32949") AnnotationAssertion( "FMA:35194") AnnotationAssertion( "GAID:256") @@ -147320,13 +145270,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pes joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ankle joint) AnnotationAssertion(Annotation( "MESH:A02.835.583.378.062") Annotation( "Wikipedia:Ankle") Annotation( "https://orcid.org/0000-0002-6601-2165") "A joint that connects the hindlimb autopod and zeugopod skeletons.") -AnnotationAssertion( "todo - accurately represent different types of ankle joint") AnnotationAssertion( "BTO:0004706") AnnotationAssertion( "EMAPA:35126") AnnotationAssertion( "FMA:35195") @@ -147352,15 +145303,16 @@ AnnotationAssertion( "ankle joint") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus joint) AnnotationAssertion(Annotation( "OBOL:automatic") "A skeletal joint that is part of a manus (hand) [Automatically generated definition].") AnnotationAssertion( "TODO check FMA - use the set class for now") -AnnotationAssertion( ) AnnotationAssertion( "EMAPA:32641") AnnotationAssertion( "MA:0000452") AnnotationAssertion( "SCTID:244546004") @@ -147376,13 +145328,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "manus joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (elbow joint) AnnotationAssertion(Annotation( "Wikipedia:Elbow") Annotation( "https://orcid.org/0000-0002-6601-2165") "A joint that connects the forelimb zeugopod and stylopod skeletons[Obol].") -AnnotationAssertion(Annotation( "HP") "In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis") AnnotationAssertion( "EMAPA:19102") AnnotationAssertion( "FMA:35289") AnnotationAssertion( "GAID:253") @@ -147404,15 +145357,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "elbow joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wrist joint) AnnotationAssertion(Annotation( "Wikipedia:Wrist") Annotation( "https://orcid.org/0000-0002-6601-2165") Annotation( "https://sourceforge.net/tracker/?group_id=76834&atid=1205376") "A joint connecting the forelimb zeugopod skeleton with the carpal skeleton.") -AnnotationAssertion(Annotation( "FMA") "in FMA this includes radio-carpal and radio-ulnar *ligaments*") -AnnotationAssertion( "EMAPA:19205") AnnotationAssertion( "FMA:321842") AnnotationAssertion( "GAID:274") AnnotationAssertion( "MA:0000460") @@ -147434,6 +145388,8 @@ AnnotationAssertion( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axillary nerve) @@ -147457,8 +145413,7 @@ AnnotationAssertion( "axillary nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -147466,7 +145421,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ncithesaurus:Pectoralis_Muscle") "Muscles of the upper chest. The term may refer to one of two muscles, the pectoralis major and pectoralis minor. The former is a thick muscle in the anterior portion of the chest. Its action involves flexion, medial rotation, and adduction of the humerus. The latter is a thin muscle located beneath the pectoralis major. Its action involves lowering the scapula and raising the ribs.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010727") Annotation( "AAO") Annotation( "AAO:MEJ") "Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO]") AnnotationAssertion( "AAO:0010727") AnnotationAssertion( "BTO:0000023") AnnotationAssertion( "CALOHA:TS-0751") @@ -147494,8 +145448,9 @@ AnnotationAssertion( "This currently groups the major and minor muscles (which have different attachment sites) as well as the AAO structure: Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus") AnnotationAssertion(rdfs:label "pectoral muscle") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ascending aorta) @@ -147524,7 +145479,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -147534,10 +145489,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (muscle of pelvic girdle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a pelvic girdle [Automatically generated definition].") -AnnotationAssertion(Annotation( "MA") "Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.") AnnotationAssertion( "UBERON:0003271") AnnotationAssertion( "EHDAA:8326") -AnnotationAssertion( "EMAPA:18184") AnnotationAssertion( "EMAPA:18185") AnnotationAssertion( "FMA:37367") AnnotationAssertion( "MA:0000537") @@ -147554,6 +145507,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of pelvic girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (muscle of pes) @@ -147572,14 +145527,13 @@ AnnotationAssertion( "UBERON:0001498") AnnotationAssertion(rdfs:label "muscle of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (muscle of arm) AnnotationAssertion(Annotation( "OBOL:automatic") "A muscle organ that is part of an arm [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion( "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)") AnnotationAssertion( "UBERON:0003272") AnnotationAssertion( "EHDAA:8277") AnnotationAssertion( "EMAPA:36053") @@ -147597,6 +145551,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of arm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (muscle of manus) @@ -147617,17 +145572,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (arch of aorta) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0004113") "The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery.") -AnnotationAssertion( "Do not confuse with aortic arch") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001196") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/arch+of+aorta") "The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001196") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20") Annotation( "http://bgee.unil.ch/") "The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]") -AnnotationAssertion( "birds have right aortic arch, mammals left.") AnnotationAssertion( "BTO:0000157") AnnotationAssertion( "EFO:0002526") AnnotationAssertion( "EHDAA2:0000132") @@ -147650,10 +145601,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "left arch 4 in human") Annotation( "embryology.ch") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -147674,14 +145625,12 @@ AnnotationAssertion( "UBERON:0001510") AnnotationAssertion(rdfs:label "skin of knee") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of leg) AnnotationAssertion(Annotation( "OBOL:automatic") "A zone of skin that is part of a leg [Automatically generated definition].") -AnnotationAssertion( "EMAPA:18156") -AnnotationAssertion( "EMAPA:18159") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37352") AnnotationAssertion( "FMA:37828") AnnotationAssertion( "MA:0000674") @@ -147694,7 +145643,8 @@ AnnotationAssertion( "UBERON:0001511") AnnotationAssertion(rdfs:label "skin of leg") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of ankle) @@ -147713,7 +145663,7 @@ AnnotationAssertion( "UBERON:0001512") AnnotationAssertion(rdfs:label "skin of ankle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of pes) @@ -147734,13 +145684,13 @@ AnnotationAssertion( "skin of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (descending aorta) AnnotationAssertion(Annotation( "GO:0035906") Annotation( "Wikipedia:Descending_aorta") "The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion( "results from fusion of left and right dorsal aortae") AnnotationAssertion( "EMAPA:18606") AnnotationAssertion( "FMA:3784") AnnotationAssertion( "MA:0002571") @@ -147761,8 +145711,6 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -147796,6 +145744,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal aorta) @@ -147855,7 +145804,6 @@ AnnotationAssertion( "skin of elbow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of wrist) @@ -147876,7 +145824,7 @@ AnnotationAssertion( "UBERON:0001518") AnnotationAssertion(rdfs:label "skin of wrist") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of manus) @@ -147897,7 +145845,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brachiocephalic artery) @@ -147939,9 +145889,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Common_carotid_artery") "A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].") AnnotationAssertion( "we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'") -AnnotationAssertion( "This class represents the adult and developing structures'") AnnotationAssertion( ) -AnnotationAssertion( "in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae") AnnotationAssertion(Annotation( "FMA:3939") "carotid artery") AnnotationAssertion( "CALOHA:TS-0116") AnnotationAssertion( "EHDAA2:0000217") @@ -147976,7 +145924,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "UBERON:cjm") "The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk.") AnnotationAssertion( ) -AnnotationAssertion( "placement of the MA class here is not strictly correct, as the MA class does not include the branches") AnnotationAssertion( "EMAPA:35749") AnnotationAssertion( "FMA:3941") AnnotationAssertion( "MA:0001928") @@ -148000,8 +145947,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:anna") "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000267") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/Internal+carotid+artery") "Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011054") Annotation( "AAO") Annotation( "PMID:12606281") "One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO]") AnnotationAssertion( "AAO:0010219") AnnotationAssertion( "AAO:0011054") AnnotationAssertion( "BTO:0004697") @@ -148035,11 +145980,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "internal carotid artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -148048,9 +145992,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "https://orcid.org/0000-0002-6601-2165") "One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta.") AnnotationAssertion( "Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010232") Annotation( "AAO") Annotation( "AAO:BJB") "Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia:Subclavian_artery") "In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005086") Annotation( "TAO") Annotation( "ZFIN:curator") "The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]") AnnotationAssertion( "AAO:0010232") AnnotationAssertion( "EHDAA2:0001933") AnnotationAssertion( "EHDAA:4357") @@ -148092,8 +146033,6 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The subclavian artery that supplies the right pectoral appendage.") AnnotationAssertion( ) -AnnotationAssertion( "in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery") -AnnotationAssertion( "proximal part arises from right 4th aortic arch in humans") AnnotationAssertion( "EHDAA2:0004514") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37384") AnnotationAssertion( "FMA:3953") @@ -148111,13 +146050,15 @@ AnnotationAssertion( "right subclavian artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left common carotid artery plus branches) AnnotationAssertion(Annotation( "UBERON:cjm") "The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax.") AnnotationAssertion( ) -AnnotationAssertion( "placement of the MA class here is not strictly correct, as the MA class does not include the branches") AnnotationAssertion( "EMAPA:35491") AnnotationAssertion( "FMA:4058") AnnotationAssertion( "MA:0001927") @@ -148137,7 +146078,6 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (popliteal vein) @@ -148229,6 +146169,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal metatarsal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (medial marginal vein) @@ -148267,13 +146209,13 @@ AnnotationAssertion( "kidney arcuate artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of hip) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "A zone of skin that is part of a hip region.") -AnnotationAssertion(Annotation( "MA") "in MA this isa hindlimb skin") AnnotationAssertion( "EMAPA:18148") AnnotationAssertion( "FMA:45282") AnnotationAssertion( "MA:0000658") @@ -148289,6 +146231,7 @@ AnnotationAssertion( "UBERON:0001554") AnnotationAssertion(rdfs:label "skin of hip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive tract) @@ -148297,11 +146240,6 @@ AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0016309") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000112") Annotation( "TAO") Annotation( "ZFIN:curator") "The alimentary or digestive tract, and associated organs.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000309") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "FMA also has a term 'gastrointestinal tract', but this includes the liver.") -AnnotationAssertion(Annotation( "MA") "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509") -AnnotationAssertion( "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this") AnnotationAssertion( "gut") AnnotationAssertion( "AAO:0010023") AnnotationAssertion( "BILA:0000083") @@ -148310,10 +146248,8 @@ AnnotationAssertion( "EHDAA2:0000726") AnnotationAssertion( "EHDAA:518") AnnotationAssertion( "EMAPA:16247") -AnnotationAssertion(Annotation( ) "FBbt:00003125") AnnotationAssertion( "FMA:45615") AnnotationAssertion( "MA:0000917") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D041981") AnnotationAssertion( "NCIT:C34082") AnnotationAssertion( "TAO:0000112") AnnotationAssertion( "TGMA:0001819") @@ -148362,9 +146298,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (upper respiratory tract) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]") AnnotationAssertion( "EHDAA2:0002136") AnnotationAssertion( "EMAPA:17669") AnnotationAssertion( "FMA:45661") @@ -148443,7 +146377,8 @@ AnnotationAssertion( "muscle of larynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -148452,12 +146387,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "VHOG:0000847") Annotation( "Wikipedia:Genioglossus_muscle") "Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000847") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/genioglossus") "Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010660") Annotation( "AAO") Annotation( "AAO:BMZ") "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO]") -AnnotationAssertion(Annotation( "2012-07-02") Annotation( "FEED") Annotation( "http://www.feedexp.org") "see Intrinsic Tongue.[FEED]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010660") Annotation( "AAO") "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000847") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7") Annotation( "http://bgee.unil.ch/") "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]") -AnnotationAssertion(Annotation( "AAO:0010660") "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.") AnnotationAssertion( "AAO:0010660") AnnotationAssertion( "EHDAA2:0000704") AnnotationAssertion( "EHDAA:9150") @@ -148479,7 +146408,7 @@ AnnotationAssertion( "genioglossus muscle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -148488,9 +146417,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "FEED:rd") "A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010663") Annotation( "AAO") Annotation( "AAO:BMZ") "Makes up part of the tongue in frogs and salamanders.[AAO]") -AnnotationAssertion(Annotation( "2012-07-02") Annotation( "FEED") Annotation( "http://www.feedexp.org") "The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010663") Annotation( "AAO") "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]") AnnotationAssertion( "AAO:0010663") AnnotationAssertion( "EMAPA:18277") AnnotationAssertion( "FMA:46691") @@ -148510,16 +146436,15 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "lingual process in horse") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extrinsic muscle of tongue) AnnotationAssertion(Annotation( "Wikipedia:Muscles_of_tongue") Annotation( "https://github.com/obophenotype/uberon/issues/331") "A muscle organ that attaches the tongue to some other structure.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000825") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)") Annotation( "http://bgee.unil.ch/") "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement") -AnnotationAssertion(Annotation( "WP") "All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus.") AnnotationAssertion( "EHDAA2:0002063") AnnotationAssertion( "EHDAA:9148") AnnotationAssertion( "EMAPA:18275") @@ -148535,16 +146460,14 @@ AnnotationAssertion( "extrinsic muscle of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "check palatoglossus") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intrinsic muscle of tongue) AnnotationAssertion(Annotation( "http://www.feedexp.org/wiki/Mammalian_Muscle_Ontology_Workshop") "The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-07-02") Annotation( "FEED") Annotation( "http://www.feedexp.org") "The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000748") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)") Annotation( "http://bgee.unil.ch/") "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone") AnnotationAssertion( "EHDAA2:0002064") AnnotationAssertion( "EHDAA:9152") AnnotationAssertion( "EMAPA:18280") @@ -148560,6 +146483,8 @@ AnnotationAssertion( "intrinsic muscle of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FEED") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -148599,17 +146524,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FEED") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (olfactory nerve) AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Olfactory_nerve") "Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010088") Annotation( "AAO") Annotation( "AAO:DSM") "Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO]") -AnnotationAssertion(Annotation( "FMA:46787") "Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787].") -AnnotationAssertion(Annotation( "MESH:A08.800.800.120.640") "The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000703") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") -AnnotationAssertion( "connects to main OB (in taxa where main/accessory distinction is important)") AnnotationAssertion(Annotation( "BIRNLEX:1319") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "1n") AnnotationAssertion( "AAO:0010088") AnnotationAssertion( "BAMS:1n") @@ -148657,15 +146578,16 @@ AnnotationAssertion( "olfactory nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left subclavian artery) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The subclavian artery that supplies the left pectoral appendage.") AnnotationAssertion( ) -AnnotationAssertion( "in humans, branches off the arch of aorta") -AnnotationAssertion( "arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37100") AnnotationAssertion( "FMA:4694") AnnotationAssertion( "MA:0002046") @@ -148684,15 +146606,15 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior vena cava) AnnotationAssertion(Annotation( "Wikipedia:Superior_vena_cava") Annotation( "http://orcid.org/0000-0002-6601-2165") "A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001195") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455") Annotation( "http://bgee.unil.ch/") "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]") -AnnotationAssertion( "The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).") AnnotationAssertion( "BTO:0002683") AnnotationAssertion( "EHDAA2:0001962") AnnotationAssertion( "EHDAA:8726") @@ -148721,13 +146643,14 @@ AnnotationAssertion( "anterior vena cava") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (internal jugular vein) AnnotationAssertion(Annotation( "Wikipedia:Internal_jugular_vein") "One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010236") Annotation( "AAO") Annotation( "AAO:BJB") "Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]") AnnotationAssertion( "AAO:0010236") AnnotationAssertion( "EHDAA2:0000877") AnnotationAssertion( "EHDAA:5407") @@ -148759,7 +146682,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Subclavian_vein") "The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010510") Annotation( "AAO") Annotation( "AAO:BJB") "Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO]") AnnotationAssertion( "AAO:0010510") AnnotationAssertion( "EHDAA2:0001934") AnnotationAssertion( "EHDAA:4455") @@ -148804,6 +146726,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchial vein) @@ -148824,6 +146748,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bronchial vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous plexus) @@ -148842,7 +146768,9 @@ AnnotationAssertion( "venous plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliary muscle) @@ -148868,16 +146796,13 @@ AnnotationAssertion( "ciliary muscle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of iris) AnnotationAssertion( "revisit this, see issue #331") -AnnotationAssertion( "The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]") -AnnotationAssertion( "in aves, stromal mesenchymal cells may migrate to the iris and become skeletal") -AnnotationAssertion( "EMAPA:35448") AnnotationAssertion( "FMA:49154") AnnotationAssertion( "MA:0001287") AnnotationAssertion( "SCTID:280888007") @@ -148891,13 +146816,11 @@ AnnotationAssertion( "muscle of iris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphincter pupillae) AnnotationAssertion(Annotation( "Wikipedia:Iris_sphincter_muscle") "A sphincter muscle that is part of the iris.") -AnnotationAssertion( "In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]") -AnnotationAssertion( "WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure") -AnnotationAssertion( "constricts iris") AnnotationAssertion( "BTO:0000656") AnnotationAssertion( "EMAPA:35788") AnnotationAssertion( "FMA:49157") @@ -148928,17 +146851,18 @@ AnnotationAssertion( "sphincter pupillae") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "BTO") ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "encircles iris") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "encircles iris") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) # Class: (dilatator pupillae) AnnotationAssertion(Annotation( "Wikipedia:Iris_dilator_muscle") "A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion( "It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina") AnnotationAssertion( "BTO:0001371") AnnotationAssertion( "EMAPA:35286") AnnotationAssertion( "FMA:49158") @@ -148973,16 +146897,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png"^^xsd:anyURI) SubClassOf(Annotation( "BTO") ) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "outer margins of iris") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "inner margins of iris") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) # Class: (lingual artery) AnnotationAssertion(Annotation( "Wikipedia:Lingual_artery") "The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010492") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the external carotid which supplies blood to the tongue.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010492") Annotation( "AAO") "relationship loss: part_of external carotid (AAO:0010218)[AAO]") AnnotationAssertion( "AAO:0010492") AnnotationAssertion( "EMAPA:36324") AnnotationAssertion( "FMA:49526") @@ -149000,8 +146922,10 @@ AnnotationAssertion( "lingual artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "AA") Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial artery) @@ -149023,6 +146947,8 @@ AnnotationAssertion( "facial artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (occipital artery) @@ -149043,12 +146969,14 @@ AnnotationAssertion( "occipital artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (maxillary artery) AnnotationAssertion(Annotation( "Wikipedia:Maxillary_artery") "An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://download.videohelp.com/vitualis/med/Vascular_Devt.html") "...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries") AnnotationAssertion( "EHDAA2:0001069") AnnotationAssertion( "EHDAA:7357") AnnotationAssertion( "EMAPA:17311") @@ -149069,14 +146997,14 @@ AnnotationAssertion( "maxillary artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ophthalmic artery) AnnotationAssertion(Annotation( "Wikipedia:Ophthalmic_artery") "The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010497") Annotation( "AAO") Annotation( "AAO:BJB") "Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010497") Annotation( "AAO") "relationship loss: part_of internal carotid (AAO:0010219)[AAO]") AnnotationAssertion( "AAO:0010497") AnnotationAssertion( "EHDAA2:0001300") AnnotationAssertion( "EHDAA:7363") @@ -149129,8 +147057,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "coronary artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal artery) @@ -149152,14 +147080,14 @@ AnnotationAssertion( "lacrimal artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (posterior communicating artery) AnnotationAssertion(Annotation( "Wikipedia:Posterior_communicating_artery") "One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005001") Annotation( "TAO") Annotation( "ZFIN:curator") "An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO]") -AnnotationAssertion( "todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery") AnnotationAssertion( "EHDAA2:0004518") AnnotationAssertion( "EHDAA:3352") AnnotationAssertion( "EMAPA:18600") @@ -149185,18 +147113,17 @@ AnnotationAssertion( "posterior communicating artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (muscle organ) AnnotationAssertion(Annotation( "GO:0007517") "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005145") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of tissue composed of contractile fibers.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001245") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75") Annotation( "http://bgee.unil.ch/") "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]") -AnnotationAssertion( "muscular") AnnotationAssertion(Annotation( "ZFA:0005145") "muscle") -AnnotationAssertion( "AAO:0011066") -AnnotationAssertion( "EMAPA:32715") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37474") AnnotationAssertion( "EV:0100146") AnnotationAssertion( "FMA:5022") @@ -149216,24 +147143,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (artery) AnnotationAssertion(Annotation( "AEO:JB") "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].") AnnotationAssertion( "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010211") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001251") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") -AnnotationAssertion( "arterial") -AnnotationAssertion( "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.") -AnnotationAssertion( ) AnnotationAssertion( "AAO:0010211") AnnotationAssertion( "AEO:0000208") AnnotationAssertion( "BTO:0000573") AnnotationAssertion( "CALOHA:TS-0054") AnnotationAssertion( "EFO:0000814") -AnnotationAssertion( "EHDAA2:0000143") AnnotationAssertion( "EHDAA2:0003253") AnnotationAssertion( "EMAPA:35147") AnnotationAssertion( "EV:0100026") @@ -149264,18 +147187,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "artery") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein) AnnotationAssertion(Annotation( "Wikipedia:Vein") "Any of the tubular branching vessels that carry blood from the capillaries toward the heart.") AnnotationAssertion( "TODO - check with MA - vein vs venous blood vessel") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010212") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001743") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") -AnnotationAssertion( "venous") -AnnotationAssertion( ) AnnotationAssertion( "venous subtree") AnnotationAssertion( "venous vessel") AnnotationAssertion( "AAO:0010212") @@ -149314,14 +147232,14 @@ AnnotationAssertion( "vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic portal vein) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Hepatic_portal_vein") Annotation( "http://sourceforge.net/tracker/?func=detail&aid=3091300&group_id=76834&atid=1205376") "A portal vein that transports nutrients from the digestive tract to the liver[Kardong].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000642") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265") Annotation( "http://bgee.unil.ch/") "Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]") -AnnotationAssertion( "In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]") AnnotationAssertion( "AAO:0010214") AnnotationAssertion( "FMA:50735") AnnotationAssertion( "MA:0002132") @@ -149384,8 +147302,7 @@ AnnotationAssertion( "dorsal aorta in Kardong") AnnotationAssertion(rdfs:label "celiac artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "dorsal aorta in primitive verts") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) @@ -149395,9 +147312,6 @@ SubClassOf(Annotation( "ISB AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Trigeminal_nerve") "Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010470") Annotation( "AAO") Annotation( "AAO:EJS") "Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000704") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "ISBN:0471888893") "the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls") AnnotationAssertion(Annotation( "BIRNLEX:869") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "5n") AnnotationAssertion( "AAO:0010470") AnnotationAssertion( "BAMS:5n") @@ -149448,15 +147362,17 @@ AnnotationAssertion( "trigeminal nerve") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial nerve) AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Facial_nerve") "Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010472") Annotation( "AAO") Annotation( "AAO:DSM") "Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000706") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:827") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "7n") AnnotationAssertion( "AAO:0010472") AnnotationAssertion( "BAMS:7n") @@ -149509,17 +147425,17 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibulocochlear nerve) AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Vestibulocochlear_nerve") "Cranial nerve that transmits sound and equilibrium (balance) information from the inner ear to the brain.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010473") Annotation( "AAO") Annotation( "AAO:DSM") "Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000695") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:890") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "8n") AnnotationAssertion( "AAO:0010473") AnnotationAssertion( "BAMS:8n") @@ -149574,15 +147490,17 @@ AnnotationAssertion( "vestibulocochlear nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glossopharyngeal nerve) AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Glossopharyngeal_nerve") "Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010474") Annotation( "AAO") Annotation( "AAO:EJS") "Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000701") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:899") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "9n") AnnotationAssertion( "AAO:0010474") AnnotationAssertion( "BAMS:9n") @@ -149631,20 +147549,13 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "sensory") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "motor") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypoglossal nerve) AnnotationAssertion(Annotation( "ISBN:080184780X") Annotation( "VHOG:0000693") Annotation( "http://orcid.org/0000-0002-6601-2165") "Cranial nerve that innervates the muscles of the tongue.") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000693") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "ISBN:080184780X") "In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010477") Annotation( "AAO") Annotation( "AAO:EJS") "Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000693") Annotation( "VHOG") Annotation( "Wikipedia:Cranial_nerves") Annotation( "http://bgee.unil.ch/") "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]") -AnnotationAssertion( "we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves") AnnotationAssertion(Annotation( "BIRNLEX:820") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "12n") AnnotationAssertion( "AAO:0010477") AnnotationAssertion( "BAMS:12n") @@ -149688,9 +147599,11 @@ AnnotationAssertion( "hypoglossal nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right pulmonary artery) @@ -149718,7 +147631,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left pulmonary artery) @@ -149746,14 +147661,14 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial vein) AnnotationAssertion(Annotation( "Wikipedia:Facial_vein") "The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010513") Annotation( "AAO") Annotation( "AAO:BJB") "Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]") -AnnotationAssertion(Annotation( "MA") "MA and NCITA also has 'anterior facial vein'") AnnotationAssertion( "AAO:0010513") AnnotationAssertion( "EMAPA:19220") AnnotationAssertion( "FMA:50874") @@ -149772,14 +147687,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facial vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (cerebral vein) AnnotationAssertion(Annotation( "Wikipedia:Cerebral_veins") "The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted].") -AnnotationAssertion( ) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37140") AnnotationAssertion( "FMA:50981") AnnotationAssertion( "GAID:530") @@ -149798,7 +147713,10 @@ AnnotationAssertion( "cerebral vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebellar vein) @@ -149819,13 +147737,12 @@ AnnotationAssertion( "cerebellar vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal ganglion) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK53171") Annotation( "https://github.com/obophenotype/uberon/issues/693") "The cranial ganglion that is associated with and extends fibers into the trigeminal nerve.") AnnotationAssertion( "consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000295") Annotation( "TAO") Annotation( "ZFIN:curator") "A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "PMID:21452441") Annotation( "XAO:0004093") "In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.") AnnotationAssertion( "AAO:0011107") AnnotationAssertion( "BAMS:5Gn") AnnotationAssertion( "BAMS:GV") @@ -149873,15 +147790,16 @@ AnnotationAssertion( "trigeminal ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ncithesaurus") ) +SubClassOf( ) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (occipital bone) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005269") "The bone at the lower, posterior part of the skull.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "PMID:11523816") "formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII") -AnnotationAssertion(Annotation( "Kardong") "fusion of basi-, exo- and supra-occipitals (and maybe tabular)") AnnotationAssertion( "EMAPA:25112") AnnotationAssertion( "FMA:52735") AnnotationAssertion( "GAID:227") @@ -149902,10 +147820,10 @@ AnnotationAssertion( "occipital bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "basi paired exo and supra occipital bones") Annotation( "MA-modified") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "interparietal (postparietal)") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:11523816") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -149914,7 +147832,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Sphenoid_bone") "An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "part of viscerocranium (facial skeleton) in FMA") AnnotationAssertion( "CALOHA:TS-2343") AnnotationAssertion( "EMAPA:18340") AnnotationAssertion( "FMA:52736") @@ -149940,21 +147857,19 @@ AnnotationAssertion( "sphenoid bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "orbito pre and basi sphenoid") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "pterygoid process") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "alisphenoid") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (temporal bone) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005272") "The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous.") AnnotationAssertion( ) -AnnotationAssertion( "In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process") -AnnotationAssertion(Annotation( "chond.") "fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)") -AnnotationAssertion(Annotation( "[WP]") "The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP].") -AnnotationAssertion(Annotation( "FMA") "Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA") AnnotationAssertion( "EHDAA:6035") AnnotationAssertion( "EMAPA:17682") AnnotationAssertion( "FMA:52737") @@ -149975,19 +147890,14 @@ AnnotationAssertion( "temporal bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "petrosal") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "squamosal plus angular") Annotation( "temporal series") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "styloid process") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ethmoid bone) AnnotationAssertion(Annotation( "Wikipedia:Ethmoid_bone") "A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001317") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/ethmoid+bone") "A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001317") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259") Annotation( "http://bgee.unil.ch/") "The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]") -AnnotationAssertion( "ethmoidal") -AnnotationAssertion( "todo - homology e.g. mesethmoid of teleost") -AnnotationAssertion(Annotation( "MA") "Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA") AnnotationAssertion( "BTO:0004140") AnnotationAssertion( "EMAPA:19018") AnnotationAssertion( "FMA:52740") @@ -150010,19 +147920,17 @@ AnnotationAssertion( "ethmoid bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg"^^xsd:anyURI) SubClassOf(Annotation( "ISBN:0073040584") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hyoid bone) AnnotationAssertion(Annotation( "Wikipedia:Hyoid_bone") "A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000684") Annotation( "AAO") Annotation( "AAO:LAP") "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000684") Annotation( "AAO") "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]") -AnnotationAssertion(Annotation( "WP") Annotation(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/548") "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia.") AnnotationAssertion( "AAO:0000684") AnnotationAssertion( "EMAPA:18650") AnnotationAssertion( "FMA:52749") @@ -150047,7 +147955,6 @@ AnnotationAssertion( "hyoid bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -150056,9 +147963,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "Wikipedia:Auditory_ossicle") Annotation( "https://github.com/obophenotype/uberon/issues/91") "One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted].") AnnotationAssertion( "This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000461") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/auditory+ossicles") "The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000461") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695") Annotation( "http://bgee.unil.ch/") "Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry.") AnnotationAssertion(Annotation( "EMAPA:17824") Annotation( "Wikipedia:Auditory_ossicle") "ossicle") AnnotationAssertion( "AAO:0011015") AnnotationAssertion( "EHDAA2:0001183") @@ -150090,16 +147994,12 @@ AnnotationAssertion( "auditory ossicle bone") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:11523816") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:11237469") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (ear) AnnotationAssertion(Annotation( "GO:0042471") Annotation( "Wikipedia:Ear") "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000330") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/ear") "The organ of hearing and of equilibrium. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000330") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)") Annotation( "http://bgee.unil.ch/") "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]") -AnnotationAssertion( "auricular") AnnotationAssertion( "AAO:0011014") AnnotationAssertion( "BIRNLEX:1062") AnnotationAssertion( "BTO:0000368") @@ -150134,18 +148034,15 @@ AnnotationAssertion( "ear") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) # Class: (external ear) AnnotationAssertion(Annotation( "GO:0042473") Annotation( "Wikipedia:External_ear") "Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO].") AnnotationAssertion(Annotation( "Wikipedia") ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000311") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000311") Annotation( "VHOG") Annotation( "DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)") Annotation( "http://bgee.unil.ch/") "Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]") -AnnotationAssertion(Annotation( "XAO") "in XAO this includes and is only the tympanum") AnnotationAssertion( "auricular region") AnnotationAssertion( "AAO:0011037") AnnotationAssertion( "BIRNLEX:1705") @@ -150179,6 +148076,7 @@ AnnotationAssertion( "external ear") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150188,8 +148086,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (petrous part of temporal bone) AnnotationAssertion(Annotation( "Wikipedia:Petrous_part_of_the_temporal_bone") "The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001553") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]") -AnnotationAssertion( "derivative of prootic and opisthotic") AnnotationAssertion(Annotation( "VHOG:0001553") "petrosal") AnnotationAssertion( "EHDAA2:0001452") AnnotationAssertion( "EMAPA:17683") @@ -150220,8 +148116,6 @@ SubClassOf(Annotation( "FMA # Class: (orbit of skull) AnnotationAssertion(Annotation( "TAO:0001410") Annotation( "Wikipedia:Orbit_(anatomy)") Annotation( "http://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001410") Annotation( "TAO") Annotation( "TAO:MAH") "Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]") -AnnotationAssertion(Annotation( "FMA") "in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit") AnnotationAssertion( "BTO:0004687") AnnotationAssertion( "FMA:53074") AnnotationAssertion( "GAID:223") @@ -150244,7 +148138,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "orbit of skull") +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) @@ -150254,7 +148150,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001082") "The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve).") AnnotationAssertion( "resolve facial VII vs geniculate (see EHDAA2)") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000707") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]") AnnotationAssertion(Annotation( "Wikipedia:Geniculate_ganglion") "geniculate") AnnotationAssertion( "BAMS:GgVII") AnnotationAssertion( "EFO:0003669") @@ -150294,16 +148189,17 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ncithesaurus") ) -SubClassOf(Annotation( "check for multi-species") Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2:0004623") Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2:0004623") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2:0000491") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glossopharyngeal ganglion) AnnotationAssertion(Annotation( "MP:0001096") "The group of neuron cell bodies associated with the ninth cranial nerve.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000702") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000710") AnnotationAssertion( "EHDAA:2838") AnnotationAssertion( "EMAPA:16795") @@ -150326,21 +148222,14 @@ AnnotationAssertion( "glossopharyngeal ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) -SubClassOf(Annotation( "dorsal") Annotation( "EHDAA2") Annotation( "ISBN:0471888893") Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ventrolateral") Annotation( "EHDAA2") Annotation( "ISBN:0471888893") Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurocranium) AnnotationAssertion(Annotation( "PMID:11523816") Annotation( "TAO:MAH") Annotation( "Wikipedia:Neuroranium") Annotation( "ZFA:0001580") "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001580") Annotation( "TAO") Annotation( "TAO:MAH") "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]") -AnnotationAssertion( "neurocranial") -AnnotationAssertion( "It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton") -AnnotationAssertion(Annotation( "WP") "The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].") -AnnotationAssertion(Annotation( "MA") "It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...") -AnnotationAssertion( "AAO:0010153") -AnnotationAssertion( "EHDAA2:0000243") -AnnotationAssertion( "EMAPA:17681") AnnotationAssertion( "FMA:53672") AnnotationAssertion( "MA:0000317") AnnotationAssertion( "SCTID:361731002") @@ -150368,8 +148257,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nail) AnnotationAssertion(Annotation( "Wikipedia:Nail_(anatomy)") Annotation( "https://github.com/obophenotype/uberon/issues/120") "A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].") -AnnotationAssertion( "Use this class for both the nails of primates and the homologous claws of mammals such as mouse.") -AnnotationAssertion( "A primate's nail consists of the unguis alone; the subunguis has disappeared") AnnotationAssertion( "BTO:0001719") AnnotationAssertion( "CALOHA:TS-2034") AnnotationAssertion( "EFO:0000956") @@ -150398,18 +148285,12 @@ AnnotationAssertion( "The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]") AnnotationAssertion(rdfs:label "nail") SubClassOf( ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal cavity) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.") AnnotationAssertion( "define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000314") Annotation( "AAO") Annotation( "AAO:LAP") "Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia:Nasal_cavity") "a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000271") Annotation( "VHOG") Annotation( "DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)") Annotation( "http://bgee.unil.ch/") "Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]") -AnnotationAssertion(Annotation( "HP") "in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures") AnnotationAssertion( "AAO:0000314") AnnotationAssertion( "BTO:0002096") AnnotationAssertion( "EHDAA2:0001226") @@ -150454,9 +148335,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Jaw") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton which includes upper and lower jaw skeletons.") AnnotationAssertion( "TODO - move ZFA:0001227 (it is the entire jaw skeleton).") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001227") Annotation( "TAO") Annotation( "ZFIN:curator") "Skeletal and cartilage elements of the first pharyngeal arch.[TAO]") -AnnotationAssertion( "There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).") -AnnotationAssertion(Annotation( "FMA") "in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates") AnnotationAssertion( "AAO:0000988") AnnotationAssertion( "BTO:0001749") AnnotationAssertion( "EMAPA:35455") @@ -150487,19 +148365,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "jaw skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper jaw region) AnnotationAssertion(Annotation( "Wikipedia:Upper_jaw") Annotation( "http://orcid.org/0000-0002-6601-2165") "Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000620") Annotation( "AAO") Annotation( "AAO:LAP") "Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000454") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "Note isa/partof difference MA/FMA") AnnotationAssertion( "AAO:0000620") AnnotationAssertion( "EHDAA2:0002118") AnnotationAssertion( "EHDAA2:0004607") @@ -150525,17 +148401,16 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "upper jaw region") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (lower jaw region) AnnotationAssertion(Annotation( "Wikipedia:Lower_jaw") "Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000272") Annotation( "AAO") Annotation( "AAO:LAP") "Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000453") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "Note isa/partof difference MA/FMA") AnnotationAssertion( "AAO:0000272") AnnotationAssertion( "EFO:0003660") AnnotationAssertion( "EHDAA2:0001018") @@ -150559,18 +148434,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "lower jaw region") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Mandibular_prominence") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane.") -AnnotationAssertion( "blepharic") -AnnotationAssertion( "palpebral") -AnnotationAssertion( "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.") -AnnotationAssertion(Annotation( "MA") "Consider adding 'eye surface', like MA") -AnnotationAssertion(Annotation( "FMA") "FMA divides this into skin, fascia, conjunctiva") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0002241") AnnotationAssertion( "EHDAA2:0000487") AnnotationAssertion( "EHDAA:9037") @@ -150597,6 +148469,7 @@ AnnotationAssertion( "eyelid") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "multiple") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150606,7 +148479,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:csmith") Annotation( "MP:0001081") Annotation( "PMID:9362461") "The groups of nerve cell bodies associated with the twelve cranial nerves.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000013") Annotation( "TAO") Annotation( "ZFIN:curator") "Ganglion which is located in the head.[TAO]") AnnotationAssertion( "UBERON:0003213") AnnotationAssertion( "UBERON:0026601") AnnotationAssertion( "BIRNLEX:2597") @@ -150644,7 +148516,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cranial ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear nucleus) @@ -150673,6 +148547,8 @@ AnnotationAssertion( "cochlear nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150680,14 +148556,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FEED:rd") Annotation( "https://github.com/obophenotype/uberon/issues/256") "A muscular organ in the floor of the mouth.") AnnotationAssertion( "in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000419") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/tongue") "A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-07-02") Annotation( "FEED") Annotation( "http://www.feedexp.org") "Muscular organ in the floor of the mouth.[FEED]") -AnnotationAssertion(Annotation( "GO:0043586") "The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000419") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)") Annotation( "http://bgee.unil.ch/") "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]") -AnnotationAssertion( "glossal") -AnnotationAssertion( "lingual") -AnnotationAssertion( "Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods") -AnnotationAssertion( "The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions") AnnotationAssertion( "AAO:0010360") AnnotationAssertion( "BTO:0001385") AnnotationAssertion( "CALOHA:TS-1050") @@ -150721,15 +148589,16 @@ AnnotationAssertion( "tongue") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg"^^xsd:anyURI) SubClassOf(Annotation( "GO") ) +SubClassOf( ) SubClassOf(Annotation( "BTO") Annotation( "EHDAA2") Annotation( "FMA") Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "anterior 2/3") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial synchondrosis) @@ -150743,6 +148612,7 @@ AnnotationAssertion( "cranial synchondrosis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (papilla of tongue) @@ -150767,12 +148637,6 @@ SubClassOf(Annotation( "FMA # Class: (taste bud) AnnotationAssertion(Annotation( "http://periowiki.wikispot.org/Taste_bud_histology") "A specialized receptor organ that is a collection of cells spanning the gustatory epithelium.") -AnnotationAssertion(Annotation( "http://periowiki.wikispot.org/Taste_bud_histology") ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010573") Annotation( "AAO") Annotation( "AAO:EJS") "A chemoreceptive organ.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000130") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/taste+bud") "One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000130") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]") -AnnotationAssertion( "In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish.") -AnnotationAssertion( "arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL)") AnnotationAssertion( "AAO:0010573") AnnotationAssertion( "BIRNLEX:4101") AnnotationAssertion( "BTO:0000989") @@ -150803,8 +148667,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "taste bud") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png"^^xsd:anyURI) -SubClassOf(Annotation( "cjm") ) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIF") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://dev.biologists.org/content/128/22/4573.full") ObjectSomeValuesFrom( )) @@ -150814,9 +148678,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nasopharynx) AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002251") "The section of the pharynx that lies above the soft palate.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000375") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/nasopharynx") "The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG]") -AnnotationAssertion( "nasopharyngeal") -AnnotationAssertion( "In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane") AnnotationAssertion( "BTO:0000662") AnnotationAssertion( "CALOHA:TS-0663") AnnotationAssertion( "EHDAA2:0001239") @@ -150844,7 +148705,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasopharynx") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150852,8 +148713,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cavity of pharynx) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical space that is enclosed by a pharynx.") -AnnotationAssertion( "See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship") -AnnotationAssertion( "TOODO check") AnnotationAssertion( "AAO:0010435") AnnotationAssertion( "BSA:0000113") AnnotationAssertion( "BTO:0002097") @@ -150869,13 +148728,14 @@ AnnotationAssertion(Annotation( "UBERON:0001731") AnnotationAssertion(rdfs:label "cavity of pharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tonsillar ring) -AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002379") "The circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils.") +AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002379") "The circular lymphoid tissue formed by the lingual, pharyngeal, and faucial tonsils.") AnnotationAssertion( "FMA:55070") AnnotationAssertion( "MA:0000752") AnnotationAssertion( "NCIT:C73468") @@ -150894,16 +148754,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsillar ring") AnnotationAssertion(rdfs:seeAlso ) -SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx) AnnotationAssertion(Annotation( "Wikipedia:Larynx") Annotation( "http://orcid.org/0000-0002-6601-2165") "A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration.") -AnnotationAssertion(Annotation( "2012-07-02") Annotation( "FEED") Annotation( "http://www.feedexp.org") "An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000268") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001279") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241") Annotation( "http://bgee.unil.ch/") "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]") -AnnotationAssertion( "laryngeal") AnnotationAssertion( "AAO:0000268") AnnotationAssertion( "BTO:0001208") AnnotationAssertion( "CALOHA:TS-0532") @@ -150933,8 +148789,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150942,8 +148797,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (laryngeal cartilage) AnnotationAssertion(Annotation( "MP:0002256") "The cartilaginous structures that support the larynx.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001550") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241") Annotation( "http://bgee.unil.ch/") "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0003660") AnnotationAssertion( "EHDAA:8157") AnnotationAssertion( "EMAPA:18697") @@ -150965,8 +148818,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -150985,12 +148839,13 @@ AnnotationAssertion( "UBERON:0001743") AnnotationAssertion(rdfs:label "ligament of larynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphoid tissue) AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_tissue") "Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].") -AnnotationAssertion(Annotation( "lampreys lack organized lymphoid tissue") Annotation( "NCBIBook:NBK27108") ) AnnotationAssertion( "BTO:0000753") AnnotationAssertion( "CALOHA:TS-0584") AnnotationAssertion( "FMA:55220") @@ -151009,8 +148864,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphoid tissue") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK27108") ObjectSomeValuesFrom( )) @@ -151029,6 +148884,8 @@ AnnotationAssertion( "secondary nodular lymphoid tissue") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151048,6 +148905,9 @@ AnnotationAssertion( "UBERON:0001746") AnnotationAssertion(rdfs:label "capsule of thyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parenchyma of thyroid gland) @@ -151069,6 +148929,10 @@ AnnotationAssertion(Annotation( "UBERON:0001747") AnnotationAssertion(rdfs:label "parenchyma of thyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -151087,7 +148951,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capsule of parathyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (parenchyma of parathyroid gland) @@ -151103,6 +148970,7 @@ AnnotationAssertion( "UBERON:0001749") AnnotationAssertion(rdfs:label "parenchyma of parathyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -151111,7 +148979,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "MGI:anna") "A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta.") AnnotationAssertion( "TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal") -AnnotationAssertion(Annotation( "ncit") "this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye") AnnotationAssertion( "EMAPA:35462") AnnotationAssertion( "FMA:55605") AnnotationAssertion( "GAID:901") @@ -151132,7 +148999,7 @@ AnnotationAssertion( "lacrimal apparatus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "HPO:pr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151142,10 +149009,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (dentine) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000069") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005143") Annotation( "TAO") Annotation( "ZFIN:curator") "Mineralized collagen containing substance that forms the tooth structure.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001589") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)") Annotation( "http://bgee.unil.ch/") "Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]") -AnnotationAssertion( "dentinal") -AnnotationAssertion( "Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]") AnnotationAssertion( "BTO:0003453") AnnotationAssertion( "EMAPA:35281") AnnotationAssertion( "FMA:55628") @@ -151172,7 +149035,7 @@ AnnotationAssertion( ".") AnnotationAssertion(rdfs:label "dentine") SubClassOf(Annotation( "VSAO") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) @@ -151182,8 +149045,6 @@ AnnotationAssertion(Annotation( "current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)") AnnotationAssertion(Annotation( "PMID:19730686") ) AnnotationAssertion(Annotation( "PMID:19730686") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000065") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]") -AnnotationAssertion(Annotation( "MA") "part_of tooth enamel organ in MA") AnnotationAssertion( "BTO:0001844") AnnotationAssertion( "CALOHA:TS-1057") AnnotationAssertion( "EMAPA:35303") @@ -151208,17 +149069,14 @@ AnnotationAssertion( "enamel") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg"^^xsd:anyURI) SubClassOf(Annotation( "VSAO") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "85") Annotation( "Wikipedia:ENAM") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cementum) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000062") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000062") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO]") -AnnotationAssertion(Annotation( "FMA:55630") "Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630].") -AnnotationAssertion( "Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]") AnnotationAssertion( "BTO:0002525") AnnotationAssertion( "CALOHA:TS-2163") AnnotationAssertion( "EMAPA:35203") @@ -151247,8 +149105,6 @@ SubClassOf(Annotation( "PMI # Class: (dental pulp) AnnotationAssertion(Annotation( "Wikipedia:Dental_pulp") "The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005141") Annotation( "TAO") Annotation( "ZFIN:curator") "Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001469") Annotation( "VHOG") Annotation( "DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)") Annotation( "http://bgee.unil.ch/") "The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG]") AnnotationAssertion( "BTO:0000339") AnnotationAssertion( "CALOHA:TS-0195") AnnotationAssertion( "EMAPA:35274") @@ -151273,6 +149129,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dental pulp") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151281,8 +149138,6 @@ SubClassOf(Annotation( "ZFA # Class: (middle ear) AnnotationAssertion(Annotation( "GO:0042474") Annotation( "Wikipedia:Middle_ear") "The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000312") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000312") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417") Annotation( "http://bgee.unil.ch/") "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]") AnnotationAssertion( "AAO:0011065") AnnotationAssertion( "BIRNLEX:1695") AnnotationAssertion( "BTO:0002099") @@ -151317,10 +149172,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pinna) AnnotationAssertion(Annotation( "Wikipedia:Pinna_(anatomy)") Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the ear that projects from the head, connecting to the external acoustic meatus.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000460") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000460") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420") Annotation( "http://bgee.unil.ch/") "Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]") -AnnotationAssertion( "In various species, the pinna can also signal mood and radiate heat") -AnnotationAssertion( "The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch).") AnnotationAssertion( "EHDAA2:0001467") AnnotationAssertion( "EMAPA:17589") AnnotationAssertion( "EV:0100355") @@ -151354,7 +149205,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (periodontium) AnnotationAssertion(Annotation( "BTO:0001021") Annotation( "Wikipedia:Periodontium") "The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO].") -AnnotationAssertion(Annotation( "FMA") "FMA treats periodontium and periodontal ligament as the same") AnnotationAssertion( "BTO:0001021") AnnotationAssertion( "CALOHA:TS-2380") AnnotationAssertion( "GAID:216") @@ -151380,8 +149230,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "Wikipedia:Vagus_nerve") "Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010475") Annotation( "AAO") Annotation( "AAO:EJS") "Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000737") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:801") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "10n") AnnotationAssertion( "AAO:0010475") AnnotationAssertion( "BAMS:10n") @@ -151430,18 +149278,16 @@ AnnotationAssertion( "vagus nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "sensory") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "motor") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (odontogenic papilla) AnnotationAssertion(Annotation( "Wikipedia:Dental_papilla") Annotation( "ZFA:0005140") "A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000025") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005140") Annotation( "TAO") Annotation( "ZFIN:curator") "Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001465") Annotation( "VHOG") Annotation( "DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)") Annotation( "http://bgee.unil.ch/") "Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]") -AnnotationAssertion( "In humans, the dental papilla appears after 8-10 weeks intra uteral life") AnnotationAssertion( "BTO:0001839") AnnotationAssertion( "EMAPA:32892") AnnotationAssertion( "FMA:57662") @@ -151468,8 +149314,12 @@ AnnotationAssertion( "odontogenic papilla") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary duct) @@ -151499,16 +149349,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "mammary duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior chamber of eyeball) AnnotationAssertion(Annotation( "MESH:A09.371.060.067") Annotation( "MP:0005205") "The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001431") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/anterior+chamber") "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]") -AnnotationAssertion(Annotation( "EHDAA2") "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball") AnnotationAssertion( "BTO:0002084") AnnotationAssertion( "EHDAA2:0000129") AnnotationAssertion( "EHDAA:9033") @@ -151543,7 +149392,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0005197") Annotation( "Wikipedia:Uvea") "The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].") AnnotationAssertion( "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus") AnnotationAssertion(Annotation( "DOI:10.1177/0192623311409597") ) -AnnotationAssertion( "uveal") AnnotationAssertion( "CALOHA:TS-2228") AnnotationAssertion( "EMAPA:35901") AnnotationAssertion( "FMA:58103") @@ -151567,7 +149415,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "uvea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151578,10 +149428,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001322") "The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000101") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000101") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)") Annotation( "http://bgee.unil.ch/") "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]") -AnnotationAssertion( "iridial") -AnnotationAssertion( "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]") AnnotationAssertion( "AAO:0010347") AnnotationAssertion( "BTO:0000653") AnnotationAssertion( "CALOHA:TS-0491") @@ -151612,6 +149458,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "iris") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151633,6 +149480,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lacrimal canaliculus") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151641,9 +149489,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MESH:A09.371.060.217.325") Annotation( "MGI:smb") Annotation( "MP:0006000") "The smooth stratified squamous epithelium that covers the outer surface of the cornea.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002187") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-061010-3") "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]") -AnnotationAssertion( "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei") -AnnotationAssertion( "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals") AnnotationAssertion( "BTO:0000287") AnnotationAssertion( "CALOHA:TS-0173") AnnotationAssertion( "EFO:0001917") @@ -151684,6 +149529,9 @@ AnnotationAssertion( "corneal epithelium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151691,13 +149539,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Sclera") Annotation( "ZFIN:ZDB-PUB-050701-15") "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Sclera") "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001274") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/sclera") "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]") -AnnotationAssertion( "scleral") -AnnotationAssertion( "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal") -AnnotationAssertion( "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.") -AnnotationAssertion( "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].") -AnnotationAssertion( "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].") AnnotationAssertion( "AAO:0010354") AnnotationAssertion( "BTO:0001606") AnnotationAssertion( "EMAPA:19027") @@ -151724,18 +149565,17 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "sclera") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "cjm") Annotation( "ISBN:0781772214") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle of trunk) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A skeletal muscle organ that is part of the trunk region.") AnnotationAssertion( "Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.") -AnnotationAssertion( "Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.") AnnotationAssertion( "AAO:0000611") AnnotationAssertion( "EMAPA:35888") AnnotationAssertion( "FMA:58274") @@ -151757,13 +149597,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (ciliary body) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005099") Annotation( "Wikipedia:Ciliary_body") "The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000102") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)") Annotation( "http://bgee.unil.ch/") "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]") AnnotationAssertion( "AAO:0010341") AnnotationAssertion( "BTO:0000260") AnnotationAssertion( "CALOHA:TS-0694") @@ -151793,6 +149634,7 @@ AnnotationAssertion( "ciliary body") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151804,8 +149646,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Choroid") "Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].") AnnotationAssertion( "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA") AnnotationAssertion( ) -AnnotationAssertion( "choroidal") -AnnotationAssertion(Annotation( "MP") "MP treats posterior uvea and optic choroid as distinct") AnnotationAssertion( "BTO:0001829") AnnotationAssertion( "CALOHA:TS-2054") AnnotationAssertion( "EMAPA:19077") @@ -151837,7 +149677,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "optic choroid") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -151850,9 +149690,6 @@ DisjointClasses(Annotation( # Class: (substantia propria of cornea) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MESH:A09.371.060.217.228") Annotation( "MP:0005300") "The lamellated connective tissue of the cornea between the Bowman and Descemet membranes.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002189") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-061010-3") "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002189") Annotation( "TAO") "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002189") Annotation( "TAO") "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]") AnnotationAssertion( "substantia propria") AnnotationAssertion( "CALOHA:TS-1138") AnnotationAssertion( "EFO:0002514") @@ -151879,7 +149716,10 @@ AnnotationAssertion( "substantia propria of cornea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "cjm") Annotation( "ISBN:0781772214") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -151906,6 +149746,7 @@ AnnotationAssertion( "ciliary epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -151929,13 +149770,15 @@ AnnotationAssertion( "iris stroma") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal nerve) AnnotationAssertion(Annotation( "MESH:A08.800.800.720") Annotation( "MP:0001077") "The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000824") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/spinal+nerve") "Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]") AnnotationAssertion( "AAO:0011101") AnnotationAssertion( "BAMS:spin") AnnotationAssertion( "BTO:0000870") @@ -151971,12 +149814,12 @@ AnnotationAssertion( "spinal nerve") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of retina) AnnotationAssertion(Annotation( "MP:0003727") "Any of the layers that make up the retina[MP].") -AnnotationAssertion(Annotation( "MA") "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers") AnnotationAssertion( "AAO:0010353") AnnotationAssertion( "EMAPA:35742") AnnotationAssertion( "FMA:58617") @@ -151994,6 +149837,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "layer of retina") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152002,9 +149846,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Retinal_pigment_epithelium") Annotation( "ZFIN:curator") "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000144") Annotation( "TAO") Annotation( "ZFIN:curator") "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011096") Annotation( "AAO") Annotation( "ZFA:0000144") "The monolayer of pigmented epithelium covering the neural retina.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000536") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "AAO:0011096") AnnotationAssertion( "BTO:0001177") AnnotationAssertion( "CALOHA:TS-0869") @@ -152048,19 +149889,19 @@ AnnotationAssertion( "pigmented layer of retina") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial nerve) AnnotationAssertion(Annotation( "Wikipedia:Cranial_nerve") "Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.") AnnotationAssertion( "classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000641") Annotation( "TAO") Annotation( "ZFIN:curator") "Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000279") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]") -AnnotationAssertion( "See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6") AnnotationAssertion( "AAO:0000108") AnnotationAssertion( "BAMS:cran") AnnotationAssertion( "BIRNLEX:1623") @@ -152097,19 +149938,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fovea centralis) AnnotationAssertion(Annotation( "Wikipedia:Fovea") Annotation( "http://orcid.org/0000-0002-6601-2165") "A depression in the inner retinal surface within the macula lutea, the photoreceptor layer of which is entirely cones and which is specialized for maximum visual acuity.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001572") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/fovea") "A small pit in the center of the macula lutea, the area of clearest vision, where the retinal layers are spread aside, and light falls directly on the cones. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001572") Annotation( "VHOG") Annotation( "DOI:10.1017/S095252380623342X Ahnelt PK, Schubert C, Kübber-Heiss A, Schiviz A, Anger E, Independent variation of retinal S and M cone photoreceptor topographies: A survey of four families of mammals. Visual neuroscience (2006), http://www.ncbi.nlm.nih.gov/pubmed/11193946 Azuma N, Molecular cell biology on morphogenesis of the fovea and evolution of the central vision. Nihon Ganka Gakkai Zasshi (2000), DOI:10.1016/S1350-9462(00)00012-4 Ahnelt PK, Kolb H, The mammalian photoreceptor mosaic-adaptive design. Progress in Retinal and Eye Research (2000)") Annotation( "http://bgee.unil.ch/") "Definition of fovea centralis should be considered here as 'an area centralis at the visual axis' (reference 1). There is an uncertaincy of the relation, because: 1.-The fovea first appeared in evolution in the temporal retina of fishes. Then, in birds, the nasal fovea and bifoveal system with nasal and temporal foveas developed. The fovea disappeared in primitive mammals, and reappeared in primates. A residue of the fovea is conserved in the visual streak, and the disappearance and reappearance of the fovea, in primitive mammals and primates respectively, correlates with degeneration and restoration of cone pigment genes in photoreceptors (reference 2). 2.-Many retinal features (foveas, trichromacy, midget pathways and associated cell types) appear specific to primates. This has led to investigations in parallel with other mammalian models such as cat or rabbit. Correlation of the results often proves to be difficult, since an evolutionary scenario with transitions between the mammalian models is largely lacking (reference 3).[uncertain][VHOG]") -AnnotationAssertion( "foveal") -AnnotationAssertion( "The fovea is also a pit in the surface of the retinas of many types of fish, reptiles, and birds. Among mammals, it is found only in simian primates. The retinal fovea takes slightly different forms in different types of animals. For example, in primates, cone photoreceptors line the base of the foveal pit, the cells that elsewhere in the retina form more superficial layers having been displaced away from the foveal region during late fetal and early postnatal life. Other foveae may show only a reduced thickness in the inner cell layers, rather than an almost complete absence") -AnnotationAssertion( "high acuity vision") AnnotationAssertion( "fovea") AnnotationAssertion( "BIRNLEX:2543") AnnotationAssertion( "CALOHA:TS-2055") @@ -152135,6 +149971,7 @@ AnnotationAssertion( "fovea centralis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152144,8 +149981,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (photoreceptor layer of retina) AnnotationAssertion(Annotation( "Wikipedia:Layer_of_rods_and_cones") Annotation( "ZFA:0000143") "The layer within the retina where the photoreceptor cell receptor segments reside.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001165") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "we follow MA and ZFA in subdividing this into inner and outer segments") AnnotationAssertion( "EMAPA:35686") AnnotationAssertion( "FMA:58680") AnnotationAssertion( "MA:0001308") @@ -152206,13 +150041,11 @@ AnnotationAssertion( "outer limiting layer of retina") SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer nuclear layer of retina) AnnotationAssertion(Annotation( "ZFA:0001464") "The layer within the retina where the photoreceptor cell bodies reside.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001170") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "outer nuclear layer") AnnotationAssertion( "BAMS:Ronl") AnnotationAssertion( "BTO:0005600") @@ -152245,15 +150078,13 @@ AnnotationAssertion( "outer nuclear layer of retina") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "soma") Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer plexiform layer of retina) AnnotationAssertion(Annotation( "ZFA:0001330") "The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001330") Annotation( "TAO") Annotation( "ZFIN:curator") "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001171") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion(Annotation( "BTO:0003174") "external plexiform layer") AnnotationAssertion( "BAMS:Ropl") AnnotationAssertion( "BTO:0003174") @@ -152291,8 +150122,6 @@ DisjointClasses( "NLX:93816") "Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO:0003176") "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001167") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "BAMS:Rinl") AnnotationAssertion( "BTO:0003176") AnnotationAssertion( "EMAPA:19155") @@ -152337,9 +150166,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "NLX:36500") "Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Ganglion_cell_layer") "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001166") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") -AnnotationAssertion(Annotation( "NIF") "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]") AnnotationAssertion(Annotation( "FMA:58687") Annotation( "ZFA:0000024") "ganglion cell layer") AnnotationAssertion( "BAMS:Rgcl") AnnotationAssertion( "BTO:0003398") @@ -152383,7 +150209,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nerve fiber layer of retina) AnnotationAssertion(Annotation( "ISBN:0-914294-08-3") Annotation( "MGI:smb") "Layer of the retina formed by expansion of the fibers of the optic nerve.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001169") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "UBERON:0005888") AnnotationAssertion(Annotation( "ZFA:0001619") "nerve fiber layer") AnnotationAssertion( "DMBA:15652") @@ -152423,7 +150248,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0010235") "The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP].") AnnotationAssertion( "TODO - check frog/fish") -AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3") "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3].") AnnotationAssertion(Annotation( "ZFA:0001029") Annotation( ) "ILM") AnnotationAssertion( "EMAPA:36519") AnnotationAssertion( "FMA:58689") @@ -152449,19 +150273,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inner limiting layer of retina") SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner plexiform layer of retina) AnnotationAssertion(Annotation( "NLX:20558") "Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia).") -AnnotationAssertion(Annotation( "GO:0010842") "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001329") Annotation( "TAO") Annotation( "ZFIN:curator") "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001168") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") -AnnotationAssertion( "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired") AnnotationAssertion( "BAMS:Ripl") AnnotationAssertion( "BTO:0003175") AnnotationAssertion( "EMAPA:35741") @@ -152494,18 +150314,18 @@ AnnotationAssertion( "inner plexiform layer of retina") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (aqueous humor of eyeball) AnnotationAssertion(Annotation( "Wikipedia:Aqueous_humor") "A thick watery refractive medium that fills the space between the lens and the cornea[WP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000548") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/aqueous+humour") "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000548") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24") Annotation( "http://bgee.unil.ch/") "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.") AnnotationAssertion( "EHDAA2:0000139") AnnotationAssertion( "EHDAA:10196") AnnotationAssertion( "EMAPA:18232") @@ -152531,8 +150351,8 @@ AnnotationAssertion( "aqueous humor of eyeball") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "FMA def states A and P") Annotation( "located_in in EHDAA2") Annotation( "VHOG") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitreous humor) @@ -152546,7 +150366,6 @@ AnnotationAssertion( "EV:0100344") AnnotationAssertion( "FMA:58822") AnnotationAssertion( "MA:0001286") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D014822") AnnotationAssertion( "NCIT:C13323") AnnotationAssertion(Annotation( "ncithesaurus:Vitreous_Humor") "UMLS:C0229096") AnnotationAssertion( "VHOG:0000795") @@ -152590,9 +150409,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vitreous body") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "neural ectoderm of optic cup") Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitreous chamber of eyeball) @@ -152617,7 +150438,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vitreous chamber of eyeball") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sensory ganglion) @@ -152638,11 +150461,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sensory ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior segment of eyeball) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MESH:A09.371.060") Annotation( "MP:0005193") "Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).") -AnnotationAssertion(Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) AnnotationAssertion( "EMAPA:36594") AnnotationAssertion( "FMA:58865") AnnotationAssertion( "MA:0002484") @@ -152666,6 +150490,7 @@ AnnotationAssertion( "anterior segment of eyeball") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152696,6 +150521,7 @@ AnnotationAssertion( "posterior segment of eyeball") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152703,7 +150529,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epithelium of lens) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A layer of epithelial cells that is part of the eye.") -AnnotationAssertion( "this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former") AnnotationAssertion( ) AnnotationAssertion( "BTO:0001873") AnnotationAssertion( "CALOHA:TS-0543") @@ -152731,16 +150556,13 @@ AnnotationAssertion( "epithelium of lens") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (capsule of lens) AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003236") Annotation( "PMID:15483628") "The elastic, clear, membrane-like structure, that is outer most layer of the lens.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000550") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000550") Annotation( "VHOG") Annotation( "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24") Annotation( "http://bgee.unil.ch/") "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]") -AnnotationAssertion( "synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens") -AnnotationAssertion(Annotation( "FMA") "FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular") AnnotationAssertion( "EHDAA2:0000977") AnnotationAssertion( "EMAPA:18237") AnnotationAssertion( "FMA:58881") @@ -152761,10 +150583,13 @@ AnnotationAssertion( "capsule of lens") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (autonomic ganglion) @@ -152773,7 +150598,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "AEO:0001001") AnnotationAssertion( "CALOHA:TS-2340") -AnnotationAssertion( "EMAPA:17157") AnnotationAssertion( "EMAPA:18221") AnnotationAssertion( "FMA:5889") AnnotationAssertion( "MA:0000220") @@ -152793,7 +150617,8 @@ AnnotationAssertion( "autonomic ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sympathetic ganglion) @@ -152806,7 +150631,6 @@ AnnotationAssertion( "EMAPA:17157") AnnotationAssertion( "FMA:5890") AnnotationAssertion( "MA:0000226") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005728") AnnotationAssertion( "NCIT:C12467") AnnotationAssertion( "SCTID:362485003") AnnotationAssertion(Annotation( "ncithesaurus:Sympathetic_Ganglion") "UMLS:C0017071") @@ -152825,6 +150649,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "DOI:10.1101/gr.157586.113") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152833,7 +150659,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Paravertebral_ganglion") Annotation( "ZFIN:curator") "Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord.") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "UBERON:0005466") AnnotationAssertion( "EHDAA2:0001403") AnnotationAssertion( "EHDAA:5635") @@ -152860,7 +150685,9 @@ AnnotationAssertion( "paravertebral ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parasympathetic ganglion) @@ -152871,7 +150698,6 @@ AnnotationAssertion( "EMAPA:32813") AnnotationAssertion( "FMA:5894") AnnotationAssertion( "MA:0002469") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005726") AnnotationAssertion( "NCIT:C52557") AnnotationAssertion( "NLXANAT:100303") AnnotationAssertion( "SCTID:279284004") @@ -152886,7 +150712,9 @@ AnnotationAssertion( "parasympathetic ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152905,13 +150733,13 @@ AnnotationAssertion( "enteric ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve plexus) AnnotationAssertion(Annotation( "FMA:5901") Annotation( "Wikipedia:Nervous_system_plexus") Annotation( "https://github.com/obophenotype/cell-ontology/issues/1306") "Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "Made to be a subtype of junction rather than tissue to be consistent with FMA") AnnotationAssertion( "plexus") AnnotationAssertion( "AEO:0000138") AnnotationAssertion( "BTO:0000205") @@ -152938,12 +150766,10 @@ SubClassOf(Annotation( "AEO AnnotationAssertion(Annotation( "MESH:A09.371.060.200") Annotation( "MGI:csmith") Annotation( "MP:0001310") "The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball.") AnnotationAssertion( ) -AnnotationAssertion( "conjunctival") AnnotationAssertion( "AAO:0010343") AnnotationAssertion( "BTO:0003415") AnnotationAssertion( "CALOHA:TS-2232") AnnotationAssertion( "EFO:0000374") -AnnotationAssertion( "EMAPA:18233") AnnotationAssertion( "EV:0100340") AnnotationAssertion( "FMA:59011") AnnotationAssertion( "GAID:898") @@ -152967,6 +150793,7 @@ AnnotationAssertion( "conjunctiva") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) @@ -152977,7 +150804,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (spinal nerve plexus) AnnotationAssertion(Annotation( "http://www.medilexicon.com/medicaldictionary.php?t=70024") "An intermingling of fiber fascicles from adjacent spinal nerves to form a network.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000926") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436") Annotation( "http://bgee.unil.ch/") "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001899") AnnotationAssertion( "EMAPA:16987") AnnotationAssertion( "FMA:5903") @@ -152994,14 +150820,14 @@ AnnotationAssertion( "UBERON:0001813") AnnotationAssertion(rdfs:label "spinal nerve plexus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brachial nerve plexus) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Brachial_plexus") "An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified].") AnnotationAssertion( "check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000372") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/brachial+plexus") "A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000372") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436") Annotation( "http://bgee.unil.ch/") "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000180") AnnotationAssertion( "EHDAA:3782") AnnotationAssertion( "EMAPA:16988") @@ -153023,6 +150849,7 @@ AnnotationAssertion( "brachial nerve plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -153050,6 +150877,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lumbosacral nerve plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -153070,16 +150898,13 @@ AnnotationAssertion( "UBERON:0001816") AnnotationAssertion(rdfs:label "autonomic nerve plexus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal gland) AnnotationAssertion(Annotation( "Wikipedia:Lacrimal_gland") Annotation( "http://orcid.org/0000-0002-6601-2165") "The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP].") AnnotationAssertion(Annotation( "PMID:7559104") ) -AnnotationAssertion(Annotation( "FMA:59101") "Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands.") -AnnotationAssertion(Annotation( "Wikipedia:Preorbital_gland") "The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "In humans, they are situated in the upper, outer portion of each orbit") -AnnotationAssertion( "Innervation is highly complex and species-specific") AnnotationAssertion( "BTO:0000044") AnnotationAssertion( "CALOHA:TS-0512") AnnotationAssertion( "EFO:0001389") @@ -153107,8 +150932,11 @@ AnnotationAssertion( "lacrimal gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -153116,9 +150944,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000674") "Any of the coil glands of the skin that secrete sweat.") AnnotationAssertion( "TODO - check if all sweat glands are epidermal - see EMAPA:29743") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001467") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/sweat+gland") "A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001467") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101") Annotation( "http://bgee.unil.ch/") "Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]") -AnnotationAssertion( "In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation") AnnotationAssertion( "BTO:0001331") AnnotationAssertion( "CALOHA:TS-0993") AnnotationAssertion( "EMAPA:35844") @@ -153143,19 +150968,17 @@ AnnotationAssertion( "sweat gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "coiled tubular") Annotation( "Wikipedia:Tubular_gland") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebaceous gland) AnnotationAssertion(Annotation( "MP:0000647") Annotation( "Wikipedia:Sebaceous_gland") "A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].") -AnnotationAssertion( "sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001468") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/sebaceous+gland") "Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001468") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102") Annotation( "http://bgee.unil.ch/") "Sebaceous glands are also limited to mammals.[well established][VHOG]") AnnotationAssertion( "BTO:0001980") AnnotationAssertion( "CALOHA:TS-2384") AnnotationAssertion( "EMAPA:35754") @@ -153180,12 +151003,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sebaceous gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ) -SubClassOf(Annotation( "BTO") Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal cartilage) @@ -153195,7 +151018,6 @@ AnnotationAssertion( "MA:th") "EMAPA:37681") AnnotationAssertion( "FMA:59502") AnnotationAssertion( "MA:0001883") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D055171") AnnotationAssertion( "NCIT:C49593") AnnotationAssertion( "SCTID:278941001") AnnotationAssertion(Annotation( "ncithesaurus:Nasal_Cartilage") "UMLS:C0225415") @@ -153209,6 +151031,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of larynx) @@ -153236,6 +151062,8 @@ AnnotationAssertion(Annotation( "UBERON:0001824") AnnotationAssertion(rdfs:label "mucosa of larynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal cavity mucosa) @@ -153259,6 +151087,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasal cavity mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretion of lacrimal gland) @@ -153288,13 +151120,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secretion of lacrimal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gingiva) AnnotationAssertion(Annotation( "ISBN:0013002015") Annotation( "Wikipedia:Gingiva") "The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001].") AnnotationAssertion( "FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.") -AnnotationAssertion( "gingival") AnnotationAssertion( "BTO:0000519") AnnotationAssertion( "CALOHA:TS-2074") AnnotationAssertion( "EFO:0001925") @@ -153321,7 +151155,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gingiva") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "Carranza") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0013002015") ObjectSomeValuesFrom( )) @@ -153332,8 +151166,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Lip") Annotation( "http://www.medterms.com/script/main/art.asp?articlekey=9458") "One of the two fleshy folds which surround the opening of the mouth.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0007006") Annotation( "TAO") Annotation( "ZFIN:curator") Annotation( "http//:www.medterms.com/script/main/art.asp?articlekey=9458") "Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]") -AnnotationAssertion( "labial") AnnotationAssertion( "BTO:0001647") AnnotationAssertion( "CALOHA:TS-0558") AnnotationAssertion( "EMAPA:32839") @@ -153367,8 +151199,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (upper lip) AnnotationAssertion(Annotation( "TAO:0001970") Annotation( "Wikipedia:Upper_lip") "Lip that covers the upper portion of the mouth.[TAO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001750") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001970") Annotation( "TAO") Annotation( "TAO:wd") "Lip that covers the upper portion of the mouth.[TAO]") AnnotationAssertion( "UBERON:0003391") AnnotationAssertion( "EMAPA:17925") AnnotationAssertion( "FMA:59817") @@ -153388,14 +151218,14 @@ AnnotationAssertion( "upper lip") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower lip) AnnotationAssertion(Annotation( "TAO:0002060") Annotation( "Wikipedia:Lower_lip") "Lip that covers the lower portion of the mouth.[TAO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002060") Annotation( "TAO") Annotation( "TAO:wd") "Lip that covers the lower portion of the mouth.[TAO]") AnnotationAssertion( "UBERON:0003392") -AnnotationAssertion( "EHDAA2:0001020") AnnotationAssertion( "EMAPA:17909") AnnotationAssertion( "FMA:59818") AnnotationAssertion( "MA:0000921") @@ -153415,13 +151245,13 @@ AnnotationAssertion( "lower lip") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (saliva) AnnotationAssertion(Annotation( "GO:0046541") Annotation( "Wikipedia:Saliva") "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.") -AnnotationAssertion( "salivary") -AnnotationAssertion(Annotation( "GO") "We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin") AnnotationAssertion( "BTO:0001202") AnnotationAssertion( "CALOHA:TS-0891") AnnotationAssertion( "EMAPA:36536") @@ -153467,6 +151297,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct of salivary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -153498,6 +151331,7 @@ AnnotationAssertion( "Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved.") AnnotationAssertion(rdfs:label "bony labyrinth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -153506,10 +151340,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (semicircular canal) AnnotationAssertion(Annotation( "Wikipedia:Semicircular_canal") "One of three half-circular, interconnected tubes located inside each ear[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000431") Annotation( "TAO") Annotation( "ZFIN:curator") "Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001144") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414") Annotation( "http://bgee.unil.ch/") "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]") -AnnotationAssertion( "detects angular acceleration") -AnnotationAssertion(Annotation( "MA") "MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal") AnnotationAssertion( "AAO:0011098") AnnotationAssertion( "BTO:0003383") AnnotationAssertion( "CALOHA:TS-2164") @@ -153540,19 +151370,13 @@ AnnotationAssertion( "semicircular canal") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png"^^xsd:anyURI) SubClassOf(Annotation( "GO") ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "OG") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlea) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000031") Annotation( "Wikipedia:Cochlea") "The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000691") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/cochlea") "A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000691") Annotation( "VHOG") Annotation( "DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)") Annotation( "http://bgee.unil.ch/") "Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]") -AnnotationAssertion( "cochlear") -AnnotationAssertion( "The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)'") -AnnotationAssertion( "the cochlea is coiled in most mammals, monotremes being the exceptions.") -AnnotationAssertion(Annotation( "XAO") "sources vary in connection to bony labyrinth") AnnotationAssertion( "AAO:0000253") AnnotationAssertion( "BIRNLEX:1190") AnnotationAssertion( "BTO:0000267") @@ -153591,6 +151415,7 @@ AnnotationAssertion( "cochlea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "VHOG") Annotation( "XAO") Annotation( "ncit") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -153617,15 +151442,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "perilymph") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (internal ear) AnnotationAssertion(Annotation( "PMID:16217737") Annotation( "Wikipedia:Internal_ear") Annotation( "ZFIN:curator") "Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000217") Annotation( "TAO") Annotation( "ZFIN:curator") "The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000284") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366") Annotation( "http://bgee.unil.ch/") "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]") AnnotationAssertion( "AAO:0000238") AnnotationAssertion( "BIRNLEX:1196") AnnotationAssertion( "BTO:0000630") @@ -153664,9 +151486,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "internal ear") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (auricular cartilage) @@ -153682,18 +151505,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "auricular cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (membranous labyrinth) AnnotationAssertion(Annotation( "FMA:61022") Annotation( "Wikipedia:Membranous_labyrinth") "Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000729") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/membranous+labyrinth") "A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000729") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366") Annotation( "http://bgee.unil.ch/") "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]") -AnnotationAssertion(Annotation( "EMAPA") "inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now") AnnotationAssertion( "UBERON:0010113") AnnotationAssertion( "AAO:0011060") AnnotationAssertion( "EHDAA2:0000899") AnnotationAssertion( "EHDAA:4698") -AnnotationAssertion( "EMAPA:17815") AnnotationAssertion( "EV:0100367") AnnotationAssertion( "FMA:61022") AnnotationAssertion( "MA:0000242") @@ -153712,6 +151534,7 @@ AnnotationAssertion( "membranous labyrinth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -153720,7 +151543,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct.") AnnotationAssertion(Annotation( "PMID:7559104") ) -AnnotationAssertion( "chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104]") AnnotationAssertion( "EMAPA:19245") AnnotationAssertion( "FMA:61063") AnnotationAssertion( "MA:0001295") @@ -153733,6 +151555,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lacrimal drainage system") SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780674021839") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -153742,8 +151566,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cortex) AnnotationAssertion(Annotation( "Wikipedia:Cortex_(anatomy)") "Outermost layer of an organ[WP].") -AnnotationAssertion( "cortical") -AnnotationAssertion(Annotation( "FMA") "this class is used more generically than in FMA, and includes e.g. cortex of hair") AnnotationAssertion( "EFO:0000383") AnnotationAssertion( "EHDAA:9344") AnnotationAssertion( "FMA:61109") @@ -153763,8 +151585,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (utricle of membranous labyrinth) AnnotationAssertion(Annotation( "ISBN:0-8036-0655-9") Annotation( "MGI:smb") Annotation( "MP:0006090") Annotation( "PMID:15363417") Annotation( "Wikipedia:Utricle_(ear)") "The larger of the two otolith organs in the vestibule.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000289") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000289") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414") Annotation( "http://bgee.unil.ch/") "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]") AnnotationAssertion( "AAO:0000625") AnnotationAssertion( "AAO:0011109") AnnotationAssertion( "BTO:0001807") @@ -153799,8 +151619,6 @@ SubClassOf(Annotation( "Wik # Class: (saccule of membranous labyrinth) AnnotationAssertion(Annotation( "ISBN:0-8036-0655-9") Annotation( "MGI:smb") Annotation( "MP:0006089") Annotation( "PMID:15363417") Annotation( "Wikipedia:Saccule") "The smaller of the two otolith organs in the vestibule.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000374") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The most ventral chamber of the membranous labyrinth. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000374") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414") Annotation( "http://bgee.unil.ch/") "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG]") AnnotationAssertion( "AAO:0000550") AnnotationAssertion( "BTO:0001805") AnnotationAssertion( "EHDAA2:0001769") @@ -153837,8 +151655,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "Wikipedia:Cochlear_duct") "An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP].") AnnotationAssertion( "TODO - check cochlear duct vs cochlear aqueduct vs scala media") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000507") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/cochlear+duct") "The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000507") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414") Annotation( "http://bgee.unil.ch/") "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG]") AnnotationAssertion( "BIRNLEX:2562") AnnotationAssertion( "BTO:0001692") AnnotationAssertion( "CALOHA:TS-0152") @@ -153872,17 +151688,16 @@ AnnotationAssertion( "cochlear duct of membranous labyrinth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (semicircular duct) AnnotationAssertion(Annotation( "http://dictionary.reference.com/browse/semicircular+duct") "Any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium.") AnnotationAssertion( "TODO - check canal vs duct. see Wikipedia:File:Gray927.png") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000238") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58") Annotation( "http://bgee.unil.ch/") "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG]") AnnotationAssertion( "EMAPA:32830") AnnotationAssertion( "FMA:61122") AnnotationAssertion( "MA:0000251") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054776") AnnotationAssertion( "NCIT:C33528") AnnotationAssertion( "SCTID:279833009") AnnotationAssertion(Annotation( "ncithesaurus:Semicircular_Duct") "UMLS:C1323109") @@ -153893,6 +151708,7 @@ AnnotationAssertion(Annotation( "UBERON:0001856") AnnotationAssertion(rdfs:label "semicircular duct") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) @@ -153905,12 +151721,9 @@ AnnotationAssertion( "EHDAA2:0000832") AnnotationAssertion( "EHDAA:4706") AnnotationAssertion( "EMAPA:17286") -AnnotationAssertion( "EMAPA:17815") AnnotationAssertion( "FMA:61255") AnnotationAssertion( "MA:0000245") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D014722") AnnotationAssertion( "NCIT:C33871") -AnnotationAssertion( "SCTID:181188003") AnnotationAssertion(Annotation( "ncithesaurus:Vestibular_Labyrinth") "UMLS:C0042606") AnnotationAssertion( "Wikipedia:Inner_ear") AnnotationAssertion( "XAO:0004145") @@ -153922,13 +151735,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vestibular labyrinth") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebum) AnnotationAssertion(Annotation( "BTO:0001981") Annotation( "Wikipedia:Sebaceous_glands#Sebum") "Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].") -AnnotationAssertion( "The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans.") -AnnotationAssertion( "waterproofs skin") AnnotationAssertion( "BTO:0001981") AnnotationAssertion( "ENVO:02000037") AnnotationAssertion( "FMA:61304") @@ -153943,7 +151755,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sebum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilage of external ear) @@ -153961,6 +151775,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cartilage of external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of chest) @@ -153994,8 +151810,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cerebral hemisphere) AnnotationAssertion(Annotation( "FMA:61817") Annotation( "Wikipedia:Cerebral_hemisphere") "One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010480") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001639") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)") Annotation( "http://bgee.unil.ch/") "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]") AnnotationAssertion( "AAO:0010480") AnnotationAssertion( "BAMS:HEM") AnnotationAssertion( "BIRNLEX:1042") @@ -154030,6 +151844,8 @@ AnnotationAssertion( "cerebral hemisphere") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) @@ -154038,7 +151854,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "NLXANAT:20090601") "Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "NLXANAT:20090601") "Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally.") AnnotationAssertion( "BTO:0000484") AnnotationAssertion( "DHBA:10161") AnnotationAssertion( "DMBA:16002") @@ -154046,7 +151861,6 @@ AnnotationAssertion( "FMA:242199") AnnotationAssertion( "GAID:674") AnnotationAssertion( "MA:0000905") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005625") AnnotationAssertion( "NLXANAT:20090601") AnnotationAssertion( "Wikipedia:Frontal_lobe") AnnotationAssertion(Annotation( "FMA:242199") "cortex of frontal lobe") @@ -154063,6 +151877,8 @@ AnnotationAssertion( "frontal cortex") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (temporal lobe) @@ -154142,7 +151958,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:1373") "Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:61833") "Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent[FMA:61833].") AnnotationAssertion( "UBERON:0010122") AnnotationAssertion( "BAMS:CA") AnnotationAssertion( "BAMS:Cd") @@ -154180,10 +151995,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "caudate nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "true") Annotation( "EHDAA2") Annotation( "ncithesaurus") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "true") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "true") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -154192,8 +152004,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:809") "Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion.") AnnotationAssertion( "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Putamen") "Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease[Wikipedia:Putamen].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001456") Annotation( "VHOG") Annotation( "DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)") Annotation( "http://bgee.unil.ch/") "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]") AnnotationAssertion( "BAMS:PU") AnnotationAssertion( "BAMS:Pu") AnnotationAssertion( "BIRNLEX:809") @@ -154223,9 +152033,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "putamen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -154233,10 +152042,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:1241") "Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:61841") "Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA:61841]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001277") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.342") Annotation( "http://bgee.unil.ch/") "One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]") -AnnotationAssertion( "amygdalar") -AnnotationAssertion(Annotation( "MA") "MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype") AnnotationAssertion( "BAMS:AMY") AnnotationAssertion( "BAMS:Amg") AnnotationAssertion( "BAMS:Amy") @@ -154286,14 +152091,13 @@ AnnotationAssertion( "amygdala") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (island of Calleja) AnnotationAssertion(Annotation( "MP:0010010") Annotation( "PMID:80412") "One of the seven small groups of granule cells in the polymorph layer of the olfactory tubercle and one large group, the insula magna, which lies along the border between septum, nucleus accumbens and nucleus of the diagonal band.") -AnnotationAssertion(Annotation( "MP:0010010") "The islands of Calleja are located within the olfactory tubercle in most species; however, in primates these islands are located within the nucleus accumbens, since the olfactory tubercle is absent or extremely rudimentary in the brains of primates") AnnotationAssertion( "BAMS:ICj") AnnotationAssertion( "BAMS:IClj") AnnotationAssertion( "BAMS:ISC") @@ -154323,7 +152127,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "island of Calleja") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -154331,11 +152135,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nucleus accumbens) AnnotationAssertion(Annotation( "BIRNLEX:727") "A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum.") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "ISBN:0471888893") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "GO:0021768") "a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia[GO][GO:0021768].") -AnnotationAssertion( "The ventral striatopallidal complex in birds corresponds closely to its counterpart in mammals, with a nucleus accumbes present in the rostral telenceaphalon. Note that in birds, a region previously called the nucleus accumbens is now recognized as the lateral part of the bed nucleus of stria terminalis.[ISBN:0471888893]") AnnotationAssertion( "BAMS:ACB") AnnotationAssertion( "BAMS:ACC") AnnotationAssertion( "BAMS:Acb") @@ -154371,7 +152172,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus accumbens") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -154380,10 +152181,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (olfactory tubercle) AnnotationAssertion(Annotation( "NLXANAT:1005037") "Region in the ventral telencephalon, prominent in rodents, but present in all mammals, consisting of a laminated cortical part and the cap/hilus region. It is traditionally viewed as part of the olfactory cortex but recognized by some as having a striatal character. According to many authors, the structure of the OT transitions from cortical like to striatal like along the lateral medial axis. (Maryann Martone).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "MP") Annotation(rdfs:comment "EDITOR_NOTE check EHDAA2") ) -AnnotationAssertion(Annotation( "Wikipedia:Olfactory_tubercle") "The olfactory tubercle is a structure involved in Olfaction. It is present in humans, but much smaller than it is in some other animals. It is a frequent subject of research.") -AnnotationAssertion(Annotation( "MP") "Absent in primates") AnnotationAssertion( "BAMS:DLT") AnnotationAssertion( "BAMS:OLT") AnnotationAssertion( "BAMS:OT") @@ -154409,16 +152206,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory tubercle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png"^^xsd:anyURI) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2-inferred") Annotation( "MA") Annotation( "VHOG") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (phrenic nerve) AnnotationAssertion(Annotation( "VHOG:0000728") "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000728") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/phrenic+nerve") "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]") AnnotationAssertion( "BAMS:phn") AnnotationAssertion( "BTO:0001063") AnnotationAssertion( "EHDAA:4677") @@ -154443,15 +152238,13 @@ AnnotationAssertion( "phrenic nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dentate gyrus of hippocampal formation) AnnotationAssertion(Annotation( "BIRNLEX:1178") "Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "GO:0021542") "The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542].") AnnotationAssertion( "BAMS:DG") AnnotationAssertion( "BIRNLEX:1178") AnnotationAssertion( "BM:Tel-DG") @@ -154495,9 +152288,6 @@ SubClassOf(Annotation( "MA" AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Choroid_plexus") "A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces.") AnnotationAssertion( "TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001443") Annotation( "TAO") Annotation( "ZFIN:curator") "A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]") -AnnotationAssertion(Annotation( "MP:0000820") "Fringe of the tela choroidea of the brain ventricles[MP]") -AnnotationAssertion( "choroidal") AnnotationAssertion(Annotation( "PMID:23375746") Annotation( ) "CP") AnnotationAssertion( "BAMS:CHP") AnnotationAssertion( "BAMS:GHP") @@ -154533,7 +152323,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "choroid plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -154541,7 +152334,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (lateral olfactory stria) AnnotationAssertion(Annotation( "BIRNLEX:1559") "White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone).") -AnnotationAssertion(Annotation( "PMID:7437895") "In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells.") AnnotationAssertion( "BAMS:LDTR") AnnotationAssertion( "BAMS:LOTR") AnnotationAssertion( "BAMS:lo") @@ -154574,6 +152366,8 @@ AnnotationAssertion( "lateral olfactory stria") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk of phrenic nerve) @@ -154587,16 +152381,13 @@ AnnotationAssertion( "UBERON:0001889") AnnotationAssertion(rdfs:label "trunk of phrenic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain) AnnotationAssertion(Annotation( "Wikipedia:Forebrain") Annotation( "ZFIN:ZDB-PUB-961014-576") "The most anterior region of the brain including both the telencephalon and diencephalon.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010147") Annotation( "AAO") Annotation( "AAO:BJB") "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000109") Annotation( "TAO") Annotation( "ZFIN:curator") "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000109") Annotation( "TAO") "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000383") Annotation( "VHOG") Annotation( "PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)") Annotation( "http://bgee.unil.ch/") "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]") -AnnotationAssertion( "prosencephalic") AnnotationAssertion(Annotation( "BIRNLEX:1509") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "FB") AnnotationAssertion( "AAO:0010147") AnnotationAssertion( "BAMS:FB") @@ -154635,24 +152426,16 @@ AnnotationAssertion( "forebrain") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (midbrain) AnnotationAssertion(Annotation( "GO:0030901") "The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].") AnnotationAssertion( "developmental relationships need revised") -AnnotationAssertion(Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "ABA") Annotation( "pending") ) -AnnotationAssertion(Annotation( "ZFA") Annotation( "ABA") Annotation( "pending") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010149") Annotation( "AAO") Annotation( "AAO:BJB") "Middle part of the brain composed of the optic tectum and penducular region.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000128") Annotation( "TAO") Annotation( "ZFIN:curator") "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000069") Annotation( "VHOG") Annotation( "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)") Annotation( "http://bgee.unil.ch/") "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]") -AnnotationAssertion( "mesencephalic") -AnnotationAssertion(Annotation( "ABA") "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships") AnnotationAssertion(Annotation( "BIRNLEX:1667") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "MB") AnnotationAssertion( "AAO:0010149") AnnotationAssertion( "BAMS:MES") @@ -154695,18 +152478,14 @@ AnnotationAssertion( "midbrain") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (rhombomere) AnnotationAssertion(Annotation( "Wikipedia:Rhombomere") Annotation( "ZFIN:curator") "A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001064") Annotation( "TAO") Annotation( "ZFIN:curator") "A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000672") Annotation( "VHOG") Annotation( "DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)") Annotation( "http://bgee.unil.ch/") "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]") -AnnotationAssertion( "In human embryonic development, the rhombomeres are present by day 29") -AnnotationAssertion( "DHBA divides this into A(1-3),B(4),C(5-7) and D(8)") AnnotationAssertion(Annotation( "ZFA:0001064") "hindbrain segment") AnnotationAssertion(Annotation( "ZFA:0001064") "segment of hindbrain") AnnotationAssertion( "DHBA:12664") @@ -154734,26 +152513,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rhombomere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (telencephalon) AnnotationAssertion(Annotation( "AAO:0010479") Annotation( "XAO:0000012") "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "FMA:62000") "Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010479") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000079") Annotation( "TAO") Annotation( "ZFIN:curator") "The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000079") Annotation( "TAO") "relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000283") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]") -AnnotationAssertion( "cerebral") -AnnotationAssertion( "telencephalic") -AnnotationAssertion( "telenencephalic") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "In mammals the cortex covers almost the whole of the cerebral hemispheres.") -AnnotationAssertion( "In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209]") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum.") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure.") -AnnotationAssertion(Annotation( "Wikipedia:Telencephalon#Variation_among_species") "dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.") AnnotationAssertion(Annotation( "Wikipedia:Tentorium_cerebelli") "supratentorial region") AnnotationAssertion( "AAO:0010479") AnnotationAssertion( "BAMS:CB") @@ -154802,14 +152567,6 @@ SubClassOf(Annotation( "Bge # Class: (diencephalon) AnnotationAssertion(Annotation( "Wikipedia:Diencephalon") "The division of the forebrain that develops from the foremost primary cerebral vesicle.") -AnnotationAssertion(Annotation( "ZFA") Annotation( "ABA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "not well differentiated from the cerebrum. (Ariens, p. 868)") Annotation( "PMID:8932866") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000101") Annotation( "TAO") Annotation( "ZFIN:curator") "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010481") Annotation( "AAO") Annotation( "AAO:BJB") "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000318") Annotation( "VHOG") Annotation( "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)") Annotation( "http://bgee.unil.ch/") "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]") -AnnotationAssertion( "diencephalic") -AnnotationAssertion(Annotation( "ABA") "in ABA, this is part of the brain stem") AnnotationAssertion(Annotation( "BIRNLEX:1503") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "DiE") AnnotationAssertion( "AAO:0010481") AnnotationAssertion( "BAMS:DI") @@ -154863,18 +152620,15 @@ AnnotationAssertion( "diencephalon") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metencephalon) AnnotationAssertion(Annotation( "Wikipedia:Metencephalon") Annotation( "https://github.com/obophenotype/uberon/issues/300") "Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BIRNLEX:965") "Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000741") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/metencephalon") "The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000741") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") AnnotationAssertion(Annotation( "ncithesaurus:Epencephalon") Annotation( ) "epencephalon") AnnotationAssertion( "BAMS:Met") AnnotationAssertion( "BIRNLEX:965") @@ -154903,18 +152657,14 @@ AnnotationAssertion( "the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].") AnnotationAssertion(rdfs:label "metencephalon") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medulla oblongata) AnnotationAssertion(Annotation( "FMA:62004") Annotation( "GO:0021550") Annotation( "Wikipedia:Bone_marrow_of_ovary_oblongata") "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010486") Annotation( "AAO") Annotation( "AAO:BJB") "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000181") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000181") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)") Annotation( "http://bgee.unil.ch/") "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]") AnnotationAssertion( "bulb") AnnotationAssertion(Annotation( "ABA:MY") "medulla") AnnotationAssertion( "AAO:0010486") @@ -154961,7 +152711,7 @@ AnnotationAssertion( "medulla oblongata") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -154971,12 +152721,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (dorsal plus ventral thalamus) AnnotationAssertion(Annotation( "BIRNLEX:954") "Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87).") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000657") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/thalamus") "One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010483") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000657") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484") Annotation( "http://bgee.unil.ch/") "(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]") -AnnotationAssertion( "thalamic") AnnotationAssertion(Annotation( "BIRNLEX:954") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( "PMID:23375746") Annotation( ) "Th") AnnotationAssertion(Annotation( "FMA:62007") Annotation( "MA:0000179") "thalamus") AnnotationAssertion( "AAO:0010483") @@ -155020,6 +152765,7 @@ AnnotationAssertion( "dorsal plus ventral thalamus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -155027,16 +152773,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hypothalamus) AnnotationAssertion(Annotation( "Wikipedia:Hypothalamus") Annotation( "ZFIN:curator") "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "Lancelets possess a region similar to the hypothalamus (Murakami, 2005)") ) AnnotationAssertion(Annotation( "Ariens, p. 1192") ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000032") Annotation( "TAO") Annotation( "ZFIN:curator") "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010484") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000179") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]") -AnnotationAssertion( "hypothalamic") -AnnotationAssertion(Annotation( "WP") "all vertebrates contain a hypothalamus") AnnotationAssertion(Annotation( "BIRNLEX:734") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "Hy") AnnotationAssertion( "AAO:0010484") AnnotationAssertion( "BAMS:HY") @@ -155085,22 +152824,15 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") Annotation( "EHDAA2") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithalamus) AnnotationAssertion(Annotation( "BIRNLEX:1710") "Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010482") Annotation( "AAO") Annotation( "AAO:BJB") "Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000178") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000178") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG]") -AnnotationAssertion( "epithalamic") AnnotationAssertion(Annotation( "BIRNLEX:1710") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "ETh") AnnotationAssertion( "AAO:0010482") AnnotationAssertion( "BAMS:EPI") @@ -155178,14 +152910,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of small intestine) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a small intestine [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005127") Annotation( "TAO") Annotation( "ZFIN:curator") "Intestinal epithelium which lines the lumen of the mid intestine.[TAO]") AnnotationAssertion( "BTO:0001258") AnnotationAssertion( "CALOHA:TS-2104") AnnotationAssertion( "EMAPA:35778") @@ -155215,17 +152947,8 @@ SubClassOf(Annotation( "FMA # Class: (pineal body) AnnotationAssertion(Annotation( "BIRNLEX:1184") "A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "Hardisty, p. 310") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000019") Annotation( "TAO") Annotation( "ZFIN:curator") "A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010549") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000019") Annotation( "TAO") "relationship loss: part_of pineal complex (TAO:0001359)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000051") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516") Annotation( "http://bgee.unil.ch/") "The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG]") -AnnotationAssertion( "epiphyseal") -AnnotationAssertion( "epiphysial") -AnnotationAssertion( "lobulated in humans, homogeneous in mouse. Calcifies with age in humans.") AnnotationAssertion(Annotation( "BIRNLEX:1184") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "Pi") AnnotationAssertion( "AAO:0010549") AnnotationAssertion( "BAMS:PIN") @@ -155282,6 +153005,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "ZFA") Annotation( "various") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -155299,7 +153023,6 @@ AnnotationAssertion( "BM:Tel-OT") AnnotationAssertion( "DHBA:10589") AnnotationAssertion( "DMBA:17785") -AnnotationAssertion( "EMAPA:16678") AnnotationAssertion( "EMAPA:35617") AnnotationAssertion( "FMA:62046") AnnotationAssertion( "GAID:735") @@ -155331,7 +153054,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -155344,15 +153067,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0000817") Annotation( "Wikipedia:Mammary_gland") Annotation( "http://orcid.org/0000-0002-6601-2165") "A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.") AnnotationAssertion( "Originally this was classified as a female reproductive structure, as it was in the MP in 2011") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000398") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/mammary+gland") "Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000398") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224") Annotation( "http://bgee.unil.ch/") "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]") -AnnotationAssertion( "mammary") -AnnotationAssertion( "A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts") -AnnotationAssertion( "The male Dayak fruit bat has lactating mammary glands") -AnnotationAssertion( "The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.") -AnnotationAssertion( "The BTO class represents the combination of nipple plus lobe") -AnnotationAssertion( "The FMA class represents an individule lobe. The nipple is not a part") -AnnotationAssertion( "The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts") AnnotationAssertion( "BTO:0000817") AnnotationAssertion( "CALOHA:TS-0595") AnnotationAssertion( "EFO:0000854") @@ -155388,10 +153102,11 @@ AnnotationAssertion( "mammary gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobule of mammary gland) @@ -155414,6 +153129,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lobule of mammary gland") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -155422,8 +153138,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.") AnnotationAssertion( "to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001263") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224") Annotation( "http://bgee.unil.ch/") "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]") -AnnotationAssertion(Annotation( "ncit") "ncit:Milk refers specifically to cow milk") AnnotationAssertion( "BTO:0000868") AnnotationAssertion( "CALOHA:TS-0636") AnnotationAssertion( "EMAPA:36540") @@ -155446,12 +153160,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "milk") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of capillary) @@ -155472,7 +153186,7 @@ AnnotationAssertion( "UBERON:0001915") AnnotationAssertion(rdfs:label "endothelium of capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of arteriole) @@ -155488,14 +153202,13 @@ AnnotationAssertion( "UBERON:0001916") AnnotationAssertion(rdfs:label "endothelium of arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of artery) AnnotationAssertion(Annotation( "OBOL:automatic") "An endothelium that is part of an artery [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011013") Annotation( "AAO") Annotation( "XAO:curator") "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001215") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207") Annotation( "http://bgee.unil.ch/") "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]") AnnotationAssertion( "AAO:0011013") AnnotationAssertion( "BTO:0004757") AnnotationAssertion( "EMAPA:35148") @@ -155512,6 +153225,9 @@ AnnotationAssertion( "endothelium of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of venule) @@ -155526,13 +153242,13 @@ AnnotationAssertion( "UBERON:0001918") AnnotationAssertion(rdfs:label "endothelium of venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of vein) AnnotationAssertion(Annotation( "OBOL:automatic") "An endothelium that is part of a vein [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001216") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207") Annotation( "http://bgee.unil.ch/") "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]") AnnotationAssertion( "AAO:0011110") AnnotationAssertion( "BTO:0004756") AnnotationAssertion( "EMAPA:36288") @@ -155549,14 +153265,15 @@ AnnotationAssertion(Annotation( "UBERON:0001919") AnnotationAssertion(rdfs:label "endothelium of vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral geniculate body) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0004165") "The group of neurons that serve as the primary processor of visual information received from the retina via the optic tract and send processed information to the visual cortex of the occipital lobe.") AnnotationAssertion(Annotation( "Ariens, p. 1192") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO") "BTO has distinct classes for body and nucleus, but other sources treat as identical") AnnotationAssertion(Annotation( "BIRNLEX:1662") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "LGN") AnnotationAssertion( "BAMS:C.gl.") AnnotationAssertion( "BAMS:LG") @@ -155593,7 +153310,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lateral geniculate body") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -155601,8 +153318,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Preoptic_area") Annotation( "ZFIN:curator") "Area of the forebrain between the anterior commissure and optic chiasm.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000470") Annotation( "TAO") Annotation( "ZFIN:curator") "Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus. See Figure 7, Atlas of Early Zebrafish Brain Development.[TAO]") -AnnotationAssertion( "Located in the hypothalamus in amniotes[PMC4038951]") AnnotationAssertion(Annotation( "BIRNLEX:1706") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( "PMID:23375746") Annotation( ) "POA") AnnotationAssertion( "BAMS:POA") AnnotationAssertion( "BIRNLEX:1706") @@ -155646,8 +153361,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (paraventricular nucleus of hypothalamus) AnnotationAssertion(Annotation( "BIRNLEX:1407") "Nucleus in the anterior part of the hypothalamus. (MSH) * one of the magnocellular hypothalamic nuclei, an elongated plate of large, deeply staining cells located close to the third ventricle in the anterior hypothalamic area; major source of oxytocin and to a lesser extent, of antidiuretic hormone, neurohormones, which are carried to the neurohypophysis along the paraventriculohypophysial tract. (CSP).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "BIRNLEX:1407") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "Pa") AnnotationAssertion( "BAMS:PAH") AnnotationAssertion( "BAMS:PVH") @@ -155690,16 +153403,13 @@ AnnotationAssertion( "paraventricular nucleus of hypothalamus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arcuate nucleus of hypothalamus) AnnotationAssertion(Annotation( "Wikipedia:Arcuate_nucleus") "The arcuate nucleus (or infundibular nucleus) is an aggregation of neurons in the mediobasal hypothalamus, adjacent to the third ventricle and the median eminence. The arcuate nucleus includes several important populations of neurons, including: Neuroendocrine neurons, Centrally-projecting neurons and Others. [WP,unvetted].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "BTO") "the semantics of the BTO class arcuate nucleus are not clear") AnnotationAssertion(Annotation( "BIRNLEX:1638") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "ArcH") AnnotationAssertion( "BAMS:ARH") AnnotationAssertion( "BAMS:Arc") @@ -155740,7 +153450,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arcuate nucleus of hypothalamus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) @@ -155748,7 +153458,6 @@ SubClassOf(Annotation( "NIF AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Midbrain_tegmentum") "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001367") Annotation( "VHOG") Annotation( "DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)") Annotation( "http://bgee.unil.ch/") "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:1200") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "MTg") AnnotationAssertion(Annotation( "ISBN:0471888893") "tegmentum") AnnotationAssertion( "BAMS:MTg") @@ -155762,7 +153471,6 @@ AnnotationAssertion( "HBA:9002") AnnotationAssertion( "MA:0000212") AnnotationAssertion( "MAT:0000452") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D013681") AnnotationAssertion( "SCTID:362392007") AnnotationAssertion( "TAO:0000160") AnnotationAssertion(Annotation( "BIRNLEX:1200") "UMLS:C0039441") @@ -155803,11 +153511,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regional part of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gingival epithelium) AnnotationAssertion(Annotation( "BTO:0004998") "A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO].") -AnnotationAssertion( "In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva") AnnotationAssertion( "BTO:0004998") AnnotationAssertion( "FMA:62423") AnnotationAssertion( "MA:0001576") @@ -155821,13 +153531,14 @@ AnnotationAssertion( "UBERON:0001949") AnnotationAssertion(rdfs:label "gingival epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neocortex) AnnotationAssertion(Annotation( "BIRNLEX:2547") Annotation( "OldNeuroNames:754") "An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "PMID:23027930") "The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils") AnnotationAssertion( "BAMS:ISO") AnnotationAssertion( "BAMS:Iso-cortex") AnnotationAssertion( "BAMS:NCX") @@ -155898,16 +153609,14 @@ AnnotationAssertion(Annotation( "UBERON:0001951") AnnotationAssertion(rdfs:label "epithelium of nasopharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (Ammon's horn) AnnotationAssertion(Annotation( "BIRNLEX:721") "A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion( "hippocampal") -AnnotationAssertion( "Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP]") AnnotationAssertion( "UBERON:0003940") AnnotationAssertion( "UBERON:0004165") AnnotationAssertion( "BAMS:CA") @@ -155919,7 +153628,6 @@ AnnotationAssertion( "DMBA:16124") AnnotationAssertion( "EFO:0000530") AnnotationAssertion( "EHDAA2:0004443") -AnnotationAssertion( "EMAPA:32772") AnnotationAssertion( "EMAPA:32845") AnnotationAssertion( "EV:0100180") AnnotationAssertion( "FMA:62493") @@ -155985,7 +153693,6 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (cartilage of bronchus) @@ -156012,6 +153719,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cartilage of bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) @@ -156038,14 +153748,14 @@ AnnotationAssertion(Annotation( "UBERON:0001957") AnnotationAssertion(rdfs:label "submucosa of bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (terminal bronchiole epithelium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An epithelium that lines a terminal bronchiole.") AnnotationAssertion( ) -AnnotationAssertion( "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]") AnnotationAssertion( ) AnnotationAssertion( "EMAPA:36283") AnnotationAssertion( "FMA:62794") @@ -156065,14 +153775,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "terminal bronchiole epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white pulp of spleen) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0002357") "The parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies.") AnnotationAssertion( ) -AnnotationAssertion( "The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp]") AnnotationAssertion( "CALOHA:TS-1264") AnnotationAssertion( "EMAPA:35809") AnnotationAssertion( "FMA:62805") @@ -156092,6 +153801,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white pulp of spleen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -156100,7 +153810,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0002358") "The area of the spleen in which T cells surround the central arteriole.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA distinguishes periarterial (PALS) from periarteriolar (FMA:62806)") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37750") AnnotationAssertion( "FMA:62810") AnnotationAssertion( "MA:0000765") @@ -156116,6 +153825,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "periarterial lymphatic sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa-associated lymphoid tissue) @@ -156150,7 +153863,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Gut-associated_lymphoid_tissue") "Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO].") AnnotationAssertion( "phylogenetic relationships to be added") AnnotationAssertion( ) -AnnotationAssertion( "guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002).") AnnotationAssertion( "FMA:62820") AnnotationAssertion( "MA:0000136") AnnotationAssertion( "NCIT:C12936") @@ -156165,6 +153877,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gut-associated lymphoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchial-associated lymphoid tissue) @@ -156181,13 +153895,14 @@ AnnotationAssertion( "Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN:0123813611] Notes: FMA classifies this as organized, not diffuse") AnnotationAssertion(rdfs:label "bronchial-associated lymphoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0123813611") ObjectSomeValuesFrom( )) # Class: (semen) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Organism substance that is composed of sperm cells suspended in seminal fluid.") -AnnotationAssertion( "seminal") -AnnotationAssertion( "Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530).") AnnotationAssertion( "BTO:0001230") AnnotationAssertion( "CALOHA:TS-0917") AnnotationAssertion( "EMAPA:31488") @@ -156240,17 +153955,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood plasma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bile) AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c120027") Annotation( "Wikipedia:Bile") "Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.") -AnnotationAssertion( "In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.") -AnnotationAssertion( "aids the process of digestion of lipids in the small intestine") -AnnotationAssertion( "bile salts function to emulsify dietary fats and facilitate their intestinal absorption") -AnnotationAssertion( "elimination of cholesterol") -AnnotationAssertion( "major excretory route for potentially harmful exogenous lipophilic substances") -AnnotationAssertion( "many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates") -AnnotationAssertion( "protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine") AnnotationAssertion( "BTO:0000121") AnnotationAssertion( "CALOHA:TS-1172") AnnotationAssertion( "ENVO:02000023") @@ -156271,11 +153984,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bile") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "0.3% in humans") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastric juice) @@ -156296,6 +154012,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastric juice") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of esophagus) @@ -156322,7 +154040,7 @@ AnnotationAssertion(Annotation( "UBERON:0001972") AnnotationAssertion(rdfs:label "submucosa of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of esophagus) @@ -156389,7 +154107,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000468") "The epithelial layer that lines the luminal space of the esophagus.") AnnotationAssertion( "TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001499") Annotation( "TAO") Annotation( "ZFIN:curator") "Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]") AnnotationAssertion( "BTO:0001578") AnnotationAssertion( "CALOHA:TS-0698") AnnotationAssertion( "EFO:0003041") @@ -156421,6 +154138,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -156439,12 +154158,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "parenchyma of pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venule) AnnotationAssertion(Annotation( "MESH:A07.231.432.952") Annotation( "MP:0004125") "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005315") Annotation( "TAO") Annotation( "ZFIN:curator") "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]") AnnotationAssertion( "BTO:0002626") AnnotationAssertion( "EMAPA:35917") AnnotationAssertion( "FMA:63130") @@ -156468,15 +154188,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole) AnnotationAssertion(Annotation( "GO:0014830") "The smallest division of the artery located between the muscular arteries and the capillaries[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002138") Annotation( "TAO") Annotation( "ZFIN:curator") "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010253") Annotation( "AAO") Annotation( "AAO:BJB") "Small, terminal branch of an artery which generally connects to capillaries.[AAO]") AnnotationAssertion( "AAO:0010253") AnnotationAssertion( "BTO:0001997") AnnotationAssertion( "EMAPA:35146") @@ -156501,6 +154218,8 @@ AnnotationAssertion( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel) @@ -156508,11 +154227,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0001102") Annotation( "Wikipedia:Blood_vessel") "A vessel through which blood circulates in the body.") AnnotationAssertion( "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001250") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011004") Annotation( "AAO") Annotation( "AAO:EJS") "Any of the vessels through which blood circulates in the body.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001250") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") -AnnotationAssertion( "annelids have blood vessels, but this class is not applicable to annelids.") -AnnotationAssertion(Annotation( "FMA") "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX") AnnotationAssertion(Annotation( "EMAPA:35993") "vascular element") AnnotationAssertion( "AAO:0011004") AnnotationAssertion( "AEO:0000207") @@ -156550,7 +154264,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -156565,9 +154281,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Capillary") Annotation( "https://github.com/obophenotype/uberon/issues/137") "Any of the smallest blood vessels connecting arterioles with venules.") AnnotationAssertion( "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010252") Annotation( "AAO") Annotation( "AAO:BJB") "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001253") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") -AnnotationAssertion( "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs") AnnotationAssertion( "AAO:0010252") AnnotationAssertion( "BTO:0002045") AnnotationAssertion( "CALOHA:TS-2006") @@ -156598,12 +154311,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2186") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000490") Annotation( "https://github.com/obophenotype/uberon/issues/213") "The tubular intestinal glands found in the mucosal membranes.") -AnnotationAssertion(Annotation( "Wikipedia:Intestinal_crypt") "In histology, an intestinal crypt, also crypt of LieberkC "ISBN:9780521617147") "Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules") AnnotationAssertion(Annotation( "Wikipedia:Crypts_of_Lieberkuhn") "intestinal gland") AnnotationAssertion( "EMAPA:35266") AnnotationAssertion( "FMA:63621") @@ -156631,10 +154345,9 @@ AnnotationAssertion( "crypt of Lieberkuhn") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia:Tubular_gland") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "further investigation required") Annotation( "ISBN:9780521617147") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of large intestine) @@ -156689,7 +154402,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -156697,7 +154412,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FMA:63916") Annotation( "MESH:A10.272.491") Annotation( "https://github.com/obophenotype/uberon/issues/225") "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].") AnnotationAssertion( ) -AnnotationAssertion( "endothelial") AnnotationAssertion( "BTO:0000393") AnnotationAssertion( "CALOHA:TS-0278") AnnotationAssertion( "EFO:0002548") @@ -156717,16 +154431,14 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA-text-def") Annotation( "https://github.com/obophenotype/uberon/issues/225") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "UBERON:0001985") Annotation( "FMA-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placenta) AnnotationAssertion(Annotation( "Wikipedia:Placenta") Annotation( "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/06placenta.htm") "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001266") Annotation( "VHOG") Annotation( "DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)") Annotation( "http://bgee.unil.ch/") "Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]") -AnnotationAssertion( "placental") -AnnotationAssertion( "Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011") AnnotationAssertion( "BTO:0001078") AnnotationAssertion( "CALOHA:TS-0799") AnnotationAssertion( "EFO:0001407") @@ -156758,6 +154470,8 @@ AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1376") ObjectSomeValuesFrom( )) @@ -156768,8 +154482,6 @@ SubClassOf(Annotation( "ISB # Class: (feces) AnnotationAssertion(Annotation( "Wikipedia:Feces") Annotation( "http://www.merriam-webster.com/dictionary/feces") "Portion of semisolid bodily waste discharged through the anus[MW,modified].") -AnnotationAssertion(Annotation( "FMA:64183") "Excretion in semisolid state processed by the intestine.[FMA]") -AnnotationAssertion( "fecal") AnnotationAssertion( "excreta") AnnotationAssertion( "BTO:0000440") AnnotationAssertion( "CALOHA:TS-2345") @@ -156816,12 +154528,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "feces") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (papillary layer of dermis) AnnotationAssertion(Annotation( "ncithesaurus:Papillary_Dermis") "The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified].") AnnotationAssertion( "todo - check tissue composition") -AnnotationAssertion(Annotation( "FMA:64776") "Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III.") AnnotationAssertion( "EMAPA:35282") AnnotationAssertion( "FMA:64776") AnnotationAssertion( "MA:0000800") @@ -156849,6 +154562,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "papillary layer of dermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) @@ -156877,6 +154592,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reticular layer of dermis") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -156886,8 +154602,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hyaline cartilage tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000094") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.") -AnnotationAssertion(Annotation( "FMA:64783") "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000094") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]") AnnotationAssertion( "EMAPA:35414") AnnotationAssertion( "FMA:64783") AnnotationAssertion( "MA:0000109") @@ -156906,20 +154620,15 @@ AnnotationAssertion( "hyaline cartilage tissue") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO-text-def") ObjectSomeValuesFrom( )) # Class: (fibrocartilage) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000103") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.") -AnnotationAssertion(Annotation( "Wikipedia:Fibrocartilage") "A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I") -AnnotationAssertion(Annotation( "FMA:64784") "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000103") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO]") -AnnotationAssertion( "fibrocartilaginous") AnnotationAssertion( "FMA:64784") AnnotationAssertion( "MA:0000108") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D051445") AnnotationAssertion( "NCIT:C32599") AnnotationAssertion( "SCTID:91685003") AnnotationAssertion(Annotation( "ncithesaurus:Fibrocartilage") "UMLS:C0684077") @@ -156936,16 +154645,13 @@ AnnotationAssertion( "The white fibrocartilages admit of arrangement into four groups-interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized") AnnotationAssertion(rdfs:label "fibrocartilage") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (elastic cartilage tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000091") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Cartilage tissue that is flexible and contains abundant elastic fibers.") -AnnotationAssertion(Annotation( "FMA:64785") "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000091") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO]") -AnnotationAssertion(Annotation( "MA") "MA has a distinct class for yellow") AnnotationAssertion( "FMA:64785") AnnotationAssertion( "MA:0000107") AnnotationAssertion( "MA:0000485") @@ -156974,8 +154680,6 @@ SubClassOf(Annotation( "VSA # Class: (olfactory epithelium) AnnotationAssertion(Annotation( "Wikipedia:Olfactory_epithelium") "A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010158") Annotation( "AAO") Annotation( "AAO:DSM") "Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010158") Annotation( "AAO") "relationship loss: part_of principal cavity (AAO:0000992)[AAO]") AnnotationAssertion( "UBERON:0004853") AnnotationAssertion( "AAO:0010158") AnnotationAssertion( "BIRNLEX:2703") @@ -157015,13 +154719,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "olfactory epithelium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NBK26868") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NBK26868") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "NBK26868") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK55982") ObjectSomeValuesFrom( )) @@ -157041,10 +154745,10 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk of sciatic nerve) -AnnotationAssertion( "EMAPA:18577") AnnotationAssertion( "FMA:65507") AnnotationAssertion( "MA:0001178") AnnotationAssertion( "sciatic nerve trunk") @@ -157053,11 +154757,12 @@ AnnotationAssertion( "UBERON:0002004") AnnotationAssertion(rdfs:label "trunk of sciatic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enteric nervous system) AnnotationAssertion(Annotation( "GO:0048484") "The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO].") -AnnotationAssertion(Annotation( "FMA") "most sources classify this as autonomic, but in FMA it is placed directly under nervous system.") AnnotationAssertion( "BAMS:ENS") AnnotationAssertion( "BIRNLEX:1166") AnnotationAssertion( "BTO:0002506") @@ -157084,6 +154789,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enteric nervous system") +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf(Annotation( "FMA") Annotation( "MA") Annotation( "NIF") Annotation( "ZFA-isa-changed") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) @@ -157110,6 +154816,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (medulla of lymph node) @@ -157130,6 +154837,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157155,6 +154864,9 @@ AnnotationAssertion( "cardiac nerve plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracodorsal artery) @@ -157174,16 +154886,14 @@ AnnotationAssertion( "thoracodorsal artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary artery) AnnotationAssertion(Annotation( "Wikipedia:Pulmonary_artery") Annotation( "http://orcid.org/0000-0002-6601-2165") "An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010221") Annotation( "AAO") Annotation( "AAO:BJB") "Major artery which supplies blood to the lungs.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000982") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pulmonary+artery") "One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000982") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]") -AnnotationAssertion( "In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]") AnnotationAssertion( "AAO:0010221") AnnotationAssertion( "BTO:0000778") AnnotationAssertion( "CALOHA:TS-0839") @@ -157218,8 +154928,11 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -157229,8 +154942,6 @@ DisjointClasses( "MGI:anna") Annotation( "MP:0011383") "The tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage.") AnnotationAssertion( ) -AnnotationAssertion( "provides some protection from trauma and damage.") -AnnotationAssertion( "The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]") AnnotationAssertion( "EMAPA:18679") AnnotationAssertion( "FMA:66610") AnnotationAssertion( "MA:0000370") @@ -157255,17 +154966,15 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary vein) AnnotationAssertion(Annotation( "GO:0060577") "Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010521") Annotation( "AAO") Annotation( "AAO:BJB") "Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001133") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pulmonary+vein") "One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]") -AnnotationAssertion(Annotation( "MP:0002726,MGI:cwg") "the veins that return oxygenated blood from the lungs to the left atrium of the heart") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001133") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]") -AnnotationAssertion( ) AnnotationAssertion( "AAO:0010521") AnnotationAssertion( "BTO:0001799") AnnotationAssertion( "CALOHA:TS-0840") @@ -157295,9 +155004,11 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (portal vein) @@ -157333,7 +155044,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (synovial membrane of synovial joint) AnnotationAssertion(Annotation( "Wikipedia:Synovial_membrane") "Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints).") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001282") Annotation( "VHOG") Annotation( "PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)") Annotation( "http://bgee.unil.ch/") "Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG]") AnnotationAssertion(Annotation( "FMA:66762") "synovial layer") AnnotationAssertion(Annotation( "AEO:0000181") "synovial membrane") AnnotationAssertion(Annotation( "BTO:0001823") Annotation( "VHOG:0001282") "synovium") @@ -157367,8 +155077,9 @@ AnnotationAssertion( "synovial membrane of synovial joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png"^^xsd:anyURI) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GAID") ObjectSomeValuesFrom( )) @@ -157376,13 +155087,6 @@ SubClassOf(Annotation( "GAI # Class: (accessory XI nerve) AnnotationAssertion(Annotation( "BIRNLEX:812") Annotation( "http://orcid.org/0000-0002-6601-2165") "A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord.") -AnnotationAssertion(Annotation( "VHOG") Annotation( "Wikipedia") Annotation(rdfs:seeAlso "http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7") ) -AnnotationAssertion(Annotation( "ISBN:080184780X") Annotation( "XAO:0004214") "A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000699") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010476") Annotation( "AAO") Annotation( "AAO:EJS") "Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000699") Annotation( "VHOG") Annotation( "Wikipedia:Cranial_nerves") Annotation( "http://bgee.unil.ch/") "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]") -AnnotationAssertion(Annotation( "GO") "In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve") -AnnotationAssertion(Annotation( "FMA") "FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]") AnnotationAssertion( "AAO:0010476") AnnotationAssertion( "BAMS:11n") AnnotationAssertion( "BAMS:XIn") @@ -157428,13 +155132,13 @@ AnnotationAssertion( "accessory XI nerve") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter) AnnotationAssertion(Annotation( "Wikipedia:Gray_matter") Annotation( "http://orcid.org/0000-0002-6601-2165") "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002197") Annotation( "TAO") Annotation( "ZFIN:curator") "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]") AnnotationAssertion( "AEO:0001012") AnnotationAssertion( "EHDAA2:0003136") AnnotationAssertion( "EHDAA2_RETIRED:0004658") @@ -157442,7 +155146,6 @@ AnnotationAssertion(Annotation( "FMA:67242") AnnotationAssertion( "HBA:4006") AnnotationAssertion( "MA:0001112") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066128") AnnotationAssertion( "NCIT:C32695") AnnotationAssertion( "TAO:0002197") AnnotationAssertion(Annotation( "ncithesaurus:Gray_Matter") "UMLS:C0018220") @@ -157466,16 +155169,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gray matter") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratum basale of epidermis) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001231") "The deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells.") AnnotationAssertion( ) -AnnotationAssertion( "replaces damaged cells on outside of body") -AnnotationAssertion( "consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells") AnnotationAssertion(Annotation( "Wikipedia:Malpighian_layer") "Malpighian layer") AnnotationAssertion(Annotation( ) "rete Malphighii") AnnotationAssertion( "rete Malpighii") @@ -157514,15 +155214,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratum basale of epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratum spinosum of epidermis) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001236") "The layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance.") AnnotationAssertion( ) -AnnotationAssertion( "Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum]") AnnotationAssertion(Annotation( "Wikipedia:Malpighian_layer") "Malpighian layer") AnnotationAssertion(Annotation( "Wikipedia:Malpighian") Annotation( ) "stratum Malpighii") AnnotationAssertion( "BTO:0000435") @@ -157545,17 +155248,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratum spinosum of epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratum corneum of epidermis) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0001240") "The outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010597") Annotation( "AAO") Annotation( "AAO:CAM") "The keratinized outermost layer of the epidermis, which is periodically shed.[AAO]") -AnnotationAssertion( "some oral epitehlium also has cornified layer / stratum corneum") AnnotationAssertion(Annotation( "BTO:0000344") "horny layer") AnnotationAssertion( "keratinized squame layer") AnnotationAssertion( "stratum corneum") @@ -157581,8 +155286,9 @@ AnnotationAssertion( "stratum corneum of epidermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157590,16 +155296,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hindbrain) AnnotationAssertion(Annotation( "Wikipedia:Rhombencephalon") Annotation( "ZFA:0000029") Annotation( "ZFIN:curator") "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].") -AnnotationAssertion(Annotation( "ZFA") Annotation( "ABA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "PMID:8932866") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010150") Annotation( "AAO") Annotation( "AAO:BJB") "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000029") Annotation( "TAO") Annotation( "ZFIN:curator") "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000029") Annotation( "TAO") "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000070") Annotation( "VHOG") Annotation( "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)") Annotation( "http://bgee.unil.ch/") "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]") -AnnotationAssertion( "rhombencephalic") -AnnotationAssertion(Annotation( "MA") "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps") AnnotationAssertion( "AAO:0010150") AnnotationAssertion( "BAMS:HB") AnnotationAssertion( "BIRNLEX:942") @@ -157639,8 +155337,7 @@ AnnotationAssertion( "hindbrain") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "modified-source-relation") Annotation( "ABA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) @@ -157669,14 +155366,14 @@ AnnotationAssertion( "epithelium of gall bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nipple) AnnotationAssertion(Annotation( "FMA:67771") Annotation( "Wikipedia:Nipple") "Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip.") -AnnotationAssertion( "a male mouse has no nipples - mammary tissue regresses during embryonic development") -AnnotationAssertion(Annotation( "FMA") "FMA makes this part of the breast, whereas in MA it is part of the mammary gland -") AnnotationAssertion( "BTO:0000821") AnnotationAssertion( "CALOHA:TS-2234") AnnotationAssertion( "EMAPA:36508") @@ -157705,6 +155402,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/1873") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Stedmans") ObjectSomeValuesFrom( )) @@ -157738,7 +155436,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157746,7 +155444,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (arrector muscle of hair) AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2008.12.005") "A tiny smooth muscle that connects the hair follicle with the dermis.") -AnnotationAssertion( "When contracted the arrector pili causes the raising of the hair") AnnotationAssertion( "BTO:0005132") AnnotationAssertion( "EMAPA:26775") AnnotationAssertion( "FMA:67821") @@ -157776,7 +155473,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (striated muscle tissue) AnnotationAssertion(Annotation( "CL:0000737") Annotation( "GOC:dph") Annotation( "GOC:mtg_muscle") "Muscle tissue that contains fibers that are divided by transverse bands into striations.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010762") Annotation( "AAO") Annotation( "AAO:CAM") "Voluntary muscle tissue arranged in bundles of fibers.[AAO]") AnnotationAssertion( "AAO:0010762") AnnotationAssertion( "AEO:0000140") AnnotationAssertion( "CALOHA:TS-2047") @@ -157796,22 +155492,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "striated muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebellum) AnnotationAssertion(Annotation( "BTO:0000232") Annotation( "ISBN:3764351209") Annotation( "MESH:A08.186.211.132.810.428.200") Annotation( "ZFA:0000100") Annotation( "https://sourceforge.net/tracker/index.php?func=detail&aid=3291162&group_id=76834&atid=1205376") "Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].") AnnotationAssertion(Annotation( "ISBN:0471888893") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ZFA") Annotation( "ABA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) -AnnotationAssertion(Annotation( "http://icb.oxfordjournals.org/content/42/4/743.full") ) AnnotationAssertion(Annotation( "ISBN:0471888893") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010485") Annotation( "AAO") Annotation( "AAO:BJB") "Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000100") Annotation( "TAO") Annotation( "ZFIN:curator") "Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000024") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]") -AnnotationAssertion( "cerebellar") -AnnotationAssertion( "The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]") -AnnotationAssertion(Annotation( "ABA") "almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem") AnnotationAssertion(Annotation( "Wikipedia:Tentorium_cerebelli") "infratentorial region") AnnotationAssertion( "AAO:0010485") AnnotationAssertion( "BAMS:CB") @@ -157857,9 +155546,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "NIF") Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (substantia nigra) @@ -157867,8 +155555,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:789") "Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM).") AnnotationAssertion( "TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:67947") "Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001573") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336") Annotation( "http://bgee.unil.ch/") "(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:789") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "SN") AnnotationAssertion( "BAMS:SN") AnnotationAssertion( "BIRNLEX:789") @@ -157907,8 +155593,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "multiple") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIF") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157938,14 +155624,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "bronchial artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic vessel endothelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An endothelium that is part of a lymphatic vessel [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005258") Annotation( "TAO") Annotation( "ZFIN:curator") "The vascular endothelium that lines the lymph vessels.[TAO]") AnnotationAssertion( "BTO:0004303") AnnotationAssertion( "CALOHA:TS-2156") AnnotationAssertion( "EMAPA:35533") @@ -157968,7 +155655,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphatic vessel endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157976,11 +155663,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (thyroid gland) AnnotationAssertion(Annotation( "BTO:0001379") Annotation( "Wikipedia:Thyroid") "A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010544") Annotation( "AAO") Annotation( "AAO:BJB") "Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000418") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]") -AnnotationAssertion(Annotation( "NCBITaxon:32443") Annotation( "Romer") Annotation( "Wikipedia:Thyroid_gland#Other_animals") "In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes") -AnnotationAssertion(Annotation( "NCBITaxon:7746") Annotation( "Romer") Annotation( "Wikipedia:Thyroid_gland#Other_animals") "In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)") -AnnotationAssertion(Annotation( "NCBITaxon:32523") Annotation( "Romer") Annotation( "Wikipedia:Thyroid_gland#Other_animals") "In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species") AnnotationAssertion( "AAO:0010544") AnnotationAssertion( "BTO:0001379") AnnotationAssertion( "CALOHA:TS-1047") @@ -158014,22 +155696,18 @@ AnnotationAssertion( "thyroid gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Endostyle") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pontine raphe nucleus) AnnotationAssertion(Annotation( "Wikipedia:Pontine_raphe_nucleus") "The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BAMS:PnR") AnnotationAssertion( "BAMS:RA-PONS") AnnotationAssertion( "BAMS:RPn") @@ -158054,20 +155732,15 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pontine raphe nucleus") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (lung) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Respiration organ that develops as an outpocketing of the esophagus.") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-9415-5104") Annotation( "https://github.com/obophenotype/uberon/issues/701") ) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-9415-5104") Annotation( "https://github.com/obophenotype/uberon/issues/701") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010567") Annotation( "AAO") Annotation( "AAO:SBH") "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000310") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)") Annotation( "http://bgee.unil.ch/") "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]") -AnnotationAssertion( "pulmonary") -AnnotationAssertion( "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi") AnnotationAssertion( "AAO:0000275") AnnotationAssertion( "AAO:0010567") AnnotationAssertion( "BTO:0000763") @@ -158087,7 +155760,6 @@ AnnotationAssertion( "NCIT:C12468") AnnotationAssertion( "SCTID:181216001") AnnotationAssertion(Annotation( "ncithesaurus:Lung") "UMLS:C0024109") -AnnotationAssertion( "VHOG:0000310") AnnotationAssertion( "Wikipedia:Lung") AnnotationAssertion( "XAO:0000119") AnnotationAssertion( "galen:Lung") @@ -158106,9 +155778,11 @@ AnnotationAssertion(rdfs:seeAlso AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "some species only have a single lung") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -158118,7 +155792,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ZFA:0005249") "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.") AnnotationAssertion( "see also: vascular system. Consider merging?") AnnotationAssertion( ) -AnnotationAssertion( "vascular") AnnotationAssertion( "BTO:0003718") AnnotationAssertion( "FMA:69050") AnnotationAssertion( "TAO:0005249") @@ -158140,16 +155813,11 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (embryonic structure) AnnotationAssertion(Annotation( "BTO:0000174") Annotation( "ZFIN:curator") "Anatomical structure that is part of an embryo.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000138") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001105") Annotation( "TAO") Annotation( "ZFIN:curator") "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000178") Annotation( "VSAO") Annotation( "ZFIN:curator") "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]") -AnnotationAssertion(Annotation( "FMA") "in FMA embryo is_a embryonic structure") AnnotationAssertion( "AAO:0000138") AnnotationAssertion( "BILA:0000034") AnnotationAssertion( "BTO:0000174") AnnotationAssertion( "CALOHA:TS-2110") AnnotationAssertion( "EFO:0000461") -AnnotationAssertion(Annotation( ) "FBbt:00004208") AnnotationAssertion( "FMA:69067") AnnotationAssertion( "GAID:407") AnnotationAssertion( "MESH:D004628") @@ -158173,6 +155841,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of bronchiole) @@ -158196,8 +155866,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "BTO") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -158218,6 +155889,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adrenal gland capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -158244,7 +155920,6 @@ AnnotationAssertion( "zona glomerulosa of adrenal gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -158268,11 +155943,12 @@ AnnotationAssertion( "inferior suprarenal artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (phrenic artery) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An artery that supplies the diaphragm.") -AnnotationAssertion( "In humans this includes the superior and inferior phrenic arteries") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37108") AnnotationAssertion( "FMA:69330") AnnotationAssertion( "MA:0002019") @@ -158283,11 +155959,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phrenic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (femoral artery) AnnotationAssertion(Annotation( "Wikipedia:Femoral_artery") "The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010222") Annotation( "AAO") Annotation( "AAO:BJB") "Artery which supplies blood via branches to the hindlimbs.[AAO]") AnnotationAssertion( "AAO:0010222") AnnotationAssertion( "BTO:0001624") AnnotationAssertion( "CALOHA:TS-0321") @@ -158313,7 +155990,6 @@ SubClassOf(Annotation( "FMA # Class: (truncus arteriosus) AnnotationAssertion(Annotation( "Wikipedia:Truncus_arteriosus_(embryology)") "The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.") -AnnotationAssertion(Annotation( "ncit") "assume spelling error for ncit") AnnotationAssertion( "EHDAA2:0004143") AnnotationAssertion( "EMAPA:35887") AnnotationAssertion( "FMA:70301") @@ -158330,6 +156006,7 @@ AnnotationAssertion( "truncus arteriosus") SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -158337,16 +156014,12 @@ SubClassOf(Annotation( "EHD # Class: (endocardial cushion) AnnotationAssertion(Annotation( "GO:0003197") Annotation( "Wikipedia:Atrioventricular_cushions") Annotation( "ZFIN:curator") "The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001317") Annotation( "TAO") Annotation( "ZFIN:curator") "Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001317") Annotation( "TAO") "relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000932") Annotation( "VHOG") Annotation( "DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3") Annotation( "http://bgee.unil.ch/") "(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000434") AnnotationAssertion( "EHDAA2:0004028") AnnotationAssertion( "EHDAA:2586") AnnotationAssertion( "EMAPA:16696") AnnotationAssertion( "FMA:70302") AnnotationAssertion( "MA:0000078") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054089") AnnotationAssertion( "TAO:0001317") AnnotationAssertion( "VHOG:0000932") AnnotationAssertion( "Wikipedia:Atrioventricular_cushions") @@ -158366,22 +156039,15 @@ AnnotationAssertion( "GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form") AnnotationAssertion(rdfs:label "endocardial cushion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png"^^xsd:anyURI) -SubClassOf(Annotation( "GO") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Wikipedia") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) # Class: (sinus venosus) AnnotationAssertion(Annotation( "PMID:20735616") Annotation( "Wikipedia:Sinus_venosus") "The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000154") Annotation( "TAO") Annotation( "ZFIN:curator") "Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010505") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000177") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428") Annotation( "http://bgee.unil.ch/") "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]") -AnnotationAssertion( "In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]") -AnnotationAssertion( "In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu") -AnnotationAssertion(Annotation( "ZFA:0000154") "In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract") AnnotationAssertion(Annotation( "ZFA:0000154") "inflow tract") AnnotationAssertion( "AAO:0010505") AnnotationAssertion( "EHDAA2:0001839") @@ -158445,17 +156111,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (dermis) AnnotationAssertion(Annotation( "Wikipedia:Dermis") Annotation( "ZFIN:curator") "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].") AnnotationAssertion( "Consider adding a layer-of-skin grouping class for all skin layers") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001119") Annotation( "TAO") Annotation( "ZFIN:curator") "A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000108") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1") Annotation( "http://bgee.unil.ch/") "When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]") -AnnotationAssertion( "dermal") AnnotationAssertion( "AAO:0000128") AnnotationAssertion( "BTO:0000294") AnnotationAssertion( "CALOHA:TS-2076") @@ -158488,15 +156150,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratum granulosum of epidermis) @@ -158520,24 +156184,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratum granulosum of epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypodermis) AnnotationAssertion(Annotation( "Wikipedia:Hypodermis") "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001136") Annotation( "TAO") Annotation( "ZFIN:curator") "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "FMA:70544") "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].") -AnnotationAssertion( "hypodermal") -AnnotationAssertion( "subcutaneous") -AnnotationAssertion( "subcutaneus") -AnnotationAssertion(Annotation( "BTO") "BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.") AnnotationAssertion( "BTO:0001314") AnnotationAssertion( "CALOHA:TS-2366") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37505") AnnotationAssertion( "FMA:70544") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D040521") AnnotationAssertion( "NCIT:C33645") AnnotationAssertion( "TAO:0001136") AnnotationAssertion(Annotation( "ncithesaurus:Subcutis") "UMLS:C0278403") @@ -158559,11 +156219,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hypodermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-modified") ObjectSomeValuesFrom( )) @@ -158571,7 +156232,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "Wikipedia:Hair_follicle") "A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001268") Annotation( "VHOG") Annotation( "ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3") Annotation( "http://bgee.unil.ch/") "The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG]") AnnotationAssertion( "BTO:0000554") AnnotationAssertion( "CALOHA:TS-0432") AnnotationAssertion( "EFO:0002464") @@ -158623,13 +156283,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair shaft") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "DOI:10.1016/j.cub.2008.12.005") ObjectSomeValuesFrom( )) # Class: (viscus) AnnotationAssertion(Annotation( "BTO:0001491") Annotation( "Wikipedia:Viscus") Annotation( "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14") "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010386") Annotation( "AAO") Annotation( "BTO:0001491") "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]") -AnnotationAssertion(Annotation( "FMA") "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.") AnnotationAssertion( "AAO:0010386") AnnotationAssertion( "BTO:0001491") AnnotationAssertion( "EHDAA:512") @@ -158656,7 +156315,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "viscus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cuticle of hair) @@ -158670,7 +156330,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cuticle of hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortex of hair) @@ -158690,15 +156353,13 @@ AnnotationAssertion( "cortex of hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right cardiac atrium) AnnotationAssertion(Annotation( "Wikipedia:Right_atrium") Annotation( "http://orcid.org/0000-0002-6601-2165") "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:7096") "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000328") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "AAO:0010248") AnnotationAssertion( "BTO:0001703") AnnotationAssertion( "EHDAA2:0000290") @@ -158728,16 +156389,14 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left cardiac atrium) AnnotationAssertion(Annotation( "Wikipedia:Left_atrium") Annotation( "http://orcid.org/0000-0002-6601-2165") "A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:7097") "Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]") -AnnotationAssertion(Annotation( "XAO:EJS") "The chamber of the heart that receives blood from the lungs[XAO:EJS].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000369") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "AAO:0010247") AnnotationAssertion( "BTO:0001702") AnnotationAssertion( "EHDAA2:0000275") @@ -158767,15 +156426,14 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart right ventricle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A cardiac ventricle that is in the right side of the heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000717") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "In mammals continuous with the pulmonary arteries") AnnotationAssertion( "BTO:0001630") AnnotationAssertion( "CALOHA:TS-0443") AnnotationAssertion( "EHDAA2:0000196") @@ -158803,6 +156461,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:17276708") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -158810,9 +156470,6 @@ SubClassOf(Annotation( "cjm # Class: (cardiac atrium) AnnotationAssertion(Annotation( "Wikipedia:Heart_atrium") Annotation( "http://orcid.org/0000-0002-6601-2165") "Cardiac chamber in which blood enters the heart.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000471") Annotation( "TAO") Annotation( "ZFIN:curator") "One of four heart chambers.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010246") Annotation( "AAO") Annotation( "AAO:BJB") "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000175") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428") Annotation( "http://bgee.unil.ch/") "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]") AnnotationAssertion( "AAO:0010246") AnnotationAssertion( "BTO:0000903") AnnotationAssertion( "CALOHA:TS-0437") @@ -158854,9 +156511,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cardiac ventricle) AnnotationAssertion(Annotation( "Wikipedia:Ventricle_(heart)") Annotation( "http://orcid.org/0000-0002-6601-2165") "Cardiac chamber through which blood leaves the heart.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010249") Annotation( "AAO") Annotation( "AAO:BJB") "A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000009") Annotation( "TAO") Annotation( "ZFIN:curator") "One of four heart chambers.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000435") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428") Annotation( "http://bgee.unil.ch/") "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]") AnnotationAssertion( "ventricle") AnnotationAssertion( "AAO:0010249") AnnotationAssertion( "BTO:0000862") @@ -158898,10 +156552,6 @@ SubClassOf(Annotation( "Bge AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A cardiac ventricle that is in the left side of the heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000718") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000718") Annotation( "VHOG") Annotation( "DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)") Annotation( "http://bgee.unil.ch/") "The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "In mammals continuous with aorta") AnnotationAssertion( "BTO:0001629") AnnotationAssertion( "CALOHA:TS-0439") AnnotationAssertion( "EHDAA2:0002178") @@ -158929,6 +156579,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) @@ -158936,8 +156588,6 @@ SubClassOf(Annotation( "GO" # Class: (interatrial septum) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A cardiac septum that divides the left and right atria of the heart.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000385") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/interatrial+septum") "The partition separating the right and left atria of the heart. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000385") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000838") AnnotationAssertion( "EHDAA:1896") AnnotationAssertion( "EMAPA:17011") @@ -158959,6 +156609,9 @@ AnnotationAssertion( "interatrial septum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracodorsal vein) @@ -158972,26 +156625,22 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracodorsal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA/obol") ObjectSomeValuesFrom( )) # Class: (postcranial axial skeleton) AnnotationAssertion(Annotation( "ZFA:0000317") Annotation( "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957") Annotation( "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834") "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000093") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000034") Annotation( "AAO") Annotation( "AAO:LAP") "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000317") Annotation( "TAO") Annotation( "ZFIN:curator") "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000317") Annotation( "VHOG") Annotation( "DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)") Annotation( "http://bgee.unil.ch/") "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]") AnnotationAssertion(Annotation( "FMA:71221") Annotation( "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton") "axial skeleton") AnnotationAssertion( "AAO:0000034") AnnotationAssertion( "EFO:0000942") AnnotationAssertion( "EHDAA2:0000161") AnnotationAssertion( "EHDAA:5049") -AnnotationAssertion( "EMAPA:17214") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37721") AnnotationAssertion( "FMA:71221") AnnotationAssertion( "MA:0002986") AnnotationAssertion( "MAT:0000148") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D013131") AnnotationAssertion( "MIAA:0000148") AnnotationAssertion( "TAO:0000317") AnnotationAssertion( "VHOG:0000317") @@ -159017,10 +156666,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "Wikipedia:Appendicular_skeleton") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000076") Annotation( "VSAO") Annotation( "PSPUB:0000170") Annotation( "https://orcid.org/0000-0002-6601-2165") "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000027") Annotation( "TAO") Annotation( "TAO:wd") "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000747") Annotation( "AAO") Annotation( "AAO:LAP") "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]") -AnnotationAssertion(Annotation( "FMA") "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.") AnnotationAssertion( "AAO:0000747") AnnotationAssertion( "EFO:0000951") AnnotationAssertion( "EMAPA:32729") @@ -159031,7 +156676,6 @@ AnnotationAssertion( "NCIT:C49477") AnnotationAssertion( "SCTID:322050006") AnnotationAssertion(Annotation( "ncithesaurus:Appendicular_Skeleton") "UMLS:C0222646") -AnnotationAssertion( "VHOG:0001666") AnnotationAssertion( "VSAO:0000076") AnnotationAssertion( "Wikipedia:Appendicular_skeleton") AnnotationAssertion( "XAO:0003166") @@ -159058,10 +156702,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (brain dura mater) AnnotationAssertion(Annotation( "MP:0009025") "The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000270") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000270") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:32668") -AnnotationAssertion( "EV:0100313") AnnotationAssertion( "FMA:71236") AnnotationAssertion( "MA:0000815") AnnotationAssertion( "NCIT:C49332") @@ -159078,12 +156719,11 @@ AnnotationAssertion( "brain dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (spinal dura mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A dura mater that is part of a spinal cord [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000411") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000411") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17806") AnnotationAssertion( "FMA:71237") AnnotationAssertion( "MA:0001132") @@ -159102,14 +156742,12 @@ AnnotationAssertion( "spinal dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (interventricular septum) AnnotationAssertion(Annotation( "FMA:7133") "Cardiac septum which separates the right ventricle from the left ventricle.[FMA].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000386") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/interventricular+septum") "The partition separating the right and left ventricles of the heart. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000386") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430") Annotation( "http://bgee.unil.ch/") "The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]") -AnnotationAssertion(Annotation( "ISBN:0124020607") "involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)") AnnotationAssertion( "BTO:0002483") AnnotationAssertion( "EFO:0001956") AnnotationAssertion( "EHDAA:2603") @@ -159143,12 +156781,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery) AnnotationAssertion(Annotation( "FMA:7144") Annotation( "Wikipedia:Mesentery") Annotation( "Wikipedia:Mesentery#Mesentery_.28general.29") Annotation( "https://github.com/obophenotype/uberon/issues/85") "Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon.") -AnnotationAssertion( "mesenteric") -AnnotationAssertion(Annotation( "FMA") "in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery.") AnnotationAssertion( "AAO:0011061") AnnotationAssertion( "BTO:0001380") AnnotationAssertion( "EV:0100083") @@ -159175,9 +156814,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (skin of body) AnnotationAssertion(Annotation( "UBERON:cjm") "The organ covering the body that consists of the dermis and epidermis.") -AnnotationAssertion( "consider 'integumentary system' for invertebrates") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "MA uses the term skin to refer to what is called here: zone of skin") AnnotationAssertion( "BTO:0001253") AnnotationAssertion( "CALOHA:TS-0934") AnnotationAssertion( "EFO:0000962") @@ -159212,7 +156849,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159220,8 +156859,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cardiac septum) AnnotationAssertion(Annotation( "MESH:A07.541.459") "The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.") -AnnotationAssertion( "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'") -AnnotationAssertion(Annotation( "GO") "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this") AnnotationAssertion( "EMAPA:35400") AnnotationAssertion( "FMA:7180") AnnotationAssertion( "GAID:562") @@ -159242,6 +156879,7 @@ AnnotationAssertion( "cardiac septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159249,10 +156887,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (trunk) AnnotationAssertion(Annotation( "TAO:0001115") Annotation( "UBERONREF:0000006") Annotation( "Wikipedia:Torso") "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.") -AnnotationAssertion(Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010339") Annotation( "AAO") Annotation( "AAO:BJB") "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001115") Annotation( "TAO") Annotation( "ZFIN:curator") "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]") AnnotationAssertion( "AAO:0010339") AnnotationAssertion( "BILA:0000116") AnnotationAssertion( "BTO:0001493") @@ -159290,8 +156924,6 @@ DisjointClasses( (limb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010336") Annotation( "AAO") Annotation( "AAO:BJB") "Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000336") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") AnnotationAssertion( "AAO:0010336") AnnotationAssertion( "AEO:0000172") AnnotationAssertion( "CALOHA:TS-0552") @@ -159304,7 +156936,6 @@ AnnotationAssertion( "GAID:36") AnnotationAssertion( "MA:0000007") AnnotationAssertion( "MAT:0000090") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005121") AnnotationAssertion( "MIAA:0000090") AnnotationAssertion( "NCIT:C12429") AnnotationAssertion( "SCTID:243996003") @@ -159328,18 +156959,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Sarcopterygians") ) +SubClassOf( ) SubClassOf(Annotation( "extends to stem tetrapods such as Eusthenopteron") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts.") -AnnotationAssertion( "Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000205") Annotation( "AAO") Annotation( "AAO:LAP") "Upper limb, which connects the manus with the pectoral girdle.[AAO]") -AnnotationAssertion(Annotation( "FMA") "note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb") AnnotationAssertion( "AAO:0000205") AnnotationAssertion( "BTO:0001729") AnnotationAssertion( "CALOHA:TS-2214") @@ -159382,19 +157010,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "Wikipedia:Hindlimb") Annotation( "Wikipedia:Lower_limb") "A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000219") Annotation( "AAO") Annotation( "AAO:LAP") "Lower limb, which connects the pes with the pelvic girdle.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000337") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "crural") -AnnotationAssertion(Annotation( "FMA") "note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton") AnnotationAssertion( "AAO:0000219") AnnotationAssertion( "BTO:0002345") AnnotationAssertion( "CALOHA:TS-2215") @@ -159439,15 +157064,15 @@ AnnotationAssertion( "hindlimb") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (visual system) AnnotationAssertion(Annotation( "NIFSTD:FMAID_7191") "The sensory system subserving the sense of vision.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000632") Annotation( "AAO") Annotation( "AAO:EJS") "The sensory system used for sight.[AAO]") AnnotationAssertion( "UBERON:0007036") AnnotationAssertion( "AAO:0000632") AnnotationAssertion( "BILA:0000140") @@ -159476,9 +157101,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (vestibulo-auditory system) AnnotationAssertion(Annotation( "ZFA:0001138") "Sensory system responsible for the perception of spatial orientation and auditory stimuli.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000631") Annotation( "AAO") Annotation( "AAO:EJS") "The sensory system used for balance and hearing.[AAO]") AnnotationAssertion( "AAO:0000631") -AnnotationAssertion( "EMAPA:36002") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37985") AnnotationAssertion( "FMA:78500") AnnotationAssertion( "TAO:0001138") @@ -159504,13 +157127,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000689") "The organ that functions to filter blood and to store red corpuscles and platelets.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010395") Annotation( "AAO") Annotation( "AAO:BMZ") "An organ involved in red blood cell filtration and immune response.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000120") Annotation( "VHOG") Annotation( "ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94") Annotation( "http://bgee.unil.ch/") "With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]") -AnnotationAssertion( "lienal") -AnnotationAssertion( "splenic") -AnnotationAssertion( "In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron") -AnnotationAssertion(Annotation( "PMID:20959416") "Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)") -AnnotationAssertion( "It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells") AnnotationAssertion( "AAO:0010395") AnnotationAssertion( "BTO:0001281") AnnotationAssertion( "CALOHA:TS-0956") @@ -159546,12 +157162,9 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "multiple sources - true spleen appear in jawed vertebrates") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159559,14 +157172,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0000759") Annotation( "Wikipedia:Liver") "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010111") Annotation( "AAO") Annotation( "AAO:BJB") "Organ which secretes bile and participates in formation of certain blood proteins.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010111") Annotation( "AAO") "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000257") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]") -AnnotationAssertion( "hepatic") -AnnotationAssertion( "An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).") -AnnotationAssertion( "The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.") -AnnotationAssertion( "secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].") -AnnotationAssertion(Annotation( "ZFA") "Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.") AnnotationAssertion( "AAO:0010111") AnnotationAssertion( "BTO:0000759") AnnotationAssertion( "CALOHA:TS-0564") @@ -159606,15 +157211,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg"^^xsd:anyURI) SubClassOf(Annotation( "BTO") Annotation( "EHDAA2") Annotation( "GO-def") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA-weakened") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://www.stembook.org/node/512") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159627,8 +157230,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Small_intestine") "Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001323") Annotation( "TAO") Annotation( "ZFIN:curator") "The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000055") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566") Annotation( "http://bgee.unil.ch/") "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]") AnnotationAssertion( "AAO:0010397") AnnotationAssertion( "BTO:0000651") AnnotationAssertion( "CALOHA:TS-0942") @@ -159668,8 +157269,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "2") Annotation( "cjm") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159678,7 +157279,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Nares") "Pair of nostrils.") AnnotationAssertion(Annotation( "http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html") ) -AnnotationAssertion(Annotation( "FMA") "this is a 'set of anatomical planes' in FMA") AnnotationAssertion( "FMA:72005") AnnotationAssertion( "Wikipedia:Nares") AnnotationAssertion( "nares set") @@ -159691,8 +157291,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pair of nares") EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gallbladder) @@ -159700,10 +157302,6 @@ AnnotationAssertion(Annotation( "ISBN:9780120749034") ) AnnotationAssertion(Annotation( "GOC:mr") Annotation( "ISBN:9781840761122") ) AnnotationAssertion(Annotation( "GOC:mr") Annotation( "ISBN:9781840761122") ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000221") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010114") Annotation( "AAO") Annotation( "AAO:BJB") "Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010114") Annotation( "AAO") "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000221") Annotation( "VHOG") Annotation( "DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)") Annotation( "http://bgee.unil.ch/") "The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]") AnnotationAssertion( "AAO:0010114") AnnotationAssertion( "BTO:0000493") AnnotationAssertion( "CALOHA:TS-0394") @@ -159741,13 +157339,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "gallbladder") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA") Annotation( "ZFA") Annotation( "cjm") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (artery smooth muscle tissue) @@ -159769,7 +157367,9 @@ AnnotationAssertion(Annotation( "UBERON:0002111") AnnotationAssertion(rdfs:label "artery smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle of esophagus) @@ -159812,26 +157412,17 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (kidney) -AnnotationAssertion(Annotation( "Wikipedia:Kidney") Annotation( "http://anatomy.uams.edu/anatomyhtml/kidney.html") "A paired organ of the urinary tract which has the production of urine as its primary function.") -AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:25140012") Annotation( "PMID:35003210") Annotation( "Wikipedia:Kidney") Annotation( "http://anatomy.uams.edu/anatomyhtml/kidney.html") Annotation( "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do") "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000250") Annotation( "AAO") Annotation( "AAO:BJB") "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]") -AnnotationAssertion( "renal") -AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "AAO:0000250") AnnotationAssertion( "BTO:0000671") AnnotationAssertion( "CALOHA:TS-0510") -AnnotationAssertion( "EFO:0000929") -AnnotationAssertion( "EMAPA:17373") -AnnotationAssertion( "EV:0100096") -AnnotationAssertion( "FMA:7203") AnnotationAssertion( "GAID:423") -AnnotationAssertion( "MA:0000368") AnnotationAssertion( "MAT:0000119") AnnotationAssertion( "MESH:D007668") AnnotationAssertion( "MIAA:0000119") -AnnotationAssertion( "NCIT:C12415") -AnnotationAssertion( "SCTID:181414000") AnnotationAssertion(Annotation( "ncithesaurus:Kidney") "UMLS:C0022646") AnnotationAssertion( "Wikipedia:Kidney") AnnotationAssertion( "XAO:0003267") @@ -159848,11 +157439,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159861,10 +157453,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0815318960") Annotation( "Wikipedia:Duodenum") "The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).") AnnotationAssertion(Annotation( "ZFA:0000348") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000052") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion( "duodenal") -AnnotationAssertion(Annotation( "NCBITaxon:32443") Annotation( "Wikipedia:Duodenum") "In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.") -AnnotationAssertion(Annotation( "NCBITaxon:9606") Annotation( "Wikipedia:Duodenum") "In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.") AnnotationAssertion( "AAO:0010402") AnnotationAssertion( "BTO:0000365") AnnotationAssertion( "CALOHA:TS-0214") @@ -159897,7 +157485,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb"^^xsd:anyURI) -SubClassOf(Annotation( "3") Annotation( "cjm") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159908,9 +157496,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:monikat") Annotation( "MP:0004002") "The portion of the small intestine that extends from the duodenum to the ileum.") AnnotationAssertion( "TODO consider ZFA:0001323 mid intestine, see also small intestine") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000053") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion( "jejunal") -AnnotationAssertion( "The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]") AnnotationAssertion( "BTO:0000657") AnnotationAssertion( "CALOHA:TS-0496") AnnotationAssertion( "EFO:0001333") @@ -159941,7 +157526,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb"^^xsd:anyURI) -SubClassOf(Annotation( "3") Annotation( "cjm") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159951,9 +157536,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:csmith") Annotation( "MP:0002581") "The portion of the small intestine that extends from the jejunum to the colon.") AnnotationAssertion( "TODO consider ZFA:0000706 posterior intestine, see also colon") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000647") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") -AnnotationAssertion( "ileal") -AnnotationAssertion( "The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]") AnnotationAssertion( "AAO:0010403") AnnotationAssertion( "BTO:0000620") AnnotationAssertion( "CALOHA:TS-0472") @@ -159987,14 +157569,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb"^^xsd:anyURI) -SubClassOf(Annotation( "3") Annotation( "cjm") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right ovary) AnnotationAssertion(Annotation( "OBOL:automatic") "An ovary that is part of a right side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37367") AnnotationAssertion( "FMA:7213") AnnotationAssertion( "MA:0001705") @@ -160005,12 +157586,13 @@ AnnotationAssertion( "UBERON:0002118") AnnotationAssertion(rdfs:label "right ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left ovary) AnnotationAssertion(Annotation( "OBOL:automatic") "An ovary that is part of a left side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion(Annotation( "Wikipedia:Ovary#In_other_animals") "In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37366") AnnotationAssertion( "FMA:7214") AnnotationAssertion( "MA:0001704") @@ -160021,15 +157603,13 @@ AnnotationAssertion( "UBERON:0002119") AnnotationAssertion(rdfs:label "left ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephros) AnnotationAssertion(Annotation( "GO:0048793") Annotation( "Wikipedia:Pronephros") "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000037") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011089") Annotation( "AAO") Annotation( "XAO:curator") "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000151") Annotation( "TAO") Annotation( "ZFIN:curator") "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000037") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637") Annotation( "http://bgee.unil.ch/") "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]") -AnnotationAssertion( "pronephric") AnnotationAssertion( "UBERON:0005794") AnnotationAssertion( "AAO:0011089") AnnotationAssertion( "BTO:0001541") @@ -160039,7 +157619,6 @@ AnnotationAssertion( "EMAPA:16579") AnnotationAssertion( "FMA:72170") AnnotationAssertion( "MAT:0000117") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D060910") AnnotationAssertion( "MIAA:0000117") AnnotationAssertion( "NCIT:C34280") AnnotationAssertion( "SCTID:308804007") @@ -160061,9 +157640,9 @@ AnnotationAssertion( "Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104") AnnotationAssertion(rdfs:label "pronephros") SubClassOf(Annotation( "GO") ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "OG") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160085,14 +157664,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capsule of thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortex of thymus) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0002371") "The outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes.") AnnotationAssertion(Annotation( "DOI:10.1177/0192623311409597") ) AnnotationAssertion( ) -AnnotationAssertion( "Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP]") AnnotationAssertion( "BTO:0002934") AnnotationAssertion( "EMAPA:35863") AnnotationAssertion( "FMA:72205") @@ -160109,6 +157689,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortex of thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160137,6 +157721,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "medulla of thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -160144,8 +157729,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "ncithesaurus:Thymic_Lobule") "A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified].") AnnotationAssertion( ) -AnnotationAssertion( "in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]") -AnnotationAssertion( "Lymphocytes, reticular cells and macrophages are found in the lobules") AnnotationAssertion( "FMA:72215") AnnotationAssertion( "MA:0000770") AnnotationAssertion( "NCIT:C33772") @@ -160160,6 +157743,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus lobule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160169,11 +157755,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (superior olivary complex) AnnotationAssertion(Annotation( "ISBN:0-19-502694-2") Annotation( "Wikipedia:Superior_olivary_complex") "A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion( "In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]") -AnnotationAssertion( "The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.") AnnotationAssertion( "BAMS:SOC") AnnotationAssertion( "BIRNLEX:1307") AnnotationAssertion( "DHBA:12462") @@ -160183,7 +157764,6 @@ AnnotationAssertion( "HBA:9177") AnnotationAssertion( "MA:0001026") AnnotationAssertion( "MBA:398") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D065832") AnnotationAssertion(Annotation( "BIRNLEX:1307") "UMLS:C0175427") AnnotationAssertion( "VHOG:0001381") AnnotationAssertion( "Wikipedia:Superior_olivary_complex") @@ -160200,15 +157780,14 @@ AnnotationAssertion( "superior olivary complex") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebellar cortex) AnnotationAssertion(Annotation( "BIRNLEX:1566") "The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer.") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "GO:0021695") "The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695].") AnnotationAssertion( "BAMS:CB") AnnotationAssertion( "BAMS:CBX") AnnotationAssertion( "BAMS:CbCx") @@ -160244,7 +157823,7 @@ AnnotationAssertion( "The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia)") AnnotationAssertion(rdfs:label "cerebellar cortex") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160252,7 +157831,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (subcommissural organ) AnnotationAssertion(Annotation( "PMID:9579598") Annotation( "Wikipedia:Subcommissural_organ") "The subcommissural organ is a circumventricular organ consisting of ependymal and hypendymal cells which secrete SCO-spondin[WP,partially vetted].") -AnnotationAssertion( "Hypendymal cells being part of the subcommissural organ is not axiomatized as it is rare in non-mammals. Consider using GCIs if this axiom needs to be added.") AnnotationAssertion(Annotation( "multiple") ) AnnotationAssertion( "BAMS:SCO") AnnotationAssertion( "BIRNLEX:1028") @@ -160285,6 +157863,7 @@ AnnotationAssertion( "DOI:10.1002/ar.1091260210") Annotation( "DOI:10.1007/BF00303086") Annotation( "PMID:479574") Annotation( "PMID:9579598") rdfs:comment "Occurs throughout the vertebartes [PMID:9579598, DOI:10.1002/ar.1091260210]. First appears in hagfish(Olsson). In many species, including the human, it reaches its full development during embryonic life[PMID:9579598]. During the course of phyletic evolution, one notes various changes. Indeed, in lower vertebrates, the SCO presents a greater degree of enzyme activity than the ependyma while in birds the ependyma demonstrates a more intense activity than the SCO[PMID:479574] Sometimes preceded by flexural organ[DOI:10.1007/BF00303086]. Hypendymal cells are rare in non-mammals [PMID:9579598].") AnnotationAssertion(rdfs:label "subcommissural organ") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160295,10 +157874,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GAID:577") Annotation( "GO:0021703") Annotation( "Wikipedia:Locus_ceruleus") "The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].") AnnotationAssertion( "TODO - check ZFA/pons. also GO says part of dorsorostral pons") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BAMS:CAE") AnnotationAssertion( "BAMS:LC") AnnotationAssertion( "BIRNLEX:905") @@ -160343,23 +157918,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "locus ceruleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "check ZFA") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (superior salivatory nucleus) AnnotationAssertion(Annotation( "BIRNLEX:1131") "Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BAMS:SSN") AnnotationAssertion( "BAMS:SuS") AnnotationAssertion( "BIRNLEX:1131") @@ -160386,16 +157953,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocardium) AnnotationAssertion(Annotation( "GO:0003157") "The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001320") Annotation( "TAO") Annotation( "ZFIN:curator") "Layer that lines the lumen of the heart.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010408") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]") -AnnotationAssertion(Annotation( "FMA:7280") "Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.") AnnotationAssertion( "UBERON:0006225") AnnotationAssertion( "AAO:0010408") AnnotationAssertion( "BTO:0000387") @@ -160433,7 +157997,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "endocardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) @@ -160471,8 +158035,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (right lung) AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "Wikipedia:Right_lung") "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000301") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210") Annotation( "http://bgee.unil.ch/") "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0001730") AnnotationAssertion( "EHDAA:4969") AnnotationAssertion( "EMAPA:17661") @@ -160492,12 +158054,12 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lung) AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "Wikipedia:Left_lung") "Lung which consists of the left upper lobe and left lower lobe.[FMA].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000618") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210") Annotation( "http://bgee.unil.ch/") "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0000943") AnnotationAssertion( "EHDAA:4947") AnnotationAssertion( "EMAPA:17653") @@ -160517,6 +158079,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alveolar sac) @@ -160539,6 +158103,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alveolar sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160548,7 +158115,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:cwg") Annotation( "MP:0002271") "The respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli.") AnnotationAssertion( ) -AnnotationAssertion( "In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation") AnnotationAssertion( "EMAPA:32694") AnnotationAssertion( "FMA:7341") AnnotationAssertion( "MA:0000417") @@ -160565,8 +158131,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary alveolar duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventral funiculus of spinal cord) @@ -160594,13 +158159,13 @@ AnnotationAssertion( "ventral funiculus of spinal cord") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (lobar bronchus) AnnotationAssertion(Annotation( "GO:0060482") Annotation( "Wikipedia:Secondary_bronchus") "The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi[GO].") AnnotationAssertion( ) -AnnotationAssertion( "They have relatively large lumens that are lined by respiratory epithelium. There is a smooth muscle layer below the epithelium arranged as two ribbons of muscle that spiral in opposite directions. This smooth muscle layer contains seromucous glands. Irregularly arranged plates of hyaline cartilage surround the smooth muscle. These plates give structural support to the bronchus and maintain the patency of the lumen.") AnnotationAssertion( "EHDAA:4955") AnnotationAssertion( "EHDAA:4963") AnnotationAssertion( "EHDAA:4977") @@ -160629,7 +158194,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lobar bronchus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160663,7 +158228,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -160677,9 +158242,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-397-51047-0") Annotation( "MESH:A04.411.125") Annotation( "MGI:cwg") Annotation( "MP:0002264") "The upper conducting airways of the lung; these airways arise from the terminus of the trachea.") AnnotationAssertion(Annotation( "Wikipedia") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000262") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion( "bronchial") -AnnotationAssertion( "In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue") AnnotationAssertion( "BTO:0001340") AnnotationAssertion( "CALOHA:TS-1229") AnnotationAssertion( "EFO:0000932") @@ -160718,9 +158280,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (bronchiole) AnnotationAssertion(Annotation( "ISBN:0-397-51047-0") Annotation( "MGI:cwg") Annotation( "MP:0002267") "The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching.") -AnnotationAssertion( "bronchiolar") -AnnotationAssertion(Annotation( "ISBN:0123813611") "lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer") -AnnotationAssertion(Annotation( "FMA") "In FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however, there are two distinct terms for the corresponding epithelium.") AnnotationAssertion( "BTO:0002375") AnnotationAssertion( "CALOHA:TS-2003") AnnotationAssertion( "EHDAA:8171") @@ -160730,7 +158289,6 @@ AnnotationAssertion( "EMAPA:32697") AnnotationAssertion( "FMA:7410") AnnotationAssertion( "MA:0000422") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D055745") AnnotationAssertion( "NCIT:C12684") AnnotationAssertion( "SCTID:278982001") AnnotationAssertion(Annotation( "ncithesaurus:Bronchiole") "UMLS:C0006270") @@ -160780,7 +158338,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0123813611") Annotation( "Wikipedia:Respiratory_bronchiole") "A bronchiole that is the first segment of the respiratory zone.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ISBN:0123813611") "mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts") AnnotationAssertion( "BTO:0003222") AnnotationAssertion( "EMAPA:35729") AnnotationAssertion( "FMA:7412") @@ -160808,14 +158365,12 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A portion of adipose tissue that is part of the hypodermis, beneath the dermis.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MP:0011156") "the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]") AnnotationAssertion( "UBERON:0008875") AnnotationAssertion(Annotation( "MP:0011156") "panniculus adiposus") AnnotationAssertion( "BTO:0004042") AnnotationAssertion( "EMAPA:35829") AnnotationAssertion( "FMA:74315") AnnotationAssertion( "MA:0000473") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D015434") AnnotationAssertion(Annotation( "FMA:74315") "fatty layer of subcutaneous tissue") AnnotationAssertion(Annotation( "MP:0011156") "hypodermis fat layer") AnnotationAssertion(Annotation( "FMA:74315") Annotation( "FMA:TA") Annotation( ) "panniculus adiposus (tela subcutanea)") @@ -160829,18 +158384,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subcutaneous adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (subiculum) AnnotationAssertion(Annotation( "BIRNLEX:1305") "Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion( "subicular") -AnnotationAssertion( "The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]") -AnnotationAssertion(Annotation( "ABA") "In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region") -AnnotationAssertion( "in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum") AnnotationAssertion( "BAMS:S") AnnotationAssertion( "BAMS:SUB") AnnotationAssertion( "BIRNLEX:1305") @@ -160896,7 +158447,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Lymph_node#Capsule") "Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers.") AnnotationAssertion( ) -AnnotationAssertion( "from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP]") AnnotationAssertion( "EMAPA:35524") AnnotationAssertion( "FMA:74604") AnnotationAssertion( "MA:0000739") @@ -160916,6 +158466,7 @@ AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula of lymph node) @@ -160938,15 +158489,12 @@ AnnotationAssertion( "trabecula of lymph node") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adenohypophysis) AnnotationAssertion(Annotation( "Wikipedia:Adenohypophysis") Annotation( "ZFIN:curator") "The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010540") Annotation( "AAO") Annotation( "AAO:BJB") "Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001282") Annotation( "TAO") Annotation( "ZFIN:curator") "The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000141") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5") Annotation( "http://bgee.unil.ch/") "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish") -AnnotationAssertion( "While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175].") AnnotationAssertion(Annotation( "BIRNLEX:1581") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "AHP") AnnotationAssertion( "AAO:0010540") AnnotationAssertion( "BAMS:AHY") @@ -160996,8 +158544,9 @@ AnnotationAssertion( "adenohypophysis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -161012,9 +158561,6 @@ DisjointClasses(Annotation( AnnotationAssertion(Annotation( "MP:0004164") "The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon.") AnnotationAssertion(Annotation( "http://syllabus.med.unc.edu/courseware/embryo_images/") "request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'") AnnotationAssertion(Annotation( "Ariens, p. 1192") ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010537") Annotation( "AAO") Annotation( "AAO:BJB") "The infundibular part of the pituitary gland consisting of two regions.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000142") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5") Annotation( "http://bgee.unil.ch/") "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]") -AnnotationAssertion(Annotation( "EMAPA") "todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19)") AnnotationAssertion(Annotation( "BIRNLEX:1586") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "NHP") AnnotationAssertion( "AAO:0010537") AnnotationAssertion( "BAMS:NHP") @@ -161067,6 +158613,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurohypophysis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:19084529") ObjectSomeValuesFrom( )) @@ -161077,13 +158624,7 @@ SubClassOf(Annotation( "Wik # Class: (integument) AnnotationAssertion(Annotation( "Wikipedia:Integument") "The dermis, epidermis and hypodermis.") -AnnotationAssertion( "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000239") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000029") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Surface structure that is the outer protective covering of the body.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000368") Annotation( "TAO") Annotation( "ZFIN:curator") "The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]") -AnnotationAssertion( "integumental") -AnnotationAssertion( "integumentary") AnnotationAssertion( "AAO:0000239") AnnotationAssertion( "BTO:0000634") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37504") @@ -161110,6 +158651,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integument") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161140,6 +158682,7 @@ AnnotationAssertion( "vasculature of head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of trunk) @@ -161160,6 +158703,7 @@ AnnotationAssertion( "vasculature of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of trachea) @@ -161183,13 +158727,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of eye) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726") "Vasculature that is part of the eye region.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ZFA") "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA") AnnotationAssertion( "FMA:74743") AnnotationAssertion( "SCTID:123846009") AnnotationAssertion( "TAO:0007057") @@ -161210,14 +158755,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0781772214") ObjectSomeValuesFrom( )) # Class: (musculoskeletal system) AnnotationAssertion(Annotation( "VSAO:0000031") Annotation( "VSAO:curator") Annotation( "https://github.com/obophenotype/uberon/issues/77") "Anatomical system that consists of the muscular and skeletal systems.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010546") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical system that provides locomotion and physical support to the organism.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001275") Annotation( "VHOG") Annotation( "DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)") Annotation( "http://bgee.unil.ch/") "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]") -AnnotationAssertion( "musculoskeletal") AnnotationAssertion( "AAO:0010546") AnnotationAssertion( "CALOHA:TS-1311") AnnotationAssertion( "EMAPA:32714") @@ -161242,7 +158786,7 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "check ctenophore") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -161256,10 +158800,6 @@ DisjointClasses( (mammillary body) AnnotationAssertion(Annotation( "BIRNLEX:865") "One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "Hardisty, p. 320-1") ) AnnotationAssertion( ) AnnotationAssertion(Annotation( "BIRNLEX:865") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "MMB") @@ -161300,7 +158840,7 @@ AnnotationAssertion( "mammillary body") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "ABA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO definition") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161308,7 +158848,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (fibrous joint) AnnotationAssertion(Annotation( "FMA:FMA") Annotation( "Wikipedia:Fibrous_joint") "Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005156") Annotation( "TAO") Annotation( "ZFIN:curator") "A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO]") AnnotationAssertion( "AEO:0000178") AnnotationAssertion( "EHDAA2:0003178") AnnotationAssertion( "EMAPA:35344") @@ -161347,8 +158886,6 @@ SubClassOf( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/286") "A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system.") AnnotationAssertion( "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots.") -AnnotationAssertion(Annotation( "FBbt:00007602, FBC:DOS") "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS].") -AnnotationAssertion(Annotation( "FMA") "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots") AnnotationAssertion( "FMA:5981") AnnotationAssertion( "FMA:82524") AnnotationAssertion( "NCIT:C54024") @@ -161363,7 +158900,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nerve root") SubClassOf( ) -SubClassOf(Annotation(rdfs:comment "EDITOR_NOTE we do not commit to CNS or PNS to allow for flexibility with this class") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161400,6 +158936,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macula of saccule of membranous labyrinth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161422,6 +158959,7 @@ AnnotationAssertion( "cartilaginous joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (macula of utricle of membranous labyrinth) @@ -161457,6 +158995,8 @@ AnnotationAssertion( "macula of utricle of membranous labyrinth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (synchondrosis) @@ -161479,6 +159019,10 @@ AnnotationAssertion( "synchondrosis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (symphysis) @@ -161501,7 +159045,6 @@ SubClassOf(Annotation( "FMA # Class: (synovial joint) AnnotationAssertion(Annotation( "FMA:7501") Annotation( "Wikipedia:Synovial_joint") "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005153") Annotation( "TAO") Annotation( "ZFIN:Curator") "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]") AnnotationAssertion( "AEO:0000183") AnnotationAssertion( "CALOHA:TS-2138") AnnotationAssertion( "EHDAA2:0003183") @@ -161525,13 +159068,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "synovial joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (perichondrium) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000036") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/26") "Fibrous connective tissue that surrounds cartilage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001643") Annotation( "TAO") Annotation( "TAO:wd") "Portion of connective tissue which surrounds cartilage.[TAO]") AnnotationAssertion( "AAO:0010445") AnnotationAssertion( "BTO:0005089") AnnotationAssertion( "EMAPA:35676") @@ -161558,7 +159102,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (thoracic cavity) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Thoracic_cavity") "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.") -AnnotationAssertion( "In many species, the diaphragm separates thoracic and abdominal cavities") AnnotationAssertion( "EMAPA:36497") AnnotationAssertion( "FMA:7565") AnnotationAssertion( "GAID:93") @@ -161583,15 +159126,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spiral organ of cochlea) AnnotationAssertion(Annotation( "Wikipedia:Organ_of_Corti") "The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted].") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001567") Annotation( "VHOG") Annotation( "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.33") Annotation( "http://bgee.unil.ch/") "The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG]") -AnnotationAssertion( "in basal early lizards, organized into 3 tonotopically organized areas, the outer areas lack a tectorial membrane[ISBN:9780387714691]") AnnotationAssertion( "BIRNLEX:2526") AnnotationAssertion( "BTO:0001691") AnnotationAssertion( "CALOHA:TS-0717") @@ -161604,7 +159146,6 @@ AnnotationAssertion( "NCIT:C33223") AnnotationAssertion( "SCTID:279841009") AnnotationAssertion(Annotation( "BIRNLEX:2526") Annotation( "ncithesaurus:Organ_of_Corti") "UMLS:C0029207") -AnnotationAssertion( "VHOG:0001567") AnnotationAssertion( "Wikipedia:Organ_of_Corti") AnnotationAssertion( "ncithesaurus:Spiral_Organ_of_Corti") AnnotationAssertion( "cochlear spiral organ") @@ -161626,20 +159167,16 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Scala_media") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/387") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (rib) AnnotationAssertion(Annotation( "Wikipedia:Rib") Annotation( "ZFIN:curator") "An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000538") Annotation( "TAO") Annotation( "ZFIN:curator") "Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000545") Annotation( "AAO") Annotation( "AAO:Pugener_2002") "Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO]") -AnnotationAssertion( "costal") -AnnotationAssertion( "In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body") -AnnotationAssertion( "They protect and support internal organs and enable lungs to expand by expanding the chest.") AnnotationAssertion( "AAO:0000545") AnnotationAssertion( "CALOHA:TS-2209") AnnotationAssertion( "EFO:0003066") @@ -161653,7 +159190,6 @@ AnnotationAssertion( "TAO:0000538") AnnotationAssertion(Annotation( "ncithesaurus:Rib") "UMLS:C0035561") AnnotationAssertion( "VHOG:0001154") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "VO:0012403") AnnotationAssertion( "Wikipedia:Rib") AnnotationAssertion( "ZFA:0000538") AnnotationAssertion( "galen:Rib") @@ -161668,7 +159204,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rib") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal phalanx of manus) @@ -161693,7 +159231,7 @@ AnnotationAssertion( "proximal phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (true rib) @@ -161711,15 +159249,14 @@ AnnotationAssertion( "true rib") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord) AnnotationAssertion(Annotation( "BIRNLEX:1709") "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).") AnnotationAssertion( "TODO - add superclass to unify with VNC?") -AnnotationAssertion(Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010151") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000601") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0010151") AnnotationAssertion( "BAMS:SP") AnnotationAssertion( "BAMS:Spinal") @@ -161772,21 +159309,19 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chondrocranium) AnnotationAssertion(Annotation( "Wikipedia:Chondrocranium") Annotation( "http://medical-dictionary.thefreedictionary.com/chondrocranium") "Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].") AnnotationAssertion( "we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010169") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001424") Annotation( "TAO") Annotation( "ZFIN:curator") "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]") -AnnotationAssertion( "chondrocranial") -AnnotationAssertion( "covers the brain dorsally in chondrichthyans") AnnotationAssertion( "AAO:0010169") AnnotationAssertion( "EHDAA2:0000243") AnnotationAssertion( "EMAPA:17681") @@ -161806,14 +159341,11 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nucleus pulposus) AnnotationAssertion(Annotation( "MGI:llw2") Annotation( "MP:0006392") "The jelly-like substance in the middle of the spinal disc which is a remnant of the notochord.") -AnnotationAssertion( "The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus]") -AnnotationAssertion(Annotation( "FMA") "we group two FMA classes together") AnnotationAssertion( "BTO:0003626") AnnotationAssertion( "EMAPA:18008") AnnotationAssertion( "FMA:13550") AnnotationAssertion( "FMA:76703") AnnotationAssertion( "MA:0000112") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000070614") AnnotationAssertion( "SCTID:316586000") AnnotationAssertion( "Wikipedia:Nucleus_pulposus") AnnotationAssertion(Annotation( "FMA:13550") "nucleus pulposus (diskus intervertebralis)") @@ -161828,22 +159360,22 @@ AnnotationAssertion( "Function noyes: It functions to distribute hydraulic pressure in all directions within each disc under compressive loads.") AnnotationAssertion(rdfs:label "nucleus pulposus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "mah") Annotation( "ISBN:0073040584") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vomeronasal organ) AnnotationAssertion(Annotation( "VHOG:0000665") "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000665") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/vomeronasal+organ") "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000665") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4)") Annotation( "http://bgee.unil.ch/") "(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG]") -AnnotationAssertion( "Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)") AnnotationAssertion( "AAO:0000997") AnnotationAssertion( "BTO:0002608") AnnotationAssertion( "EFO:0001934") @@ -161873,6 +159405,7 @@ AnnotationAssertion( "vomeronasal organ") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161926,6 +159459,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal horn of spinal cord") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161937,7 +159471,6 @@ DisjointClasses(Annotation( # Class: (ventral horn of spinal cord) AnnotationAssertion(Annotation( "GO:0021517") Annotation( "MP:0005112") Annotation( "Wikipedia:Anterior_horn_of_spinal_cord") Annotation( "https://sourceforge.net/tracker/?group_id=36855&atid=440764") "The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO].") -AnnotationAssertion(Annotation( "Wikipedia:Anterior_horn_of_spinal_cord") "The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord].") AnnotationAssertion( "BAMS:VH") AnnotationAssertion( "BIRNLEX:2668") AnnotationAssertion( "BTO:0005151") @@ -161979,6 +159512,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ventral horn of spinal cord") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -161988,7 +159522,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (dorsal root of spinal cord) AnnotationAssertion(Annotation( "NLXANAT:20090208") "The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion).") -AnnotationAssertion(Annotation( "Wikipedia:Posterior_root_of_spinal_nerve") "In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve].") AnnotationAssertion( "BAMS:drt") AnnotationAssertion( "BTO:0000360") AnnotationAssertion( "FMA:5980") @@ -162024,23 +159557,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory bulb) AnnotationAssertion(Annotation( "BTO:0000961") Annotation( "Wikipedia:Olfactory_bulb") "A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ISBN:0471888893") "Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010165") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]") -AnnotationAssertion(Annotation( "FMA:77624") "Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000033") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000033") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)") Annotation( "http://bgee.unil.ch/") "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb") -AnnotationAssertion( "Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos)") -AnnotationAssertion( "the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP).") AnnotationAssertion( "AAO:0010165") AnnotationAssertion( "BAMS:DLB") AnnotationAssertion( "BAMS:OB") @@ -162084,6 +159606,7 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) @@ -162094,12 +159617,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BIRNLEX:1663") Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Olfactory_tract") Annotation( "http://orcid.org/0000-0002-6601-2165") "White matter tract that contains projections from the olfactory bulb to other parts of the brain.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO:0003647") "A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647].") -AnnotationAssertion(Annotation( "Wikipedia:Olfactory_tract") "The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia].") -AnnotationAssertion(Annotation( "FMA") "Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA]") -AnnotationAssertion(Annotation( "deprecated class") Annotation( "BIRNLEX:1663") "White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone)") -AnnotationAssertion( "in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN:0471888893]") -AnnotationAssertion(Annotation( "cjm") Annotation( "ISBN:0471888893") "The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa.") AnnotationAssertion( "BAMS:olf") AnnotationAssertion( "BIRNLEX:1663") AnnotationAssertion( "BTO:0003647") @@ -162127,16 +159644,16 @@ AnnotationAssertion( "olfactory tract") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory organ) AnnotationAssertion(Annotation( "UBERON:cjm") "An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.") AnnotationAssertion( "An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint") -AnnotationAssertion( "fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint") AnnotationAssertion( "AAO:0010180") AnnotationAssertion( "BTO:0001772") -AnnotationAssertion(Annotation( ) "FBbt:00005158") AnnotationAssertion( "FMA:77659") AnnotationAssertion( "VHOG:0000287") AnnotationAssertion( "XAO:0000273") @@ -162153,8 +159670,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (periventricular zone of hypothalamus) @@ -162172,6 +159691,7 @@ AnnotationAssertion(Annotation( "UBERON:0002271") AnnotationAssertion(rdfs:label "periventricular zone of hypothalamus") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (medial zone of hypothalamus) @@ -162191,14 +159711,12 @@ AnnotationAssertion(Annotation( "UBERON:0002272") AnnotationAssertion(rdfs:label "medial zone of hypothalamus") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (reticular formation) AnnotationAssertion(Annotation( "NeuroNames:1223") "A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).") -AnnotationAssertion( "this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.") -AnnotationAssertion( "It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.") -AnnotationAssertion(Annotation( "FMA") "FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure") AnnotationAssertion( "BAMS:RET") AnnotationAssertion( "EMAPA:35188") AnnotationAssertion( "FMA:77719") @@ -162241,6 +159759,7 @@ AnnotationAssertion( "lamina of spiral limbus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (perilymphatic space) @@ -162266,7 +159785,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (stria vascularis of cochlear duct) AnnotationAssertion(Annotation( "Wikipedia:Stria_vascularis") "The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted].") -AnnotationAssertion(Annotation( "FMA") "represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps") AnnotationAssertion( "BIRNLEX:2525") AnnotationAssertion( "BTO:0001819") AnnotationAssertion( "CALOHA:TS-0982") @@ -162293,16 +159811,14 @@ AnnotationAssertion( "stria vascularis of cochlear duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "pigment cells") Annotation( "NCBIBook:NBK53175") ObjectSomeValuesFrom( )) # Class: (telencephalic ventricle) AnnotationAssertion(Annotation( "Wikipedia:Lateral_ventricle") Annotation( "https://orcid.org/0000-0002-6601-2165") "A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Lateral_ventricle") "The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP].") -AnnotationAssertion(Annotation( "GO:0021670") "The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000643") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") AnnotationAssertion( "BAMS:LV") AnnotationAssertion( "BAMS:Tel-V") AnnotationAssertion( "BIRNLEX:1263") @@ -162350,7 +159866,9 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "telencephalic ventricle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "material to immaterial") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroid plexus of fourth ventricle) @@ -162382,7 +159900,8 @@ AnnotationAssertion( "choroid plexus of fourth ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central canal of spinal cord) @@ -162423,6 +159942,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "central canal of spinal cord") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg"^^xsd:anyURI) SubClassOf(Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162433,7 +159953,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (biliary system) AnnotationAssertion(Annotation( "Wikipedia:Biliary_system") "Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).") -AnnotationAssertion( ) AnnotationAssertion( "FMA:79646") AnnotationAssertion( "GAID:279") AnnotationAssertion( "MA:0001273") @@ -162450,7 +159969,12 @@ AnnotationAssertion( "biliary system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) DisjointClasses( ) @@ -162463,11 +159987,9 @@ DisjointClasses( "MGI:anna") Annotation( "MP:0003169") Annotation( "PMID:1680563") "The division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing).") AnnotationAssertion( "TODO - check cochlear duct vs cochlear aqueduct vs scala media") -AnnotationAssertion( "EHDAA2:0000262") AnnotationAssertion( "EMAPA:35751") AnnotationAssertion( "FMA:79789") AnnotationAssertion( "MA:0002458") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D003053") AnnotationAssertion( "Wikipedia:Scala_media") AnnotationAssertion( "uberon") AnnotationAssertion( "cochlear duct") @@ -162478,13 +160000,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "scala media") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png"^^xsd:anyURI) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal mesentery) AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") Annotation( "Wikipedia:Mesentery#Development") Annotation( "ZFIN:curator") "The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005130") Annotation( "TAO") Annotation( "ZFIN:curator") "The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]") AnnotationAssertion( "EHDAA2:0004560") AnnotationAssertion( "EHDAA:3019") AnnotationAssertion( "EHDAA:3033") @@ -162505,19 +160027,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal mesentery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png"^^xsd:anyURI) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (brainstem) AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "MP:0005277") Annotation( "Wikipedia:Brainstem") Annotation( "ZFA:0001707") "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].") -AnnotationAssertion(Annotation( "we apply a strict definition") ) -AnnotationAssertion(Annotation( "ZFA") Annotation( "ABA") Annotation( "https://github.com/obophenotype/uberon/issues/378") Annotation( "pending") ) -AnnotationAssertion(Annotation( "we apply a strict definition") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002156") Annotation( "TAO") Annotation( "ISBN:3764351209") "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]") -AnnotationAssertion(Annotation( "ZFA:0001707") "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].") -AnnotationAssertion(Annotation( "MP:0005277") "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]") AnnotationAssertion( "BAMS:BS") AnnotationAssertion( "BIRNLEX:1565") AnnotationAssertion( "BTO:0000146") @@ -162554,8 +160070,7 @@ AnnotationAssertion( "'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).") AnnotationAssertion(rdfs:label "brainstem") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png"^^xsd:anyURI) -SubClassOf(Annotation( "ZFA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162570,7 +160085,6 @@ AnnotationAssertion( "CALOHA:TS-0031") AnnotationAssertion( "EFO:0001985") AnnotationAssertion( "EMAPA:32682") -AnnotationAssertion( "EV:0100043") AnnotationAssertion( "FMA:7318") AnnotationAssertion( "GAID:349") AnnotationAssertion( "MA:0000420") @@ -162594,6 +160108,8 @@ AnnotationAssertion( "alveolus of lung") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162616,12 +160132,12 @@ AnnotationAssertion(Annotation( "UBERON:0002301") AnnotationAssertion(rdfs:label "layer of neocortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (myocardium of atrium) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010493") "The atrial part of middle layer of the heart, comprised of involuntary muscle.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000602") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481") Annotation( "http://bgee.unil.ch/") "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]") AnnotationAssertion( "EFO:0003087") AnnotationAssertion( "EMAPA:32746") AnnotationAssertion( "FMA:83509") @@ -162641,6 +160157,7 @@ AnnotationAssertion( "myocardium of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (juxtaglomerular apparatus) @@ -162665,6 +160182,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "juxtaglomerular apparatus") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162675,7 +160193,6 @@ SubClassOf(Annotation( "GO" # Class: (layer of dentate gyrus) AnnotationAssertion(Annotation( "PMCID:PMC2492885") Annotation( "http://orcid.org/0000-0002-6601-2165") "One of the three layers of the dentate gyrus of the hippocampal formation.") -AnnotationAssertion( "the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885]") AnnotationAssertion( "EMAPA:35278") AnnotationAssertion( "FMA:83678") AnnotationAssertion( "MA:0002429") @@ -162685,6 +160202,9 @@ AnnotationAssertion( "UBERON:0002304") AnnotationAssertion(rdfs:label "layer of dentate gyrus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of hippocampus) @@ -162705,12 +160225,14 @@ AnnotationAssertion( "EDITOR_NOTE TODO - check NIF xref") AnnotationAssertion(rdfs:label "layer of hippocampus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal mucus) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa.") -AnnotationAssertion( "protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons") AnnotationAssertion( "BTO:0003603") AnnotationAssertion( "CALOHA:TS-0658") AnnotationAssertion( "EMAPA:36552") @@ -162726,6 +160248,8 @@ AnnotationAssertion( "EDITOR_NOTE TODO - split nasal vs respiratory tract?") AnnotationAssertion(rdfs:label "nasal mucus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroid plexus of lateral ventricle) @@ -162774,6 +160298,7 @@ AnnotationAssertion(Annotation( "UBERON:0002308") AnnotationAssertion(rdfs:label "nucleus of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus fimbria) @@ -162812,8 +160337,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hippocampus fimbria") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "Need to determine whether the fimbria is part of the fornix. Sometimes the language suggests it isn't always thought of that way, but I see no useful reason why it should be separate; it all forms one continuous white matter tract. Neuronames and others include this as part of the hippocampal formation (MM)") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162844,13 +160369,14 @@ AnnotationAssertion( "EDITOR_NOTE this layer changes in its depthwise spatial relation across its extent") AnnotationAssertion(rdfs:label "hippocampus pyramidal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain tectum) AnnotationAssertion(Annotation( "BIRNLEX:1032") "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM).") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001388") Annotation( "VHOG") Annotation( "DOI:10.1371/journal.pone.0003582 Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS ONE (2008)") Annotation( "http://bgee.unil.ch/") "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi") AnnotationAssertion( "BAMS:MTec") AnnotationAssertion( "BAMS:Tec") AnnotationAssertion( "BIRNLEX:1032") @@ -162915,22 +160441,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gray matter of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter) AnnotationAssertion(Annotation( "Wikipedia:White_matter") Annotation( "https://orcid.org/0000-0002-6601-2165") "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.") -AnnotationAssertion(Annotation( "FMA:83929") "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002142") Annotation( "TAO") Annotation( "ZFIN:curator") "Multi-tissue structure comprised largely of myelinated axons.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001764") Annotation( "VHOG") Annotation( "DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)") Annotation( "http://bgee.unil.ch/") "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]") -AnnotationAssertion(Annotation( "NIF") Annotation(rdfs:seeAlso "https://github.com/SciCrunch/NIF-Ontology/issues/83") "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex") AnnotationAssertion( "AEO:0000139") AnnotationAssertion( "AEO:0001011") AnnotationAssertion( "EMAPA:35927") AnnotationAssertion( "FMA:83929") AnnotationAssertion( "HBA:9218") AnnotationAssertion( "MA:0001135") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066127") AnnotationAssertion( "NCIT:C33892") AnnotationAssertion( "NLX:412") AnnotationAssertion( "NLXANAT:101177") @@ -162958,8 +160481,7 @@ AnnotationAssertion( "white matter") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of spinal cord) @@ -162984,16 +160506,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white matter of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesangium) AnnotationAssertion(Annotation( "Wikipedia:Mesangium") Annotation( "https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/13/") "The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.") AnnotationAssertion( ) -AnnotationAssertion( "mesangial") -AnnotationAssertion(Annotation( "MA") "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here.") AnnotationAssertion( "BTO:0002494") -AnnotationAssertion( "EMAPA:28248") AnnotationAssertion(Annotation( "MA:th") "EMAPA:36561") AnnotationAssertion( "FMA:84139") AnnotationAssertion( "MA:0002617") @@ -163007,16 +160528,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesangium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular mesangium) AnnotationAssertion(Annotation( "MESH:A05.810.453.736.520.380") Annotation( "Wikipedia:Glomerular_mesangium") "A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix.") AnnotationAssertion( ) AnnotationAssertion( "EMAPA:27961") -AnnotationAssertion( "EMAPA:28248") AnnotationAssertion( "FMA:84140") AnnotationAssertion( "GAID:430") AnnotationAssertion( "MA:0002606") @@ -163030,6 +160554,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular mesangium") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163046,7 +160571,7 @@ AnnotationAssertion( "EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus?") AnnotationAssertion(rdfs:label "extraglomerular mesangium") SubClassOf( ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163054,7 +160579,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (periventricular nucleus) AnnotationAssertion(Annotation( "Wikipedia:Periventricular_nucleus") "A thin sheet of small neurons located in the wall of the third ventricle, a composite structure of the hypothalamus.") -AnnotationAssertion(Annotation( "ZFA:0000260, GOC:MAH, ISBN:3764351209") "Diencephalic nucleus which is the periventricular part of the ventral hypothalamic zone. From Neuroanatomy of the Zebrafish Brain.") AnnotationAssertion( "FMA:84354") AnnotationAssertion( "TAO:0000260") AnnotationAssertion( "Wikipedia:Periventricular_nucleus") @@ -163071,15 +160595,11 @@ SubClassOf( (coelemic cavity lumen) AnnotationAssertion(Annotation( "BTO:0001707") "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.") -AnnotationAssertion(Annotation( "2012-09-12") Annotation( "ZFA:0001438") Annotation( "ZFA") Annotation( "ZFIN:curator") "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].") -AnnotationAssertion(Annotation( "2012-09-12") Annotation( "BTO:0001707") Annotation( "BTO") Annotation( "BTO") "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].") -AnnotationAssertion( "In mammals it forms the peritoneal, pleural, and pericardial cavities") AnnotationAssertion( "UBERON:0000169") AnnotationAssertion(Annotation( "BTO:0001707") "body cavity") AnnotationAssertion( "AEO:0000186") AnnotationAssertion( "BTO:0001707") AnnotationAssertion( "EHDAA2:0000267") -AnnotationAssertion(Annotation( ) "FBbt:00005060") AnnotationAssertion( "FMA:85006") AnnotationAssertion( "NCIT:C25444") AnnotationAssertion( "RETIRED_EHDAA2:0003186") @@ -163104,7 +160624,7 @@ AnnotationAssertion( "EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct") AnnotationAssertion(rdfs:label "coelemic cavity lumen") SubClassOf( ) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of back) @@ -163123,7 +160643,7 @@ AnnotationAssertion( "muscle of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (epithelium of urethra) @@ -163144,8 +160664,12 @@ AnnotationAssertion(Annotation( "UBERON:0002325") AnnotationAssertion(rdfs:label "epithelium of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "GO") ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of urethra) @@ -163164,11 +160688,11 @@ AnnotationAssertion( "lamina propria of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk of intercostal nerve) -AnnotationAssertion( "EMAPA:18227") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37720") AnnotationAssertion( "FMA:85315") AnnotationAssertion( "MA:0001176") @@ -163178,17 +160702,12 @@ AnnotationAssertion( "UBERON:0002327") AnnotationAssertion(rdfs:label "trunk of intercostal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (notochord) AnnotationAssertion(Annotation( "ISBN:0815318960") Annotation( "Wikipedia:Notochord") Annotation( "http://tolweb.org/Chordata/2499") Annotation( "https://github.com/obophenotype/uberon/issues/25") Annotation( "https://github.com/obophenotype/uberon/issues/271") "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000032") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000135") Annotation( "TAO") Annotation( "ZFIN:curator") "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000327") Annotation( "AAO") Annotation( "AAO:LAP") "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000327") Annotation( "AAO") "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000199") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]") -AnnotationAssertion( "notochordal") -AnnotationAssertion( "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.") AnnotationAssertion( "AAO:0000327") AnnotationAssertion( "BTO:0001768") AnnotationAssertion( "CALOHA:TS-0690") @@ -163224,6 +160743,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) SubClassOf(Annotation( "PMID:15890825") ) SubClassOf(Annotation( "VSAO") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163236,15 +160757,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (somite) AnnotationAssertion(Annotation( "DOI:10.1111/j.1439-0426.2012.01987.x") Annotation( "Wikipedia:Somite") "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.") -AnnotationAssertion( "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk") AnnotationAssertion(Annotation( "PMID:17237766") ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010569") Annotation( "AAO") Annotation( "AAO:EJS") "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000155") Annotation( "TAO") Annotation( "ZFIN:curator") "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000155") Annotation( "TAO") "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000155") Annotation( "TAO") "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010569") Annotation( "AAO") "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000191") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)") Annotation( "http://bgee.unil.ch/") "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]") -AnnotationAssertion( "somitic") AnnotationAssertion(Annotation( "GO:0001756") "mesodermal cluster") AnnotationAssertion( "AAO:0010569") AnnotationAssertion( "AEO:0001015") @@ -163302,6 +160815,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163317,8 +160831,6 @@ DisjointClasses( "ISBN:0-683-40008-8") Annotation( "MP:0001725") Annotation( "PMID:9144284") Annotation( "Wikipedia:Umbilical_cord") "The connecting cord from the developing embryo to the placenta.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Umbilical_cord") "The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP].") -AnnotationAssertion( "umbilical") AnnotationAssertion( "BTO:0001415") AnnotationAssertion( "CALOHA:TS-1078") AnnotationAssertion( "EFO:0001415") @@ -163360,8 +160872,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001134") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pulmonary+trunk") "An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001134") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481") Annotation( "http://bgee.unil.ch/") "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001576") AnnotationAssertion( "EHDAA:9831") AnnotationAssertion( "EMAPA:17015") @@ -163392,7 +160902,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0072024") Annotation( "Wikipedia:Macula_densa") "The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "not part of a nephron or distal tubule in MA and FMA") AnnotationAssertion( "BTO:0003940") AnnotationAssertion( "EMAPA:28399") AnnotationAssertion( "FMA:86333") @@ -163407,7 +160916,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macula densa") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) @@ -163429,6 +160938,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endometrial stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of bronchus) @@ -163460,9 +160972,9 @@ AnnotationAssertion(Annotation( "UBERON:0002338") AnnotationAssertion(rdfs:label "lamina propria of bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of lobar bronchus) @@ -163485,6 +160997,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of lobar bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163510,7 +161025,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of segmental bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163523,12 +161040,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neural crest) AnnotationAssertion(Annotation( "MP:0009846") "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].") -AnnotationAssertion( "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).") -AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "PMID:17377535") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000045") Annotation( "TAO") Annotation( "ZFIN:curator") "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010578") Annotation( "AAO") Annotation( "AAO:EJS") "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]") -AnnotationAssertion(Annotation( "PMID:11523831") "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000057") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)") Annotation( "http://bgee.unil.ch/") "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]") AnnotationAssertion( "AAO:0010578") AnnotationAssertion( "BTO:0001764") AnnotationAssertion( "CALOHA:TS-0676") @@ -163541,7 +161052,6 @@ AnnotationAssertion( "MIAA:0000066") AnnotationAssertion( "NCIT:C34222") AnnotationAssertion( "SCTID:361462002") -AnnotationAssertion( "TAO:0000045") AnnotationAssertion(Annotation( "ncithesaurus:Neural_Crest") "UMLS:C0027789") AnnotationAssertion( "VHOG:0000057") AnnotationAssertion( "Wikipedia:Neural_crest") @@ -163560,18 +161070,19 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "neural crest") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "XAO") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:11523831") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:11523831") ObjectSomeValuesFrom( )) # Class: (abdomen musculature) AnnotationAssertion(Annotation( "OBOL:automatic") "Set of all muscles in abdomen.") -AnnotationAssertion( "distinction between abdomen muscle and abdomen musculature") AnnotationAssertion( "FMA:71294") AnnotationAssertion( "FMA:86917") AnnotationAssertion( "TAO:0001327") @@ -163588,7 +161099,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "abdomen musculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (descending thoracic aorta) @@ -163605,6 +161117,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "descending thoracic aorta") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163614,9 +161127,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neurectoderm) AnnotationAssertion(Annotation( "Wikipedia:Neuroectoderm") "Embryonic ectoderm that gives rise to nervous tissue.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000150") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]") -AnnotationAssertion( "neurectodermal") -AnnotationAssertion( "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here") AnnotationAssertion( "AAO:0011074") AnnotationAssertion( "BILA:0000039") AnnotationAssertion( "CALOHA:TS-1212") @@ -163625,7 +161135,6 @@ AnnotationAssertion( "EHDAA:255") AnnotationAssertion( "EMAPA:16073") AnnotationAssertion( "EV:0100004") -AnnotationAssertion(Annotation( ) "FBbt:00001057") AnnotationAssertion( "FMA:87657") AnnotationAssertion( "MAT:0000176") AnnotationAssertion( "MIAA:0000176") @@ -163648,14 +161157,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurectoderm") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) # Class: (thoracic vertebra) AnnotationAssertion(Annotation( "OBOL:automatic") "A thoracic vertebra endochondral element that is composed primarily of a bone tissue.") AnnotationAssertion( ) -AnnotationAssertion( "Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs") AnnotationAssertion( "EMAPA:18011") AnnotationAssertion( "FMA:9139") AnnotationAssertion( "GAID:244") @@ -163677,16 +161185,16 @@ AnnotationAssertion( "thoracic vertebra") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicardium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005057") Annotation( "TAO") Annotation( "ZFIN:curator") "External layer of the heart.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010409") Annotation( "AAO") Annotation( "AAO:BJB") "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]") -AnnotationAssertion( "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]") AnnotationAssertion( "AAO:0010409") AnnotationAssertion( "EHDAA2:0002202") AnnotationAssertion( "FMA:9461") @@ -163711,6 +161219,7 @@ AnnotationAssertion( "EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.") AnnotationAssertion(rdfs:label "epicardium") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "multiple") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-inferred") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163719,16 +161228,12 @@ SubClassOf(Annotation( "FMA # Class: (myocardium) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005329") "The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000083") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010410") Annotation( "AAO") Annotation( "AAO:BJB") "The middle layer of the heart, consisting of cardiac muscle.[AAO]") -AnnotationAssertion( "myocardial") AnnotationAssertion( "AAO:0010410") AnnotationAssertion( "BSA:0000089") AnnotationAssertion( "BTO:0000901") AnnotationAssertion( "CALOHA:TS-0440") AnnotationAssertion( "EFO:0000819") AnnotationAssertion( "EHDAA2:0004150") -AnnotationAssertion( "EMAPA:32688") AnnotationAssertion( "EV:0100022") AnnotationAssertion( "FMA:9462") AnnotationAssertion( "GAID:173") @@ -163759,15 +161264,16 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "myocardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (conducting system of heart) AnnotationAssertion(Annotation( "GO:0003161") "The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO].") AnnotationAssertion( "EHDAA2 divides the system from the tissue") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001271") Annotation( "VHOG") Annotation( "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)") Annotation( "http://bgee.unil.ch/") "The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]") AnnotationAssertion( "EFO:0003909") AnnotationAssertion( "EHDAA2:0004185") AnnotationAssertion( "EMAPA:35428") @@ -163794,8 +161300,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "conducting system of heart") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -163843,8 +161349,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "sinoatrial node") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163855,7 +161361,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Atrioventricular_node") "An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001474") Annotation( "VHOG") Annotation( "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)") Annotation( "http://bgee.unil.ch/") "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]") AnnotationAssertion( "BTO:0005689") AnnotationAssertion( "EFO:0000276") AnnotationAssertion( "EHDAA2:0004183") @@ -163893,8 +161398,9 @@ AnnotationAssertion( "atrioventricular node") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163933,7 +161439,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif"^^xsd:anyURI) SubClassOf(Annotation( "cjm") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163963,8 +161469,7 @@ AnnotationAssertion( "cardiac Purkinje fiber") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") Annotation( "GO") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -163972,8 +161477,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pelvic region of trunk) AnnotationAssertion(Annotation( "Wikipedia:Pelvis") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/720") "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.") -AnnotationAssertion( "pelvic") -AnnotationAssertion(Annotation( "MA") "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs") AnnotationAssertion( "BTO:0001006") AnnotationAssertion( "CALOHA:TS-2227") AnnotationAssertion( "EFO:0002805") @@ -164027,10 +161530,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "VHOG:0001257") "A serous membrane that lines the peritoneal cavity[VHOG,modified].") AnnotationAssertion( "TODO - in ZFA is_a epithelium") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005120") Annotation( "TAO") Annotation( "ZFIN:curator") "An epithelium that lines the peritoneal cavity.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010814") Annotation( "AAO") Annotation( "AAO:JMG") "Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]") -AnnotationAssertion( "peritoneal") -AnnotationAssertion(Annotation( "MA") "todo: check MA/EMAPA.") AnnotationAssertion( "AAO:0010814") AnnotationAssertion( "BTO:0001472") AnnotationAssertion( "CALOHA:TS-2072") @@ -164056,13 +161555,13 @@ AnnotationAssertion( "peritoneum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibrous pericardium) AnnotationAssertion(Annotation( "FMA:9586") "Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA].") -AnnotationAssertion( "most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]") AnnotationAssertion( "EMAPA:19029") AnnotationAssertion( "FMA:9586") AnnotationAssertion( "MA:0002738") @@ -164076,6 +161575,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fibrous pericardium") SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) @@ -164083,17 +161583,10 @@ SubClassOf(Annotation( "WP" # Class: (meninx) AnnotationAssertion(Annotation( "FMA:9589") Annotation( "Wikipedia:Meninx") Annotation( "http://www.shsu.edu/~bio_mlt/Chap15.html") "Membrane organ that surrounds the brain and the spinal cord.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001295") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/meninges") "Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001295") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") -AnnotationAssertion( "meningeal") -AnnotationAssertion( "Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).") -AnnotationAssertion(Annotation( "FMA") Annotation(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/1261") "Not consider part of the CNS/neuraxis in FMA") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0000144") AnnotationAssertion( "CALOHA:TS-1177") AnnotationAssertion( "EFO:0000867") AnnotationAssertion( "EMAPA:32660") -AnnotationAssertion( "EV:0100312") AnnotationAssertion( "FMA:9589") AnnotationAssertion( "GAID:687") AnnotationAssertion( "MA:0001113") @@ -164119,15 +161612,14 @@ AnnotationAssertion( "meninx") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (pia mater) AnnotationAssertion(Annotation( "NLXANAT:090209") "The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals.") AnnotationAssertion( "consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system") -AnnotationAssertion(Annotation( "Wikipedia:Pia_mater") "delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater].") AnnotationAssertion( "BTO:0001635") AnnotationAssertion( "EHDAA2:0004318") AnnotationAssertion( "EHDAA:1367") @@ -164142,7 +161634,6 @@ AnnotationAssertion( "EHDAA:6566") AnnotationAssertion( "EHDAA:6583") AnnotationAssertion( "EMAPA:32663") -AnnotationAssertion( "EV:0100315") AnnotationAssertion( "FMA:9590") AnnotationAssertion( "GAID:693") AnnotationAssertion( "MA:0001116") @@ -164165,13 +161656,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "check-aves") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arachnoid mater) AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Arachnoid_mater") "A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space.") -AnnotationAssertion(Annotation( "ISBN:0471888893") ) AnnotationAssertion( "BTO:0001636") AnnotationAssertion( "CALOHA:TS-0052") AnnotationAssertion( "EMAPA:32659") @@ -164204,13 +161694,9 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "NLXANAT:090206") "Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections.") AnnotationAssertion(Annotation( "ISBN:0073040584") ) -AnnotationAssertion(Annotation( "Wikipedia:Dura_mater") "the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater].") -AnnotationAssertion( "capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288") -AnnotationAssertion( "some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]") AnnotationAssertion( "BTO:0001637") AnnotationAssertion( "CALOHA:TS-2008") AnnotationAssertion( "EMAPA:32664") -AnnotationAssertion( "EV:0100313") AnnotationAssertion( "FMA:9592") AnnotationAssertion( "GAID:691") AnnotationAssertion( "MA:0001115") @@ -164233,17 +161719,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "PMID:16496288") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tympanic membrane) AnnotationAssertion(Annotation( "PMID:11237469") Annotation( "Wikipedia:Tympanic_membrane") "A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted].") AnnotationAssertion(Annotation( "Wikipedia") ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001146") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001146") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418") Annotation( "http://bgee.unil.ch/") "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG]") -AnnotationAssertion( "The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum") -AnnotationAssertion(Annotation( "PMID:11237469") "most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint.") AnnotationAssertion( "EMAPA:19062") AnnotationAssertion( "FMA:9595") AnnotationAssertion( "GAID:870") @@ -164306,6 +161787,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate gland) @@ -164313,7 +161797,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0030850") Annotation( "Wikipedia:Prostate") "The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.") AnnotationAssertion( "TODO - FMA treats the gland as part of the prostate - see also FMA:74119.") AnnotationAssertion( ) -AnnotationAssertion( "prostatic") AnnotationAssertion( "BTO:0001129") AnnotationAssertion( "CALOHA:TS-0828") AnnotationAssertion( "EFO:0000858") @@ -164345,6 +161828,7 @@ AnnotationAssertion( "prostate gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164377,15 +161861,13 @@ AnnotationAssertion( "endocrine gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adrenal gland) AnnotationAssertion(Annotation( "BTO:0000047") Annotation( "Wikipedia:Adrenal_gland") "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010551") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001141") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9") Annotation( "http://bgee.unil.ch/") "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]") -AnnotationAssertion( "The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole") -AnnotationAssertion( "suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.") AnnotationAssertion( "AAO:0010551") AnnotationAssertion( "BTO:0000047") AnnotationAssertion( "CALOHA:TS-0016") @@ -164401,7 +161883,6 @@ AnnotationAssertion( "NCIT:C12666") AnnotationAssertion( "SCTID:181127006") AnnotationAssertion(Annotation( "ncithesaurus:Adrenal_Gland") "UMLS:C0001625") -AnnotationAssertion( "VHOG:0001141") AnnotationAssertion( "Wikipedia:Adrenal_gland") AnnotationAssertion( "XAO:0000164") AnnotationAssertion( "galen:AdrenalGland") @@ -164425,21 +161906,17 @@ AnnotationAssertion( "adrenal gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) # Class: (thymus) AnnotationAssertion(Annotation( "NLM:thymus") Annotation( "Wikipedia:Thymus") "Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.") AnnotationAssertion( "check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010548") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000253") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558") Annotation( "http://bgee.unil.ch/") "A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]") -AnnotationAssertion( "thymic") AnnotationAssertion( "AAO:0010548") AnnotationAssertion( "BTO:0001374") AnnotationAssertion( "CALOHA:TS-1043") @@ -164478,11 +161955,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164495,8 +161974,6 @@ AnnotationAssertion(Annotation( "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs") AnnotationAssertion( "consider placement of NCIT:C53466 medullary bone") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001218") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)") Annotation( "http://bgee.unil.ch/") "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]") -AnnotationAssertion( "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]") AnnotationAssertion( "AAO:0011007") AnnotationAssertion( "BTO:0000141") AnnotationAssertion( "BTO:0000829") @@ -164530,14 +162007,17 @@ AnnotationAssertion( "bone marrow") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tonsil) AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002380") "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx.") -AnnotationAssertion( "the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region") AnnotationAssertion( ) AnnotationAssertion( "BTO:0001387") AnnotationAssertion( "CALOHA:TS-1053") @@ -164563,7 +162043,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil") -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164590,7 +162070,10 @@ AnnotationAssertion( "metacarpal bone") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164629,15 +162112,16 @@ AnnotationAssertion( "defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)") AnnotationAssertion(rdfs:label "cranial muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of neck) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any muscle that is part of the cervical (neck) region.") AnnotationAssertion( ) -AnnotationAssertion( "EMAPA:36050") AnnotationAssertion( "FMA:9617") AnnotationAssertion( "GAID:149") AnnotationAssertion( "MA:0000587") @@ -164686,6 +162170,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of abdomen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164693,7 +162179,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Trapezius_muscle") "A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000834") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345") Annotation( "http://bgee.unil.ch/") "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]") AnnotationAssertion( "EMAPA:18183") AnnotationAssertion( "FMA:9626") AnnotationAssertion( "MA:0002398") @@ -164712,11 +162197,13 @@ AnnotationAssertion( "trapezius muscle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "posterior border of the lateral third of the clavicle acromion process and spine of scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "posterior border of the lateral third of the clavicle acromion process and spine of scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "dbpedia") ObjectSomeValuesFrom( )) @@ -164745,21 +162232,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoralis major") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "lateral pectoral nerve and medial pectoral nerveClavicular head: C5 and C6Sternocostal head: C7 C8 and T1") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "anterior surface of the sternum and the superior six costal cartilages and the aponeurosis of the external oblique muscle") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "anterior surface of the medial half of the clavicle") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Lateral lip of intertubercular groove of the humerus") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (connective tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000017") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/23") "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000098") Annotation( "AAO") Annotation( "AAO:LAP") "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001641") Annotation( "TAO") Annotation( "TAO:wd") "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000017") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]") -AnnotationAssertion(Annotation( "MA") "MA also has set of connective tissues") AnnotationAssertion( "AAO:0000098") AnnotationAssertion( "BTO:0000421") AnnotationAssertion( "CALOHA:TS-2009") @@ -164790,14 +162274,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "connective tissue") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle tissue) AnnotationAssertion(Annotation( "GO:0060537") Annotation( "Wikipedia:Muscle_tissue") Annotation( "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764") "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000306") Annotation( "AAO") Annotation( "AAO:LAP") "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]") AnnotationAssertion( "AAO:0000306") AnnotationAssertion( "AEO:0000122") AnnotationAssertion( "CALOHA:TS-0642") @@ -164821,18 +162302,16 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (forelimb zeugopod) AnnotationAssertion(Annotation( "PHENOSCAPE:curators") "The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000341") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000341") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here") AnnotationAssertion( "BTO:0001447") AnnotationAssertion( "CALOHA:TS-2205") AnnotationAssertion( "EFO:0003053") @@ -164886,13 +162365,14 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes) AnnotationAssertion(Annotation( "Wikipedia:Foot") Annotation( "Wikipedia:Pes_(anatomy)") "Distal portion of the hind limb, including tarsal region, metatarsal region and digits.") -AnnotationAssertion( "pedal") AnnotationAssertion( "BTO:0000476") AnnotationAssertion( "CALOHA:TS-0377") AnnotationAssertion( "EFO:0003065") @@ -164930,13 +162410,14 @@ AnnotationAssertion( "pes") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A digit that is part of a manus (hand).") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000857") Annotation( "AAO") Annotation( "AAO:LAP") "One of the fingers of the manus.[AAO]") AnnotationAssertion( "UBERON:0000028") AnnotationAssertion( "AAO:0000857") AnnotationAssertion( "BTO:0004669") @@ -164967,7 +162448,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "manual digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -164975,10 +162456,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Haematopoiesis") "Anatomical system that is involved in the production of hematopoietic cells.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011002") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical system that consists of the blood and blood forming tissues.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001624") Annotation( "VHOG") Annotation( "DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)") Annotation( "http://bgee.unil.ch/") "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]") -AnnotationAssertion( "hematopoietic") -AnnotationAssertion(Annotation( "WP") "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes") AnnotationAssertion( "AAO:0011002") AnnotationAssertion( "BTO:0000570") AnnotationAssertion( "CALOHA:TS-0449") @@ -165016,9 +162493,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hematopoietic system") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) DisjointClasses( ) @@ -165060,8 +162538,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nasolacrimal duct) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0008969") "The paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000664") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256") Annotation( "http://bgee.unil.ch/") "The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG]") -AnnotationAssertion( "the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue") AnnotationAssertion(Annotation( "VHOG:0000664") "nasolacrimal duct - posterior naris") AnnotationAssertion( "AAO:0000643") AnnotationAssertion( "EHDAA2:0001237") @@ -165086,7 +162562,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasolacrimal duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165099,14 +162577,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (bile duct) AnnotationAssertion(Annotation( "Wikipedia:Bile_duct") Annotation( "http://orcid.org/0000-0002-6601-2165") "Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.") -AnnotationAssertion(Annotation( "ZFA:0001100, ZFA:curator") "A duct that carries bile from the liver to the intestine.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000212") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/bile+duct") "Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000212") Annotation( "VHOG") Annotation( "DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)") Annotation( "http://bgee.unil.ch/") "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA") AnnotationAssertion( "AAO:0011019") AnnotationAssertion( "BTO:0000122") AnnotationAssertion( "CALOHA:TS-0075") -AnnotationAssertion( "EHDAA2:0000741") AnnotationAssertion( "EMAPA:35171") AnnotationAssertion( "EV:0100091") AnnotationAssertion( "FMA:9706") @@ -165132,7 +162605,9 @@ AnnotationAssertion( "bile duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165142,16 +162617,9 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000098") "The triangular flat bone of the nasal septum.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000308") Annotation( "TAO") Annotation( "ZFIN:curator") "Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000633") Annotation( "AAO") Annotation( "AAO:LAP") "Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000308") Annotation( "TAO") "relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000308") Annotation( "TAO") "relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]") -AnnotationAssertion(Annotation( "Wikipedia:Vomer#In_other_animals") "In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]") -AnnotationAssertion(Annotation( "2012-09-06") Annotation( "TAO:0000308") Annotation( "TAO") Annotation( "Curator") "The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]") AnnotationAssertion( "AAO:0000633") AnnotationAssertion( "FMA:9710") AnnotationAssertion( "MA:0001496") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D055172") AnnotationAssertion( "NCIT:C33888") AnnotationAssertion( "SCTID:272678009") AnnotationAssertion( "TAO:0000308") @@ -165169,16 +162637,14 @@ AnnotationAssertion( "vomer") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "palatal series") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus) AnnotationAssertion(Annotation( "Wikipedia:Hand") Annotation( "Wikipedia:Manus_(anatomy)") "Distal segment of the fore limb, including carpal region, metacarpal region and digits.") -AnnotationAssertion( "like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton") -AnnotationAssertion( "manual") AnnotationAssertion( "AAO:0010803") AnnotationAssertion( "BTO:0004668") AnnotationAssertion( "CALOHA:TS-2213") @@ -165214,6 +162680,8 @@ AnnotationAssertion( "manus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165236,15 +162704,17 @@ AnnotationAssertion( "the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax") AnnotationAssertion(rdfs:label "parietal pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral pleura) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Pulmonary_pleurae") "The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Visceral_pleura") "Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura].") -AnnotationAssertion(Annotation( "FMA") "FMA treats this as part of the lungs") AnnotationAssertion( "EHDAA2:0002205") AnnotationAssertion( "EMAPA:16777") AnnotationAssertion( "FMA:9734") @@ -165267,16 +162737,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visceral pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pleural cavity) AnnotationAssertion(Annotation( "Wikipedia:Pleural_cavity") Annotation( "https://github.com/obophenotype/uberon/issues/86") "The fluid-filled cavity that lies between the visceral and parietal pleurae.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000581") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206") Annotation( "http://bgee.unil.ch/") "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]") -AnnotationAssertion( "The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning") -AnnotationAssertion(Annotation( "EHDAA2") "the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86") AnnotationAssertion( "BTO:0004422") AnnotationAssertion( "EHDAA2:0001475") AnnotationAssertion( "EMAPA:16773") @@ -165300,15 +162771,16 @@ AnnotationAssertion( "pleural cavity") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (immune system) AnnotationAssertion(Annotation( "Wikipedia:Immune_system") "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001247") Annotation( "VHOG") Annotation( "PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)") Annotation( "http://bgee.unil.ch/") "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]") AnnotationAssertion( "AAO:0011003") AnnotationAssertion( "BILA:0000104") AnnotationAssertion( "BTO:0005810") @@ -165346,7 +162818,6 @@ AnnotationAssertion(Annotation( "FMA:9868") AnnotationAssertion( "RETIRED_EHDAA2:0001443") AnnotationAssertion( "SCTID:361326002") -AnnotationAssertion( "TAO:0000054") AnnotationAssertion( "uberon") AnnotationAssertion( "pericardium") AnnotationAssertion( "UBERON:0002406") @@ -165355,26 +162826,23 @@ AnnotationAssertion( "pericardial sac") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (pericardium) AnnotationAssertion(Annotation( "Wikipedia:Pericardium") Annotation( "http://orcid.org/0000-0002-6601-2165") "The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010817") Annotation( "AAO") Annotation( "AAO:JMG") "Peritoneum that surrounds the heart.[AAO]") -AnnotationAssertion( "pericardial") -AnnotationAssertion(Annotation( "FMA") "In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity") -AnnotationAssertion(Annotation( "ZFA") "this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)") -AnnotationAssertion(Annotation( "FMA") "we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium") AnnotationAssertion( "AAO:0010817") AnnotationAssertion( "BSA:0000090") AnnotationAssertion( "BTO:0000717") AnnotationAssertion( "CALOHA:TS-0761") AnnotationAssertion( "EFO:0000820") AnnotationAssertion( "EHDAA:5376") -AnnotationAssertion( "EMAPA:16133") AnnotationAssertion( "EV:0100023") AnnotationAssertion( "FMA:9869") AnnotationAssertion( "GAID:569") @@ -165384,7 +162852,6 @@ AnnotationAssertion( "NCIT:C13005") AnnotationAssertion( "RETIRED_EHDAA2:0001443") AnnotationAssertion( "SCTID:181295003") -AnnotationAssertion( "TAO:0000054") AnnotationAssertion(Annotation( "ncithesaurus:Pericardium") "UMLS:C0031050") AnnotationAssertion( "VHOG:0001280") AnnotationAssertion( "Wikipedia:Pericardium") @@ -165400,6 +162867,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pericardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165431,6 +162899,8 @@ AnnotationAssertion( "parietal serous pericardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pericardial fluid) @@ -165438,7 +162908,6 @@ AnnotationAssertion(Annotation( "BTO:0001016") AnnotationAssertion( "FMA:9887") AnnotationAssertion( "MA:0002530") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000069236") AnnotationAssertion( "Wikipedia:Pericardial_fluid") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0002409") @@ -165446,15 +162915,13 @@ AnnotationAssertion( "pericardial fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autonomic nervous system) AnnotationAssertion(Annotation( "GO:0048483") "The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000396") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000033") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000396") Annotation( "VHOG") Annotation( "DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)") Annotation( "http://bgee.unil.ch/") "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib") AnnotationAssertion( "AAO:0000033") AnnotationAssertion( "BIRNLEX:1123") AnnotationAssertion( "BTO:0002507") @@ -165465,7 +162932,6 @@ AnnotationAssertion( "EMAPA:16984") AnnotationAssertion( "FMA:65553") AnnotationAssertion( "GAID:706") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0002126") AnnotationAssertion( "MA:0000219") AnnotationAssertion( "MESH:D001341") AnnotationAssertion( "NCIT:C12673") @@ -165500,7 +162966,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (clitoris) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0003127") "The small, erectile body located at the anterior end of the vulva.") -AnnotationAssertion( "clitoral") AnnotationAssertion( "BTO:0002020") AnnotationAssertion( "EHDAA2:0000255") AnnotationAssertion( "EHDAA:9360") @@ -165523,6 +162988,8 @@ AnnotationAssertion( "clitoris") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg"^^xsd:anyURI) SubClassOf(Annotation( "Wikipedia") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -165534,10 +163001,7 @@ AnnotationAssertion(Annotation( "Consider changing name to make distinction from inferred superclass 'vertebral element' clear") AnnotationAssertion( "we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones") AnnotationAssertion(Annotation( "Wikipedia") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001189") Annotation( "TAO") Annotation( "ZFIN:curator") "Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000691") Annotation( "AAO") Annotation( "AAO:Pugener_and_Maglia_2008") "Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]") AnnotationAssertion( "AAO:0000691") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006196") AnnotationAssertion( "CALOHA:TS-2352") AnnotationAssertion( "EFO:0001371") AnnotationAssertion( "EMAPA:32740") @@ -165561,7 +163025,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165569,7 +163035,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A vertebra that is located in the cervical region of the vertebral column.") AnnotationAssertion( ) -AnnotationAssertion( "In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.") AnnotationAssertion( "EMAPA:17674") AnnotationAssertion( "FMA:9915") AnnotationAssertion( "GAID:235") @@ -165590,8 +163055,10 @@ AnnotationAssertion( "cervical vertebra") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail) @@ -165626,7 +163093,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "CARO:0002001") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/29") "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000403") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)") Annotation( "http://bgee.unil.ch/") "(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]") AnnotationAssertion( "UBERON:0007029") AnnotationAssertion( "AEO:0000154") AnnotationAssertion( "BILA:0000118") @@ -165638,7 +163104,6 @@ AnnotationAssertion( "EHDAA:6520") AnnotationAssertion( "EMAPA:17524") AnnotationAssertion( "EV:0100151") -AnnotationAssertion(Annotation( ) "FBbt:00004969") AnnotationAssertion( "FMA:72979") AnnotationAssertion( "HAO:0000421") AnnotationAssertion( "MA:0000014") @@ -165667,6 +163132,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integumental system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165697,11 +163163,6 @@ SubClassOf( (cartilage tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000040") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/37") Annotation( "https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5") "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000060") Annotation( "AAO") Annotation( "AAO:LAP") "A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001501") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000040") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000060") Annotation( "AAO") "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001207") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)") Annotation( "http://bgee.unil.ch/") "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]") AnnotationAssertion( "AAO:0000060") AnnotationAssertion( "AEO:0000087") AnnotationAssertion( "BTO:0000206") @@ -165742,7 +163203,6 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "cartilage tissue") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165766,7 +163226,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basal ganglion) @@ -165789,16 +163252,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "basal ganglion") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampal formation) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment].") -AnnotationAssertion(Annotation( "NIF") "The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO") "BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.") AnnotationAssertion( "BAMS:HPF") AnnotationAssertion( "BAMS:Hi") AnnotationAssertion( "BAMS:HiF") @@ -165830,7 +163291,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hippocampal formation") SubClassOf( ) -SubClassOf(Annotation( "GO") Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MBA-indirect") Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Hippocampus") ObjectSomeValuesFrom( )) @@ -165838,10 +163298,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "BIRNLEX:1256") "Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000110") Annotation( "TAO") Annotation( "ZFIN:curator") "Fluid-filled brain cavity. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011043") Annotation( "AAO") Annotation( "UBERON:0002422") "Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO]") -AnnotationAssertion(Annotation( "GO:0021592") "The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000006") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0011043") AnnotationAssertion( "BAMS:4V") AnnotationAssertion( "BAMS:V4") @@ -165892,14 +163348,14 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatobiliary system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the digestive system that contains the liver and the biliary system.") -AnnotationAssertion(Annotation( "ZFIN:curator") "System responsible for the production and movement of bile[ZFIN:curator].") -AnnotationAssertion( "The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]") AnnotationAssertion( "AAO:0011056") AnnotationAssertion( "CALOHA:TS-1308") AnnotationAssertion( "EFO:0000800") @@ -165927,6 +163383,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatobiliary system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -165941,8 +163398,6 @@ DisjointClasses( "https://orcid.org/0000-0002-6601-2165") "An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.") AnnotationAssertion( "consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)") -AnnotationAssertion(Annotation( "ZFA:0000816") "The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].") -AnnotationAssertion(Annotation( "PMID:16488870") "the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme") AnnotationAssertion( "AAO:0010357") AnnotationAssertion( "BTO:0001775") AnnotationAssertion( "CALOHA:TS-0715") @@ -165965,12 +163420,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oral epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AAO-modified") ObjectSomeValuesFrom( )) # Class: (visceral serous pericardium) AnnotationAssertion(Annotation( "Wikipedia:Visceral_pericardium") "Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].") -AnnotationAssertion( "EMAPA:16589") AnnotationAssertion( "EMAPA:19032") AnnotationAssertion( "FMA:84882") AnnotationAssertion( "MA:0000484") @@ -165990,6 +163447,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visceral serous pericardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166001,7 +163460,6 @@ AnnotationAssertion( "BTO:0000508") AnnotationAssertion( "CALOHA:TS-1037") AnnotationAssertion( "EMAPA:17747") -AnnotationAssertion( "EMAPA:17748") AnnotationAssertion( "FMA:9619") AnnotationAssertion( "MA:0000548") AnnotationAssertion(Annotation( "OBOL:automatic") "anterior thoracic region muscle organ") @@ -166020,6 +163478,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chest muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (arm skin) @@ -166034,12 +163494,12 @@ AnnotationAssertion(Annotation( "UBERON:0002427") AnnotationAssertion(rdfs:label "arm skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb bone) AnnotationAssertion(Annotation( "OBOL:automatic") "A bone that is part of a limb [Automatically generated definition].") -AnnotationAssertion( "the formal definition is very inclusive, and includes sesamoids") -AnnotationAssertion(Annotation( "NCIT") "NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle") AnnotationAssertion( "EFO:0000945") AnnotationAssertion( "MAT:0000151") AnnotationAssertion( "MIAA:0000151") @@ -166055,7 +163515,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "limb bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical lymph node) @@ -166075,13 +163537,12 @@ AnnotationAssertion( "cervical lymph node") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striatum) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "Wikipedia:Striatum") "A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion( "striatal") -AnnotationAssertion(Annotation( "FMA") "FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen") AnnotationAssertion( "BAMS:STR") AnnotationAssertion( "BAMS:Str") AnnotationAssertion( "BAMS:Striatum") @@ -166120,18 +163581,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "striatum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "NIF") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral hemisphere white matter) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "White matter that is part of a cerebral hemisphere.") -AnnotationAssertion( "sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere") -AnnotationAssertion(Annotation( "BTO") "The BTO class is inconsistent as it is part of the brain and spinal cord.") AnnotationAssertion( "BAMS:cw") AnnotationAssertion( "BIRNLEX:711") AnnotationAssertion( "BTO:0000236") @@ -166157,6 +163615,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cerebral hemisphere white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axillary nerve trunk) @@ -166170,6 +163630,8 @@ AnnotationAssertion(Annotation( "UBERON:0002442") AnnotationAssertion(rdfs:label "axillary nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroidal blood vessel) @@ -166195,14 +163657,14 @@ AnnotationAssertion( "cannot find singular in FMA, using Set class") AnnotationAssertion(rdfs:label "choroidal blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens fiber) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A region of the lens consisting of packed elongated enucleate cells packed with crystallin.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000444") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Fibres resembling a ribbon and arranged in very thin plates in the lens. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000444") Annotation( "VHOG") Annotation( "DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)") Annotation( "http://bgee.unil.ch/") "(...) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG]") AnnotationAssertion( "BTO:0000724") AnnotationAssertion( "CALOHA:TS-0544") AnnotationAssertion( "EHDAA:4745") @@ -166228,14 +163690,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lens fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (patella) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") Annotation( "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=3470151&group_id=76834") "A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad].") AnnotationAssertion( ) -AnnotationAssertion( "patellar") AnnotationAssertion( "EMAPA:35668") AnnotationAssertion( "FMA:24485") AnnotationAssertion( "GAID:203") @@ -166259,14 +163723,16 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (decidua) AnnotationAssertion(Annotation( "MP:0004256") Annotation( "PMID:11433360") "The maternal uterine-derived portion of the placenta.") AnnotationAssertion( "TODO - check mp syn") -AnnotationAssertion( "formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua]") AnnotationAssertion( "BTO:0001360") AnnotationAssertion( "CALOHA:TS-0193") AnnotationAssertion( "EMAPA:35269") @@ -166297,7 +163763,7 @@ AnnotationAssertion( "decidua") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "maternal") Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166305,8 +163771,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Uterine_glands") "The mucous secreting gland associated with the mucuous membrane lining the uterus.") AnnotationAssertion( ) -AnnotationAssertion( "simple or branched tubular") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0003433") AnnotationAssertion( "BTO:0004518") AnnotationAssertion( "EMAPA:29919") @@ -166331,6 +163795,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MP") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Tubular_gland") ObjectSomeValuesFrom( )) @@ -166338,7 +163805,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "Wikipedia:Internal_thoracic_artery") "An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "MA has both mammary and thoracic") AnnotationAssertion( "EHDAA2:0000880") AnnotationAssertion( "EHDAA:8585") AnnotationAssertion( "EMAPA:18617") @@ -166360,7 +163826,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "internal thoracic artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166368,8 +163834,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intersomitic artery) AnnotationAssertion(Annotation( "MP:0010662") "The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries.") -AnnotationAssertion(Annotation( "ZFA:0001061") "Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000225") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612") Annotation( "http://bgee.unil.ch/") "Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]") AnnotationAssertion( "UBERON:0006001") AnnotationAssertion( "EHDAA2:0000882") AnnotationAssertion( "EHDAA:4340") @@ -166411,12 +163875,12 @@ AnnotationAssertion( "spinal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vesical vein) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Vesical_veins") "A tributary of the iliac vein that drains the urinary bladder.") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37205") AnnotationAssertion( "MA:0002263") AnnotationAssertion( "SCTID:12683000") @@ -166431,11 +163895,12 @@ AnnotationAssertion( "vesical vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve trunk) -AnnotationAssertion(Annotation( "FMA:5913") "Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913].") AnnotationAssertion( "UBERON:0001147") AnnotationAssertion( "BTO:0000927") AnnotationAssertion( "EHDAA:4675") @@ -166452,18 +163917,14 @@ AnnotationAssertion( "UBERON:0002464") AnnotationAssertion(rdfs:label "nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (lymphoid system) AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010522") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000842") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627") Annotation( "http://bgee.unil.ch/") "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]") -AnnotationAssertion( "lymphoid") -AnnotationAssertion( "The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]") -AnnotationAssertion( "The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]") -AnnotationAssertion(Annotation( "https://github.com/obophenotype/mouse-anatomy-ontology/issues/51") "We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.") AnnotationAssertion( "UBERON:0002096") AnnotationAssertion( "EHDAA2:0001043") AnnotationAssertion( "EHDAA:8677") @@ -166516,6 +163977,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intestine secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus mucosa) @@ -166525,7 +163988,6 @@ AnnotationAssertion( "EMAPA:26981") AnnotationAssertion( "FMA:62996") AnnotationAssertion( "MA:0002680") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000071041") AnnotationAssertion( "NCIT:C32538") AnnotationAssertion( "SCTID:362127004") AnnotationAssertion(Annotation( "ncithesaurus:Esophageal_Mucosa") "UMLS:C0227176") @@ -166550,12 +164012,12 @@ AnnotationAssertion(Annotation( "UBERON:0002469") AnnotationAssertion(rdfs:label "esophagus mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (autopod region) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/303") Annotation( "https://orcid.org/0000-0002-6601-2165") "Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.") AnnotationAssertion(Annotation( "MA:0002714") "autopod") AnnotationAssertion( "BTO:0004359") AnnotationAssertion( "EFO:0000877") @@ -166586,14 +164048,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "autopod region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (zeugopod) AnnotationAssertion(Annotation( "PHENOSCAPE:curators") Annotation( "https://github.com/obophenotype/uberon/issues/101") "The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).") -AnnotationAssertion( "zeugopodial") AnnotationAssertion( "middle part of limb") AnnotationAssertion( "EFO:0000878") AnnotationAssertion( "FMA:83016") @@ -166617,6 +164080,7 @@ AnnotationAssertion( "There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]") AnnotationAssertion(rdfs:label "zeugopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166624,10 +164088,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (stylopod) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The proximal free limb segment. Includes as parts the stylopod skeleton.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "stylopodial") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group") AnnotationAssertion( "proximal part of limb") AnnotationAssertion( "EFO:0000879") AnnotationAssertion( "FMA:83014") @@ -166645,22 +164105,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stylopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (orbitosphenoid) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0004457") "The bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000345") Annotation( "AAO") Annotation( "AAO:LAP") "Endochondral ossification of the lateral sides of the braincase.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") Annotation( "ZFIN:curator") "Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000345") Annotation( "AAO") "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000253") Annotation( "TAO") "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]") AnnotationAssertion( "AAO:0000345") AnnotationAssertion( "EMAPA:18719") AnnotationAssertion( "FMA:52869") @@ -166687,9 +164138,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166698,7 +164152,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (dorsal lateral geniculate nucleus) AnnotationAssertion(Annotation( "http://www.medilexicon.com/medicaldictionary.php?t=61422") "The main division of the lateral geniculate body; consists of two magnocellular layers [TA] (strata magnocellularia [TA]) and four parvocellular layers [TA] (strata parvocellularia [TA]) and serves as a processing station in the major pathway from the retina to the cerebral cortex, receiving fibers from the optic tract and giving rise to the geniculocalcarine radiation to the visual cortex in the occipital lobe.") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "BIRNLEX:1595") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "DLG") AnnotationAssertion( "BAMS:DLG") AnnotationAssertion( "BAMS:LGd") @@ -166727,7 +164180,7 @@ AnnotationAssertion(Annotation( "NeuroNames:353") Annotation( ) "nucleus geniculatus lateralis dorsalis") AnnotationAssertion( "UBERON:0002479") AnnotationAssertion(rdfs:label "dorsal lateral geniculate nucleus") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) @@ -166735,7 +164188,6 @@ SubClassOf(Annotation( "NIF AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000047") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.") AnnotationAssertion( "see https://github.com/obophenotype/uberon/issues/27") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000047") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]") AnnotationAssertion( "CALOHA:TS-2011") AnnotationAssertion( "EMAPA:35179") AnnotationAssertion( "FMA:224804") @@ -166781,9 +164233,6 @@ SubClassOf( (bone marrow cavity) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000065") Annotation( "PMID:10709991") "The medullary cavities of the bones where bone marrow is stored.") -AnnotationAssertion(Annotation( "DOI:10.1177/0192623311409597") ) -AnnotationAssertion( "Located in the main shaft (cortical bone) of a long bone (diaphysis) (consisting mostly of compact bone), the medullary cavity has walls composed of spongy bone (cancellous bone) and is lined with a thin, vascular membrane (endosteum)[Wikipedia:Bone_marrow_of_ovaryry_cavity]") -AnnotationAssertion(Annotation( "FMA") "not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone'") AnnotationAssertion( "FMA:75147") AnnotationAssertion( "FMA:83698") AnnotationAssertion( "MA:0002783") @@ -166820,13 +164269,15 @@ AnnotationAssertion( "prostate duct") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:18977204") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontal suture) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A suture that connects the two frontal bones of the skull.") -AnnotationAssertion( "in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted]") AnnotationAssertion( "EMAPA:19226") AnnotationAssertion( "EMAPA:35358") AnnotationAssertion( "FMA:52989") @@ -166848,7 +164299,7 @@ AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) SubClassOf( ) -SubClassOf(Annotation( "two halves of the frontal bone") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (long bone) @@ -166876,8 +164327,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (acromion) AnnotationAssertion(Annotation( "VSAO:0005067") "Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000826") Annotation( "AAO") Annotation( "AAO:LAP") "Anterior rounded projection of the pars acromialis of the scapula.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000826") Annotation( "AAO") "relationship loss: part_of pars acromialis (AAO:0000752)[AAO]") AnnotationAssertion( "AAO:0000826") AnnotationAssertion( "EMAPA:25119") AnnotationAssertion( "FMA:23260") @@ -166905,7 +164354,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (deltopectoral crest) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0004353") "A rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches.") -AnnotationAssertion( "In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad]") AnnotationAssertion( "AAO:0000736") AnnotationAssertion( "EMAPA:25052") AnnotationAssertion( "FMA:23418") @@ -166929,7 +164377,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "deltopectoral crest") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166951,6 +164401,7 @@ AnnotationAssertion( "cochlear labyrinth") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166976,6 +164427,7 @@ AnnotationAssertion( "iris epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -166996,6 +164448,7 @@ AnnotationAssertion( "abdominal lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (mesenteric lymph node) @@ -167018,13 +164471,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula carnea) AnnotationAssertion(Annotation( "MGI:monikat") Annotation( "MP:0004067") "The supporting bundles of muscular fibers lining the walls of the ventricles of the heart.") -AnnotationAssertion(Annotation( "WP") "The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented") -AnnotationAssertion(Annotation( "MP") "Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea.") AnnotationAssertion( "EMAPA:18626") AnnotationAssertion( "FMA:7269") AnnotationAssertion( "MA:0002831") @@ -167043,7 +164496,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trabecula carnea") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "WP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167052,7 +164505,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "PMID:20959416") Annotation( "Wikipedia:Corpus_luteum") "A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID].") AnnotationAssertion(Annotation( "PMID:20959416") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "PMID:20959416") "maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum") AnnotationAssertion( "BTO:0000292") AnnotationAssertion( "CALOHA:TS-0181") AnnotationAssertion( "EMAPA:29886") @@ -167076,7 +164528,8 @@ AnnotationAssertion( "corpus luteum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg"^^xsd:anyURI) SubClassOf(Annotation( "PMID:20959416") ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167087,8 +164540,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0001958") Annotation( "GO_REF:0000034") Annotation( "VSAO:0000145") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/54") "Replacement bone that forms within cartilage.") AnnotationAssertion( "placement in this class to be inferred") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000145") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Replacement bone that forms within cartilage.[VSAO]") -AnnotationAssertion(Annotation( "ZFA") "some structures, e.g. in ZFA are both intramembrane and endochondral") AnnotationAssertion( "AAO:0010776") AnnotationAssertion( "AEO:0000083") AnnotationAssertion( "BTO:0002157") @@ -167109,6 +164560,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167116,8 +164568,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intramembranous bone) AnnotationAssertion(Annotation( "GO:0001957") Annotation( "Wikipedia:Intramembranous_ossification") Annotation( "https://github.com/obophenotype/uberon/issues/267") "Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001644") Annotation( "TAO") Annotation( "TAO:wd") "Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]") -AnnotationAssertion(Annotation( "2012-09-06") Annotation( "TAO:0001644") Annotation( "TAO") Annotation( "Curator") "[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]") AnnotationAssertion( "EMAPA:36615") AnnotationAssertion( "TAO:0001644") AnnotationAssertion( "Wikipedia:Intramembranous_ossification") @@ -167134,7 +164584,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (periosteum) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010971") "The thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints.") -AnnotationAssertion( "periosteal") AnnotationAssertion( "BTO:0001022") AnnotationAssertion( "EMAPA:35681") AnnotationAssertion( "FMA:24041") @@ -167152,6 +164601,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "periosteum") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cf/Bone_growth.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167159,7 +164609,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (basicranium) AnnotationAssertion(Annotation( "Wikipedia:Base_of_skull") "The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof.") -AnnotationAssertion( "basicranial") AnnotationAssertion( "FMA:52801") AnnotationAssertion( "MA:0002840") AnnotationAssertion( "MESH:D019291") @@ -167188,7 +164637,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MGI:llw2") Annotation( "MP:0002894") "The crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane).") AnnotationAssertion( "Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001676") Annotation( "VHOG") Annotation( "PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)") Annotation( "http://bgee.unil.ch/") "In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG]") AnnotationAssertion( "EFO:0003539") AnnotationAssertion( "GAID:883") AnnotationAssertion( "MA:0002841") @@ -167209,9 +164657,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "otolith organ") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167234,7 +164682,9 @@ AnnotationAssertion( "elastic tissue") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica media) @@ -167266,7 +164716,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "NCIT:C33820") Annotation( "Wikipedia:Tunica_intima") "The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].") AnnotationAssertion( "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure") AnnotationAssertion( "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts") -AnnotationAssertion(Annotation( "Wikipedia") Annotation( "Wikipedia:Tunica_intima") "The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]") AnnotationAssertion( "BTO:0002012") AnnotationAssertion( "EMAPA:36297") AnnotationAssertion( "FMA:55589") @@ -167286,9 +164735,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tunica intima") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "check for exceptions, e.g. capillaries") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) # Class: (pancreatic lymph node) @@ -167309,12 +164759,12 @@ AnnotationAssertion( "pancreatic lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb segment) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.") AnnotationAssertion( "TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition") -AnnotationAssertion(Annotation( "FMA") "FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z") AnnotationAssertion( "FMA:241863") AnnotationAssertion( "MA:0002889") AnnotationAssertion( "NCIT:C38630") @@ -167329,6 +164779,8 @@ AnnotationAssertion( "UBERON:0002529") AnnotationAssertion(rdfs:label "limb segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167337,18 +164789,13 @@ DisjointClasses( (gland) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0002163") "An organ that functions as a secretory or excretory organ.") -AnnotationAssertion( ) -AnnotationAssertion( "glandular") AnnotationAssertion( "AAO:0000212") AnnotationAssertion( "AEO:0000096") AnnotationAssertion( "BTO:0000522") AnnotationAssertion( "EFO:0000797") AnnotationAssertion( "EHDAA2:0003096") AnnotationAssertion( "EHDAA:2161") -AnnotationAssertion( "EHDAA:4475") -AnnotationAssertion( "EHDAA:6522") AnnotationAssertion( "EMAPA:18425") -AnnotationAssertion(Annotation( ) "FBbt:00100317") AnnotationAssertion( "FMA:7146") AnnotationAssertion( "FMA:86294") AnnotationAssertion( "HAO:0000375") @@ -167380,7 +164827,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Epiblast") Annotation( "ZFIN:curator") "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].") AnnotationAssertion( "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000243") Annotation( "VHOG") Annotation( "DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)") Annotation( "http://bgee.unil.ch/") "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]") AnnotationAssertion( "BTO:0004593") AnnotationAssertion( "FMA:296704") AnnotationAssertion( "MAT:0000067") @@ -167407,8 +164853,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0001445") "The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node.") AnnotationAssertion( "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011104") Annotation( "AAO") Annotation( "ISBN:0815318960") Annotation( "OMD:tail+bud") "Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000201") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]") AnnotationAssertion( "AAO:0011104") AnnotationAssertion( "BTO:0001445") AnnotationAssertion( "EFO:0002748") @@ -167432,8 +164876,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "post-anal tail bud") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arthropod sensillum) @@ -167442,7 +164885,6 @@ AnnotationAssertion(Annotation( "this term should be ceded to the arthropod anatomy ontology") AnnotationAssertion( "BTO:0001237") AnnotationAssertion( "EFO:0000939") -AnnotationAssertion(Annotation( ) "FBbt:00007152") AnnotationAssertion( "HAO:0000933") AnnotationAssertion( "MAT:0000163") AnnotationAssertion( "MIAA:0000163") @@ -167476,14 +164918,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hermaphrodite gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch) AnnotationAssertion(Annotation( "PMID:16313389") Annotation( "ZFA:yb") Annotation( "http://orcid.org/0000-0002-6601-2165") "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010359") Annotation( "AAO") Annotation( "NLM:branchial+arch") "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000155") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]") -AnnotationAssertion( "Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering") AnnotationAssertion( "AAO:0010359") AnnotationAssertion( "BTO:0001785") AnnotationAssertion( "EFO:0000959") @@ -167516,10 +164958,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://tolweb.org/Chordata/2499") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) # Class: (lateral line system) @@ -167527,15 +164969,10 @@ SubClassOf(Annotation( "PMI AnnotationAssertion(Annotation( "ISBN:0471209627") Annotation( "ISBN:0815318960") Annotation( "Wikipedia:Lateral_line_system") Annotation( "http://orcid.org/0000-0002-6601-2165") "A line of sensory organs and associated structures along the sides of fish and amphibia that detect vibrations and pressure changes.") AnnotationAssertion( "we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO") AnnotationAssertion(Annotation( "http://tolweb.org/Amniota") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000034") Annotation( "TAO") Annotation( "ZFIN:curator") "A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000975") Annotation( "AAO") Annotation( "AAO:EJS") "Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000975") Annotation( "AAO") "relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001243") Annotation( "VHOG") Annotation( "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195") Annotation( "http://bgee.unil.ch/") "The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG]") AnnotationAssertion( "AAO:0000269") AnnotationAssertion( "AAO:0000975") AnnotationAssertion( "EFO:0000941") AnnotationAssertion( "MAT:0000249") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D053403") AnnotationAssertion( "MIAA:0000249") AnnotationAssertion( "TAO:0000034") AnnotationAssertion( "VHOG:0001243") @@ -167559,14 +164996,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (digit) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/420") "A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).") -AnnotationAssertion( "this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000944") Annotation( "VHOG") Annotation( "DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)") Annotation( "http://bgee.unil.ch/") "Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]") -AnnotationAssertion( "digital") AnnotationAssertion( "AAO:0011126") AnnotationAssertion( "EFO:0000881") AnnotationAssertion( "EMAPA:32725") -AnnotationAssertion(Annotation( "GAT") "FMA:85518") AnnotationAssertion( "MA:0000690") AnnotationAssertion( "MAT:0000285") AnnotationAssertion( "MIAA:0000285") @@ -167587,7 +165019,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -167597,13 +165030,10 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK53175/") Annotation( "https://github.com/obophenotype/uberon/issues/135") Annotation( "https://github.com/seger/aao/issues/4") Annotation( "https://orcid.org/0000-0002-6601-2165") Annotation( "https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/") "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.") AnnotationAssertion( "Do not merge with neurogenic placode") -AnnotationAssertion(Annotation( "PMID:11523831") "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons") -AnnotationAssertion( "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass") AnnotationAssertion(Annotation( "FMA:293966") Annotation( "PMID:22512454") Annotation( ) "ectodermal placode") AnnotationAssertion(Annotation( "Wikipedia:Placode") "placode") AnnotationAssertion( "AAO:0010466") AnnotationAssertion( "EFO:0001650") -AnnotationAssertion( "FMA:293966") AnnotationAssertion( "MAT:0000369") AnnotationAssertion( "MIAA:0000369") AnnotationAssertion( "XAO:0000305") @@ -167621,13 +165051,9 @@ SubClassOf(Annotation( "PMI AnnotationAssertion(Annotation( "Wikipedia:Larva") "A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.") AnnotationAssertion( "TODO discriminate between stages and organisms") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002048") Annotation( "TAO") Annotation( "TAO:wd") "Whole organism that is premetamorphic or a very immature individual.[TAO]") -AnnotationAssertion( "larval") AnnotationAssertion( "AEO:0000126") AnnotationAssertion( "BTO:0000707") -AnnotationAssertion(Annotation( ) "FBbt:00001727") AnnotationAssertion( "HAO:0000459") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D007814") AnnotationAssertion( "TAO:0002048") AnnotationAssertion( "Wikipedia:Larva") AnnotationAssertion(Annotation( "TAO:0002048") "larval organism") @@ -167651,7 +165077,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "larva") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior hypothalamic region) @@ -167696,9 +165124,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intermediate hypothalamic region) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com") "The portion of the hypothalamus located generally internal to the region of the infundibulum.") -AnnotationAssertion( "See notes for pars intermedia of adenohypophysis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0006000") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-001018-1") Annotation( "ZFIN:ZDB-PUB-020730-6") Annotation( "ZFIN:ZDB-PUB-081114-19") "Brain structure that lies perpendicular to the longitudinal axis of the embryonic neural tube, is continuous with the rostral hypothalamic proliferation and whose most lateral extent is deflected dorsally within the inferior lobe.[TAO]") -AnnotationAssertion(Annotation( "TA") "In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami") AnnotationAssertion(Annotation( "BIRNLEX:1015") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "IHR") AnnotationAssertion( "BAMS:IHR") AnnotationAssertion( "BIRNLEX:1015") @@ -167746,7 +165171,9 @@ AnnotationAssertion( "UBERON:0002561") AnnotationAssertion(rdfs:label "lumen of central nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limbic lobe) @@ -167759,7 +165186,6 @@ AnnotationAssertion( "DHBA:12155") AnnotationAssertion( "FMA:72719") AnnotationAssertion( "HBA:4219") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D065726") AnnotationAssertion( "SCTID:279215006") AnnotationAssertion(Annotation( "BIRNLEX:1128") "UMLS:C0458337") AnnotationAssertion( "Wikipedia:Limbic_lobe") @@ -167783,14 +165209,6 @@ SubClassOf(Annotation( "FMA # Class: (cochlear nuclear complex) AnnotationAssertion(Annotation( "Wikipedia:Cochlear_nuclei") "The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion( "WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla") AnnotationAssertion( "BAMS:CN") AnnotationAssertion( "BIRNLEX:1151") AnnotationAssertion( "BM:Me-Co") @@ -167809,8 +165227,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cochlear nuclear complex") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "MA") Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regional part of brain) @@ -167833,6 +165251,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regional part of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (preoptic periventricular nucleus) @@ -167862,25 +165283,17 @@ AnnotationAssertion(Annotation( "NeuroNames:379") "periventricular nucleus, anterior portion") AnnotationAssertion( "UBERON:0002622") AnnotationAssertion(rdfs:label "preoptic periventricular nucleus") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (median preoptic nucleus) AnnotationAssertion(Annotation( "Wikipedia:Preoptic_area#Median_preoptic_nucleus") "The median preoptic nucleus is located along the midline in a position significantly dorsal to the other 3 preoptic nuclei, at least in the macaca fascicularis brain. It wraps around the top (dorsal), front, and bottom (ventral) surfaces of the anterior commissure. The median preoptic nucleus generates thirst. Drinking decreases noradrenaline release in the median preoptic nucleus.") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "BIRNLEX:1208") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "MnPO") AnnotationAssertion( "BAMS:MEPO") AnnotationAssertion( "BAMS:MnPO") AnnotationAssertion( "BIRNLEX:1208") AnnotationAssertion( "BM:MPO") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006168") AnnotationAssertion( "DHBA:13063") AnnotationAssertion( "FMA:62323") AnnotationAssertion( "HBA:4548") @@ -167896,8 +165309,7 @@ AnnotationAssertion(Annotation( "UBERON:0002625") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "median preoptic nucleus") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -167905,9 +165317,6 @@ SubClassOf(Annotation( "Wik # Class: (septal nuclear complex) AnnotationAssertion(Annotation( "BIRNLEX:1313") "Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone).") -AnnotationAssertion(Annotation( "MP:0012682") "Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala.") -AnnotationAssertion(Annotation( "Wikipedia:Septal_nuclei") "The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds & Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei].") -AnnotationAssertion(Annotation( "NIF") "in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass") AnnotationAssertion( "BAMS:SptN") AnnotationAssertion( "BIRNLEX:1313") AnnotationAssertion( "DHBA:10350") @@ -167930,16 +165339,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "septal nuclear complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) # Class: (anteroventral periventricular nucleus) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion(Annotation( "BIRNLEX:1401") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "AVPe") AnnotationAssertion( "BAMS:AVPV") AnnotationAssertion( "BAMS:AVPe") @@ -167957,16 +165363,13 @@ AnnotationAssertion(Annotation( "NeuroNames:382") "ventral periventricular hypothalamic nucleus") AnnotationAssertion( "UBERON:0002690") AnnotationAssertion(rdfs:label "anteroventral periventricular nucleus") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (metathalamus) AnnotationAssertion(Annotation( "Wikipedia:Metathalamus") "The metathalamus is a composite structure of the thalamus, consisting of the medial geniculate nucleus and the lateral geniculate nucleus. [WP,unvetted].") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "FMA") "we follow FMA in making this a subtype of nucleus, but in fact it is a group containing two nuclei") AnnotationAssertion(Annotation( "BIRNLEX:1461") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "MTh") AnnotationAssertion( "BAMS:GENd") AnnotationAssertion( "BAMS:MTh") @@ -167978,7 +165381,6 @@ AnnotationAssertion( "FMA:62023") AnnotationAssertion( "MA:0000868") AnnotationAssertion( "MBA:1008") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005829") AnnotationAssertion( "SCTID:361550004") AnnotationAssertion( "Wikipedia:Metathalamus") AnnotationAssertion(Annotation( "BIRNLEX:1461") "neuronames:351") @@ -167993,8 +165395,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metathalamus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1b/ThalamicNuclei.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (corticospinal tract) @@ -168006,7 +165407,6 @@ AnnotationAssertion( "BIRNLEX:1464") AnnotationAssertion( "BM:CST") AnnotationAssertion( "BM:Me-PyT") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006132") AnnotationAssertion( "DHBA:12776") AnnotationAssertion( "DMBA:17756") AnnotationAssertion( "EMAPA:36600") @@ -168036,8 +165436,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "corticospinal tract") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png"^^xsd:anyURI) -SubClassOf(Annotation( "In NIFSTD this is a tract of brain but this leads to issues due to its overlap with the spinal cord") ) -SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -168048,7 +165447,6 @@ AnnotationAssertion( "BIRNLEX:1499") AnnotationAssertion( "FMA:71166") AnnotationAssertion( "MA:0003081") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066193") AnnotationAssertion( "NCIT:C12892") AnnotationAssertion( "SCTID:180960003") AnnotationAssertion(Annotation( "BIRNLEX:1499") Annotation( "ncithesaurus:Cervical_Spinal_Cord") "UMLS:C0581619") @@ -168064,7 +165462,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibulocochlear nerve root) @@ -168087,7 +165487,9 @@ AnnotationAssertion( "UBERON:0002731") AnnotationAssertion(rdfs:label "vestibulocochlear nerve root") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basal forebrain) @@ -168101,7 +165503,6 @@ AnnotationAssertion( "EMAPA:35164") AnnotationAssertion( "FMA:77700") AnnotationAssertion( "HBA:4300") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066187") AnnotationAssertion( "PBA:128012976") AnnotationAssertion( "Wikipedia:Basal_forebrain") AnnotationAssertion(Annotation( "BIRNLEX:1560") "neuronames:1997") @@ -168128,6 +165529,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regional part of cerebellar cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior hypothalamic region) @@ -168157,7 +165560,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (left parietal lobe) AnnotationAssertion(Annotation( "BIRNLEX:1728") "Parietal lobe of the left hemisphere of the brain.") -AnnotationAssertion( ) AnnotationAssertion( "BIRNLEX:1728") AnnotationAssertion( "FMA:72974") AnnotationAssertion( "SCTID:314147009") @@ -168166,6 +165568,8 @@ AnnotationAssertion( "UBERON:0002802") AnnotationAssertion(rdfs:label "left parietal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right parietal lobe) @@ -168179,6 +165583,8 @@ AnnotationAssertion( "UBERON:0002803") AnnotationAssertion(rdfs:label "right parietal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left limbic lobe) @@ -168190,6 +165596,8 @@ AnnotationAssertion( "UBERON:0002804") AnnotationAssertion(rdfs:label "left limbic lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right limbic lobe) @@ -168200,6 +165608,8 @@ AnnotationAssertion( "UBERON:0002805") AnnotationAssertion(rdfs:label "right limbic lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left temporal lobe) @@ -168212,6 +165622,8 @@ AnnotationAssertion( "UBERON:0002808") AnnotationAssertion(rdfs:label "left temporal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right temporal lobe) @@ -168224,6 +165636,8 @@ AnnotationAssertion( "UBERON:0002809") AnnotationAssertion(rdfs:label "right temporal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right frontal lobe) @@ -168236,12 +165650,13 @@ AnnotationAssertion( "UBERON:0002810") AnnotationAssertion(rdfs:label "right frontal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left frontal lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A frontal cortex that is part of a left cerebral hemisphere.") -AnnotationAssertion( ) AnnotationAssertion( "BIRNLEX:1787") AnnotationAssertion( "FMA:72970") AnnotationAssertion( "SCTID:314142003") @@ -168250,12 +165665,13 @@ AnnotationAssertion( "UBERON:0002811") AnnotationAssertion(rdfs:label "left frontal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left cerebral hemisphere) AnnotationAssertion(Annotation( "OBOL:automatic") "A cerebral hemisphere that is in the left side of a brain.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "BIRNLEX:1795") AnnotationAssertion( "FMA:61819") AnnotationAssertion( "NCIT:C32955") @@ -168268,11 +165684,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right cerebral hemisphere) AnnotationAssertion(Annotation( "OBOL:automatic") "A cerebral hemisphere that is in the right side of a brain.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "BIRNLEX:1797") AnnotationAssertion( "FMA:67292") AnnotationAssertion( "NCIT:C33472") @@ -168285,14 +165702,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibulocochlear ganglion) AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003703") "The group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia.") AnnotationAssertion( "Consider follow MA naming scheme.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000588") Annotation( "TAO") Annotation( "ZFIN:curator") "The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000696") Annotation( "VHOG") Annotation( "PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010)") Annotation( "http://bgee.unil.ch/") "(During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG]") -AnnotationAssertion(Annotation( "Wikipedia:Cochlear_nerve") "The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus") AnnotationAssertion(Annotation( "ZFA:0000588") "SAG") AnnotationAssertion( "BIRNLEX:2564") AnnotationAssertion( "EFO:0003543") @@ -168330,9 +165746,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vestibulocochlear ganglion") SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK53175") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (ventral cochlear nucleus) @@ -168367,7 +165783,6 @@ AnnotationAssertion( "ventral cochlear nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (dorsal cochlear nucleus) @@ -168403,7 +165818,6 @@ AnnotationAssertion( "dorsal cochlear nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) # Class: (anteroventral cochlear nucleus) @@ -168466,6 +165880,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical dorsal root ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic dorsal root ganglion) @@ -168488,20 +165904,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic dorsal root ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypoglossal nucleus) AnnotationAssertion(Annotation( "BIRNLEX:2644") "Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453).") -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BAMS:12") AnnotationAssertion( "BAMS:12N") AnnotationAssertion( "BAMS:XII") @@ -168537,13 +165946,12 @@ AnnotationAssertion( "hypoglossal nucleus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of lateral olfactory tract) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BAMS:LOT") AnnotationAssertion( "BAMS:NLOT") AnnotationAssertion( "BIRNLEX:2702") @@ -168568,14 +165976,14 @@ AnnotationAssertion( "part of amygdala in FMA but this leads to inconsistency when combined with ABA partitions") AnnotationAssertion(rdfs:label "nucleus of lateral olfactory tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory cortex) AnnotationAssertion(Annotation( "BIRNLEX:2707") "Aggregate brain region defined as those areas of cerebral cortex receiving direct synaptic input from the olfactory bulb (Price, 1973). It usually includes the piriform cortex and sometimes other areas.") AnnotationAssertion( "consider relationship: receives_input_from UBERON:0002264 olfactory bulb") -AnnotationAssertion(Annotation( "BTO:0001446") "That portion of the cerebral cortex that, with the palaeocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archaeocortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals[BTO:0001446].") -AnnotationAssertion(Annotation( "GO:0021989") "The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO][GO:0021989].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000325") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)") Annotation( "http://bgee.unil.ch/") "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]") AnnotationAssertion( "BAMS:OLF") AnnotationAssertion( "BIRNLEX:2707") AnnotationAssertion( "BTO:0001446") @@ -168636,7 +166044,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray726_central_sulcus.svg"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/b6/Central_sulcus.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (longitudinal fissure) @@ -168676,7 +166087,6 @@ SubClassOf(Annotation( "FMA # Class: (trigeminal nucleus) AnnotationAssertion(Annotation( "OBOL:automatic") "A nucleus of brain that is part of a trigeminal nuclear complex.") -AnnotationAssertion(Annotation( "GO") Annotation( "https://github.com/obophenotype/mouse-anatomy-ontology/issues/58") "massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.") AnnotationAssertion( "BM:V") AnnotationAssertion( "BTO:0001074") AnnotationAssertion( "CALOHA:TS-2077") @@ -168703,7 +166113,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trigeminal nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gustatory epithelium) @@ -168715,7 +166126,9 @@ AnnotationAssertion( "UBERON:0002926") AnnotationAssertion(rdfs:label "gustatory epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dentate gyrus polymorphic layer) @@ -168735,12 +166148,13 @@ AnnotationAssertion(Annotation( "UBERON:0002928") AnnotationAssertion(rdfs:label "dentate gyrus polymorphic layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (granular layer of cerebellar cortex) AnnotationAssertion(Annotation( "GO:0021681") "The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BIRNLEX:779") AnnotationAssertion( "BTO:0004425") AnnotationAssertion( "CALOHA:TS-1247") @@ -168765,15 +166179,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "granular layer of cerebellar cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (molecular layer of cerebellar cortex) AnnotationAssertion(Annotation( "GO:0021679") "The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells.") AnnotationAssertion( "revisit logical definition after using brain layer patterns") -AnnotationAssertion( "Compare with ZFA:0000636 - cerebellar crest, which is also composed of parallel fibers but located in a more restricted nucleus within the cerebellum") AnnotationAssertion( "BAMS:thf") AnnotationAssertion( "BIRNLEX:810") AnnotationAssertion( "CALOHA:TS-1248") @@ -168798,13 +166213,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "molecular layer of cerebellar cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Purkinje cell layer of cerebellar cortex) AnnotationAssertion(Annotation( "GO:0021680") "The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells.") -AnnotationAssertion(Annotation( "ABA") ) AnnotationAssertion( "BIRNLEX:818") AnnotationAssertion( "BTO:0004909") AnnotationAssertion( "EMAPA:35223") @@ -168832,19 +166248,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Purkinje cell layer of cerebellar cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pontine tegmentum) AnnotationAssertion(Annotation( "BIRNLEX:923") "Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).") AnnotationAssertion( ) -AnnotationAssertion( "involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]") AnnotationAssertion( "BAMS:PTg") AnnotationAssertion( "BIRNLEX:923") AnnotationAssertion( "DHBA:12416") AnnotationAssertion( "FMA:71108") AnnotationAssertion( "HBA:9135") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D065821") AnnotationAssertion( "SCTID:362401009") AnnotationAssertion(Annotation( "BIRNLEX:923") "UMLS:C0228426") AnnotationAssertion( "Wikipedia:Pontine_tegmentum") @@ -168866,6 +166283,7 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -168875,7 +166293,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (septum) AnnotationAssertion(Annotation( "Wikipedia:Septum") "A wall, dividing a cavity or structure into smaller ones[WP].") -AnnotationAssertion( "septal") AnnotationAssertion( "AAO:0011127") AnnotationAssertion( "FMA:86461") AnnotationAssertion( "Wikipedia:Septum") @@ -168913,6 +166330,7 @@ AnnotationAssertion( "thoracic spinal cord") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal nerve fibers) @@ -168931,13 +166349,13 @@ AnnotationAssertion(Annotation( "UBERON:0003041") AnnotationAssertion(rdfs:label "trigeminal nerve fibers") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory placode) AnnotationAssertion(Annotation( "Wikipedia:Nasal_placode") Annotation( "XAO:0000005") "A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000186") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]") AnnotationAssertion( "AAO:0011076") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006222") AnnotationAssertion( "EFO:0003420") AnnotationAssertion( "EHDAA2:0001232") AnnotationAssertion( "EHDAA:1504") @@ -168961,18 +166379,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic") AnnotationAssertion(rdfs:label "olfactory placode") -SubClassOf(Annotation( "NCBIBook:NBK53171") Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ear vesicle) AnnotationAssertion(Annotation( "MP:0009806") Annotation( "Wikipedia:Otic_vesicle") "An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000051") Annotation( "TAO") Annotation( "ZFIN:curator") "Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001148") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001148") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413") Annotation( "http://bgee.unil.ch/") "The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]") -AnnotationAssertion(Annotation( "MP") "MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305") AnnotationAssertion( "UBERON:0004373") AnnotationAssertion( "AAO:0011080") AnnotationAssertion( "BTO:0002661") @@ -168999,15 +166412,18 @@ AnnotationAssertion( "ear vesicle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain-hindbrain boundary) AnnotationAssertion(Annotation( "GO:0021555") "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.") AnnotationAssertion( "consider adding class for organizer. Consider adding separate class for isthmus as a structure") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000649") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]") AnnotationAssertion( "AAO:0011064") AnnotationAssertion( "DMBA:16810") AnnotationAssertion( "EHDAA2:0004395") @@ -169034,19 +166450,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "midbrain-hindbrain boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ZFA") Annotation( "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (periderm) -AnnotationAssertion(Annotation( "ISBN:9780878932504") "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001185") Annotation( "TAO") Annotation( "ZFIN:curator") "The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001185") Annotation( "TAO") "relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]") -AnnotationAssertion( "In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]") -AnnotationAssertion( "In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis") -AnnotationAssertion( "Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0003377") +AnnotationAssertion(Annotation( "ISBN:9780878932504") Annotation( "PMID:25133425") Annotation( "PMID:35582825") "The outermost layer (or layers, depending on the species) of embryonic skin, essential for the development of the epidermis and establishment of the barrier functions. The periderm derives from the outer layer of the ectoderm.") AnnotationAssertion( "EHDAA2:0001846") AnnotationAssertion( "EHDAA:6538") AnnotationAssertion( "FMA:295662") @@ -169056,26 +166469,21 @@ AnnotationAssertion(Annotation( "VHOG:0001680") AnnotationAssertion( "XAO:0000029") AnnotationAssertion( "ZFA:0001185") -AnnotationAssertion(Annotation( "EHDAA2:0001846") "skin periderm") AnnotationAssertion( "uberon") -AnnotationAssertion(Annotation( "ZFA:0001185") "EVL") -AnnotationAssertion( "epidermis epithelial layer") -AnnotationAssertion( "epidermis outer layer") -AnnotationAssertion(Annotation( "MP:0013530") "epitrichium") -AnnotationAssertion( "periderm") +AnnotationAssertion(Annotation( "ZFA:0001185") Annotation( ) "EVL") +AnnotationAssertion(Annotation( "ZFA:0001185") "enveloping layer") +AnnotationAssertion(Annotation( "MP:0013530") Annotation( "PMID:28722897") "epitrichium") AnnotationAssertion( "UBERON:0003055") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "periderm") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (pre-chordal neural plate) AnnotationAssertion(Annotation( "XB:curator") "The portion of neural plate anterior to the mid-hindbrain junction.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001200") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "AAO:0011084") AnnotationAssertion( "TAO:0007016") AnnotationAssertion( "VHOG:0001200") @@ -169085,14 +166493,14 @@ AnnotationAssertion( "anterior neural plate") AnnotationAssertion( "UBERON:0003056") AnnotationAssertion(rdfs:label "pre-chordal neural plate") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (chordal neural plate) AnnotationAssertion(Annotation( "XB:curator") "The portion of neural plate posterior to the mid-hindbrain junction.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001201") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "TAO:0007017") AnnotationAssertion( "VHOG:0001201") AnnotationAssertion( "XAO:0000046") @@ -169101,15 +166509,13 @@ AnnotationAssertion( "posterior neural plate") AnnotationAssertion( "UBERON:0003057") AnnotationAssertion(rdfs:label "chordal neural plate") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (presomitic mesoderm) AnnotationAssertion(Annotation( "ZFIN:curator") "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000279") Annotation( "TAO") Annotation( "ZFIN:curator") "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000559") Annotation( "VHOG") Annotation( "DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)") Annotation( "http://bgee.unil.ch/") "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]") AnnotationAssertion( "AAO:0011086") AnnotationAssertion( "EFO:0001982") AnnotationAssertion( "EMAPA:16189") @@ -169131,22 +166537,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presomitic mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (pronephric duct) AnnotationAssertion(Annotation( "Wikipedia:Pronephric_duct") "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000150") Annotation( "TAO") Annotation( "ZFIN:curator") "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000082") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000082") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686") Annotation( "http://bgee.unil.ch/") "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]") AnnotationAssertion( "AAO:0011088") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0005991") AnnotationAssertion( "NCIT:C34279") AnnotationAssertion( "SCTID:361406002") AnnotationAssertion( "TAO:0000150") AnnotationAssertion(Annotation( "ncithesaurus:Pronephric_Duct") "UMLS:C1283945") -AnnotationAssertion( "VHOG:0000082") AnnotationAssertion( "Wikipedia:Pronephric_duct") AnnotationAssertion( "XAO:0000063") AnnotationAssertion( "ZFA:0000150") @@ -169159,6 +166562,7 @@ AnnotationAssertion( "The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]") AnnotationAssertion(rdfs:label "pronephric duct") SubClassOf(Annotation( "GO") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) @@ -169166,11 +166570,6 @@ SubClassOf(Annotation( "XAO # Class: (blood island) AnnotationAssertion(Annotation( "Wikipedia:Blood_island_of_umbilical_vesicle") "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000094") Annotation( "TAO") Annotation( "ZFIN:curator") "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011006") Annotation( "AAO") Annotation( "AAO:EJS") "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000094") Annotation( "TAO") "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000085") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)") Annotation( "http://bgee.unil.ch/") "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac") AnnotationAssertion( "ventral lateral plate mesoderm") AnnotationAssertion( "AAO:0011006") AnnotationAssertion( "EFO:0003489") @@ -169196,8 +166595,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood island") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -169205,9 +166603,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0838580343") Annotation( "MP:0004387") "A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue.") AnnotationAssertion( "TODO - check; developmental relationship to anterior hypoblast in ZFA?") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000060") Annotation( "TAO") Annotation( "ZFIN:curator") "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000086") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000086") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)") Annotation( "http://bgee.unil.ch/") "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]") AnnotationAssertion( "UBERON:0004881") AnnotationAssertion(Annotation( "XAO:0000079") "head mesenchyme") AnnotationAssertion(Annotation( "XAO:0000079") "head mesoderm") @@ -169226,16 +166621,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prechordal plate") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:16313393") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intermediate mesoderm) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "Wikipedia:Intermediate_mesoderm") "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010575") Annotation( "AAO") Annotation( "AAO:EJS") "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000087") Annotation( "VHOG") Annotation( "Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43") Annotation( "http://bgee.unil.ch/") "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').") AnnotationAssertion( "AAO:0010575") AnnotationAssertion( "EMAPA:16056") AnnotationAssertion( "EMAPA:16178") @@ -169260,8 +166652,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intermediate mesoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "AAO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) @@ -169271,10 +166662,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pharyngeal arch 2) AnnotationAssertion(Annotation( "PMID:12784288") Annotation( "ZFIN:yb") Annotation( "https://github.com/obophenotype/uberon/issues/258") "The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010363") Annotation( "AAO") Annotation( "XAO:EJS") "The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000297") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "in XAO, develops from visceral pouch 2") -AnnotationAssertion( "2"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010363") AnnotationAssertion( "EHDAA2:0000050") AnnotationAssertion( "EHDAA:611") @@ -169312,7 +166699,6 @@ SubClassOf( (dorsolateral placode) AnnotationAssertion(Annotation( "ZFIN:curator") "Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000103") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)") Annotation( "http://bgee.unil.ch/") "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]") AnnotationAssertion( "TAO:0001310") AnnotationAssertion( "VHOG:0000103") AnnotationAssertion( "XAO:0000187") @@ -169328,7 +166714,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (axial mesoderm) AnnotationAssertion(Annotation( "GO:0048318") Annotation( "Wikipedia:Chordamesoderm") "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000107") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]") AnnotationAssertion( "AAO:0011017") AnnotationAssertion( "EFO:0003647") AnnotationAssertion( "TAO:0001204") @@ -169343,8 +166728,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "axial mesoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -169352,9 +166736,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (otic placode) AnnotationAssertion(Annotation( "NCBIBook:NBK53175") Annotation( "Wikipedia:Otic_placode") "A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000138") Annotation( "TAO") Annotation( "ZFIN:curator") "Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000235") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]") -AnnotationAssertion(Annotation( "NCBIBook:NBK53175") "With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991).") AnnotationAssertion( "AAO:0011079") AnnotationAssertion( "EFO:0003429") AnnotationAssertion( "EHDAA2:0001339") @@ -169381,16 +166762,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "otic placode") -SubClassOf(Annotation( "invaginates") Annotation( "NCBIBook:NBK53175") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal placode complex) AnnotationAssertion(Annotation( "PMID:22512454") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/693") "A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion.") -AnnotationAssertion(Annotation( "XAO") "The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000162") Annotation( "TAO") Annotation( "ZFIN:curator") "The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000109") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)") Annotation( "http://bgee.unil.ch/") "The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]") -AnnotationAssertion( "Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'") AnnotationAssertion( "EFO:0003433") AnnotationAssertion( "EHDAA2:0004209") AnnotationAssertion( "TAO:0000162") @@ -169412,7 +166789,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (eye primordium) AnnotationAssertion(Annotation( "GO:0046619") Annotation( "ZFA:0000570") "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.") -AnnotationAssertion(Annotation( "GO") "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.") AnnotationAssertion( "UBERON:0005060") AnnotationAssertion( "AAO:0011038") AnnotationAssertion( "EFO:0003541") @@ -169437,13 +166813,17 @@ AnnotationAssertion( "eye primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PMID:16496288") Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic cup) AnnotationAssertion(Annotation( "MP:0004269") Annotation( "Wikipedia:Optic_cup_(embryology)") Annotation( "ZFA:0001202") "Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000167") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]") AnnotationAssertion( "BTO:0005351") AnnotationAssertion( "EHDAA2:0001303") AnnotationAssertion( "EHDAA:2912") @@ -169464,6 +166844,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "optic cup") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -169471,9 +166852,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (lens placode) AnnotationAssertion(Annotation( "Wikipedia:Lens_placode") Annotation( "ZFIN:curator") "A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000122") Annotation( "TAO") Annotation( "ZFIN:curator") "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000166") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]") -AnnotationAssertion(Annotation( "NCBIBook:NBK53175") "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)") AnnotationAssertion( "AAO:0011055") AnnotationAssertion( "EFO:0003494") AnnotationAssertion( "EHDAA2:0000982") @@ -169499,31 +166877,27 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric duct) AnnotationAssertion(Annotation( "Wikipedia:Mesonephric_duct") Annotation( "ZFIN:curator") Annotation( "https://github.com/obophenotype/uberon/issues/28") "Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].") AnnotationAssertion( "Consider adding subclasses for male and female specific variants") AnnotationAssertion( "TODO - mesonephric portion of the nephric duct") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000637") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000082") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000082") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686") Annotation( "http://bgee.unil.ch/") "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]") -AnnotationAssertion( "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.") AnnotationAssertion( "AAO:0000637") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0005990") AnnotationAssertion( "EHDAA2:0001243") AnnotationAssertion( "EHDAA:1590") -AnnotationAssertion( "EMAPA:16577") AnnotationAssertion( "GAID:1315") AnnotationAssertion( "MESH:D014928") AnnotationAssertion( "NCIT:C26469") AnnotationAssertion( "SCTID:308800003") AnnotationAssertion( "TAO:0000546") AnnotationAssertion(Annotation( "ncithesaurus:Mesonephric_Duct") "UMLS:C0043204") -AnnotationAssertion( "VHOG:0000082") AnnotationAssertion( "Wikipedia:Mesonephric_duct") AnnotationAssertion( "XAO:0000242") AnnotationAssertion( "ZFA:0000546") @@ -169539,16 +166913,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesonephric duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "GO") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (neural plate) AnnotationAssertion(Annotation( "ISBN:0815318960") Annotation( "OMD:neural+plate") Annotation( "Wikipedia:Neural_plate") Annotation( "ZFIN:curator") "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000132") Annotation( "TAO") Annotation( "ZFIN:curator") "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000068") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "AAO:0011072") AnnotationAssertion( "BTO:0001765") AnnotationAssertion( "DHBA:10153") @@ -169557,7 +166929,6 @@ AnnotationAssertion( "EHDAA:902") AnnotationAssertion( "EMAPA:35593") AnnotationAssertion( "FMA:293879") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054258") AnnotationAssertion( "NCIT:C34225") AnnotationAssertion( "RETIRED_EHDAA2:0001252") AnnotationAssertion( "TAO:0000132") @@ -169576,7 +166947,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural plate") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png"^^xsd:anyURI) -SubClassOf(Annotation( "GO") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "GOTAX:0000352") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -169584,7 +166956,6 @@ SubClassOf(Annotation( "Bge # Class: (posterior neural tube) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001383") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "AAO:0011082") AnnotationAssertion( "TAO:0007037") AnnotationAssertion( "VHOG:0001383") @@ -169593,7 +166964,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003076") AnnotationAssertion(rdfs:label "posterior neural tube") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) @@ -169601,9 +166972,6 @@ DisjointClasses(Annotation( # Class: (paraxial mesoderm) AnnotationAssertion(Annotation( "GO:0048339") Annotation( "https://github.com/obophenotype/uberon/issues/30") "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010568") Annotation( "AAO") Annotation( "AAO:EJS") "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000114") Annotation( "VHOG") Annotation( "DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)") Annotation( "http://bgee.unil.ch/") "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)") AnnotationAssertion( "AAO:0010568") AnnotationAssertion( "EFO:0003515") AnnotationAssertion( "EMAPA:16183") @@ -169627,8 +166995,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paraxial mesoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) @@ -169636,10 +167005,6 @@ SubClassOf(Annotation( "Bge # Class: (epibranchial placode) AnnotationAssertion(Annotation( "VHOG:0000117") "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000117") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000117") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]") -AnnotationAssertion(Annotation( "NCBIBook:NBK53175") "Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively") -AnnotationAssertion(Annotation( "XAO") "in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group") AnnotationAssertion( "AAO:0011036") AnnotationAssertion( "EFO:0003455") AnnotationAssertion( "FMA:293968") @@ -169655,14 +167020,12 @@ AnnotationAssertion( "epibranchial placode") SubClassOf(Annotation( "NCBIBook:NBK53175") Annotation( "ZFA") ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior neural tube) AnnotationAssertion( "TODO - add grouping class for the anterior end of the neural tube at all stages") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001384") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "AAO:0011012") AnnotationAssertion( "TAO:0007038") AnnotationAssertion( "VHOG:0001384") @@ -169671,18 +167034,13 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003080") AnnotationAssertion(rdfs:label "anterior neural tube") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral plate mesoderm) AnnotationAssertion(Annotation( "MP:0010117") Annotation( "Wikipedia:Lateral_plate_mesoderm") "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010574") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000118") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000118") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)") Annotation( "http://bgee.unil.ch/") "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "subclass of mesoderm in ZFA.") AnnotationAssertion( "UBERON:0006258") AnnotationAssertion( "AAO:0010574") AnnotationAssertion( "EHDAA2:0000919") @@ -169708,19 +167066,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lateral plate mesoderm") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") Annotation( "VHOG") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (myotome) AnnotationAssertion(Annotation( "AEO:0001018") "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.") AnnotationAssertion( "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001056") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001244") Annotation( "VHOG") Annotation( "DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]") AnnotationAssertion( "AAO:0011067") AnnotationAssertion( "AEO:0001018") AnnotationAssertion( "BTO:0000742") @@ -169753,15 +167110,12 @@ AnnotationAssertion( "myotome") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png"^^xsd:anyURI) SubClassOf(Annotation( "AEO") ) -SubClassOf(Annotation( "WP") Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk neural crest) AnnotationAssertion(Annotation( "ISBN:0815318960") Annotation( "Wikipedia:Trunk_neural_crest") "Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010582") Annotation( "AAO") Annotation( "AAO:EJS") "Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000062") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "AAO:0010582") AnnotationAssertion( "EFO:0003605") AnnotationAssertion( "EHDAA2:0001901") @@ -169777,7 +167131,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk neural crest") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -169785,9 +167141,6 @@ SubClassOf(Annotation( "ZFA AnnotationAssertion(Annotation( "ZFIN:curator") "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.") AnnotationAssertion( "should probably be merged with heart rudiment.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000028") Annotation( "TAO") Annotation( "ZFIN:curator") "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011044") Annotation( "AAO") Annotation( "XAO:curator") "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000028") Annotation( "TAO") "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]") AnnotationAssertion( "AAO:0011044") AnnotationAssertion( "BTO:0001887") AnnotationAssertion( "NCIT:C34276") @@ -169810,8 +167163,6 @@ SubClassOf(Annotation( "XAO # Class: (caudal artery) AnnotationAssertion(Annotation( "Wikipedia:Caudal_artery") Annotation( "ZFIN:curator") "Extension of the dorsal aorta in the tail.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000011") Annotation( "TAO") Annotation( "ZFIN:curator") "Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011023") Annotation( "AAO") Annotation( "ISBN:0-226-55763-4") "The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]") AnnotationAssertion( "AAO:0011023") AnnotationAssertion( "EFO:0003472") AnnotationAssertion( "TAO:0000011") @@ -169826,17 +167177,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "caudal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sclerotome) AnnotationAssertion(Annotation( "Wikipedia:Sclerotome") Annotation( "XB:curator") Annotation( "https://github.com/obophenotype/uberon/issues/316") "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010571") Annotation( "AAO") Annotation( "AAO:EJS") "Skeletogenic portion of somites.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000680") Annotation( "VHOG") Annotation( "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)") Annotation( "http://bgee.unil.ch/") "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "part_of somite in XAO") AnnotationAssertion( "AAO:0010571") AnnotationAssertion( "AEO:0000212") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006255") AnnotationAssertion( "EHDAA2:0003439") AnnotationAssertion( "EMAPA:31159") AnnotationAssertion( "FMA:295652") @@ -169864,9 +167214,6 @@ SubClassOf(Annotation( "ZFA # Class: (thyroid primordium) AnnotationAssertion(Annotation( "http://emedicine.medscape.com/article/845125-overview") "The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus.") -AnnotationAssertion(Annotation( "ZFIN:curator") "Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator].") -AnnotationAssertion(Annotation( "PMID:16313389") "In all vertebrates the thyroid arises from the ventral aspect of the second pouch") -AnnotationAssertion(Annotation( "EHDAA2") "Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm") AnnotationAssertion( "AAO:0011106") AnnotationAssertion( "BTO:0004709") AnnotationAssertion( "EHDAA2:0002033") @@ -169884,6 +167231,7 @@ AnnotationAssertion( "thyroid primordium") SubClassOf(Annotation( "ZFA") ) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) @@ -169891,8 +167239,6 @@ SubClassOf(Annotation( "ISB # Class: (optic stalk) AnnotationAssertion(Annotation( "ISBN:0-914294-08-3") Annotation( "MP:0004268") "The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000223") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/optic+stalk") "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000223") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]") AnnotationAssertion( "AAO:0011077") AnnotationAssertion( "EHDAA2:0001318") AnnotationAssertion( "EHDAA:3816") @@ -169914,6 +167260,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "optic stalk") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -169921,9 +167268,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cranial neural crest) AnnotationAssertion(Annotation( "MGI:anna") "Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010580") Annotation( "AAO") Annotation( "AAO:EJS") "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001194") Annotation( "TAO") Annotation( "ZFIN:curator") "Neural crest that is part of the head.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000063") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "AAO:0010580") AnnotationAssertion( "EFO:0003645") AnnotationAssertion( "EHDAA2:0004420") @@ -169946,18 +167290,18 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cranial neural crest") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (female organism) AnnotationAssertion(Annotation( "CARO:0000028") "Gonochoristic organism that can produce female gametes.") -AnnotationAssertion( ) AnnotationAssertion( "AAO:0010030") AnnotationAssertion( "BILA:0000028") AnnotationAssertion( "CARO:0000028") -AnnotationAssertion(Annotation( ) "FBbt:00007011") AnnotationAssertion( "FMA:67812") AnnotationAssertion( "HAO:0000028") AnnotationAssertion( "SCTID:362608006") @@ -169981,7 +167325,6 @@ AnnotationAssertion(Annotation( "AAO:0010033") AnnotationAssertion( "BILA:0000027") AnnotationAssertion( "CARO:0000027") -AnnotationAssertion(Annotation( ) "FBbt:00007004") AnnotationAssertion( "FMA:67811") AnnotationAssertion( "HAO:0000027") AnnotationAssertion( "SCTID:362609003") @@ -170003,7 +167346,6 @@ SubClassOf( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/24") "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.") AnnotationAssertion( "consider obsoleting. See issue/1305") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000292") Annotation( "TAO") Annotation( "ZFIN:curator") "Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]") AnnotationAssertion( "AAO:0010337") AnnotationAssertion( "AEO_RETIRED:0000010") AnnotationAssertion( "EHDAA2_RETIRED:0003010") @@ -170027,7 +167369,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (compound organ) AnnotationAssertion(Annotation( "CARO:0000024") "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.") -AnnotationAssertion( "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs") AnnotationAssertion( "AAO:0010015") AnnotationAssertion( "AEO:0000024") AnnotationAssertion( "BILA:0000024") @@ -170052,9 +167393,6 @@ SubClassOf( "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up") Annotation( "https://en.wikipedia.org/wiki/Mesenchyme") Annotation( "https://github.com/obophenotype/uberon/issues/1641") "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.") AnnotationAssertion( "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000393") Annotation( "TAO") Annotation( "ZFIN:curator") "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010427") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]") -AnnotationAssertion( "mesenchymal") AnnotationAssertion( "AAO:0010427") AnnotationAssertion( "AEO:0000145") AnnotationAssertion( "BTO:0001393") @@ -170081,15 +167419,13 @@ AnnotationAssertion( "mesenchyme") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (otic region) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000189") Annotation( "TAO") Annotation( "TAO:MAH") "Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010208") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000189") Annotation( "TAO") "relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO]") -AnnotationAssertion( "UBERONREF:0000007 has this as a syn for otic capsule") AnnotationAssertion( "AAO:0010208") AnnotationAssertion( "TAO:0000189") AnnotationAssertion( "XAO:0003175") @@ -170105,7 +167441,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (sphenoid region) AnnotationAssertion(Annotation( "TAO:0000290") Annotation( "UBERONREF:0000007") "Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010207") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO]") AnnotationAssertion( "AAO:0010207") AnnotationAssertion( "TAO:0000290") AnnotationAssertion( "XAO:0003174") @@ -170120,8 +167455,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (olfactory region) AnnotationAssertion(Annotation( "TAO:0000351") "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000351") Annotation( "TAO") Annotation( "TAO:MAH") "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010206") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]") AnnotationAssertion( "AAO:0010206") AnnotationAssertion( "EFO:0003525") AnnotationAssertion( "NCIT:C98765") @@ -170142,8 +167475,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Skull_roof") Annotation( "ZFA:0000863") "Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].") AnnotationAssertion( "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007") AnnotationAssertion(Annotation( "ISBN:0073040584") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000863") Annotation( "TAO") Annotation( "ZFIN:curator") "Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010154") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]") AnnotationAssertion( "AAO:0010154") AnnotationAssertion( "TAO:0000863") AnnotationAssertion( "VHOG:0001665") @@ -170165,17 +167496,12 @@ AnnotationAssertion( "UBERON:0003113") AnnotationAssertion(rdfs:label "dermatocranium") SubClassOf( ) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch 3) AnnotationAssertion(Annotation( "MP:0006339") "The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010365") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000298") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "in XAO, called branchial arch 1 and df VP3") -AnnotationAssertion( "3"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010365") AnnotationAssertion( "EHDAA2:0000069") AnnotationAssertion( "EHDAA:1080") @@ -170206,10 +167532,6 @@ SubClassOf( (pharyngeal arch 4) AnnotationAssertion(Annotation( "MP:0006340") "Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010366") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000299") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "in XAO, called branchial arch 2 and df VP4") -AnnotationAssertion( "4"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010366") AnnotationAssertion( "EHDAA2:0000086") AnnotationAssertion( "EHDAA:1663") @@ -170241,11 +167563,6 @@ SubClassOf( (pharyngeal arch 5) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010367") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001204") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion( "A fifth arch never establishes itself in amniotes") -AnnotationAssertion(Annotation( "XAO") "in XAO, called branchial arch 3 and df VP5") -AnnotationAssertion( "5"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010367") AnnotationAssertion( "FMA:293045") AnnotationAssertion( "SCTID:308771006") @@ -170269,9 +167586,6 @@ SubClassOf( (pharyngeal arch 6) AnnotationAssertion(Annotation( "MP:0006347") "The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010368") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001205") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion( "6"^^xsd:nonNegativeInteger) AnnotationAssertion( "UBERON:0004349") AnnotationAssertion( "AAO:0010368") AnnotationAssertion( "EHDAA2:0004075") @@ -170301,8 +167615,6 @@ SubClassOf( (pharyngeal arch artery 1) AnnotationAssertion(Annotation( "MP:0010355") "The vessels formed within the first pair of branchial arches in embryogenesis.") -AnnotationAssertion( "Disappears early in development in tetrapods") -AnnotationAssertion(Annotation( "ZFA") "ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas") AnnotationAssertion( "UBERON:0004371") AnnotationAssertion( "AAO:0010415") AnnotationAssertion( "EHDAA2:0000007") @@ -170329,13 +167641,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery 1") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch artery 2) AnnotationAssertion(Annotation( "MP:0010356") "The vessels formed within the second pair of branchial arches in embryogenesis.") -AnnotationAssertion(Annotation( "Wikipedia:Aortic_arches#Arches_1_and_2") "The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010418") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]") AnnotationAssertion( "UBERON:0004372") AnnotationAssertion( "AAO:0010418") AnnotationAssertion( "EHDAA2:0000051") @@ -170362,14 +167674,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery 2") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch artery 3) AnnotationAssertion(Annotation( "MP:0006356") "The vessels formed within the third pair of branchial arches in embryogenesis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005007") Annotation( "TAO") Annotation( "ZFIN:curator") "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]") -AnnotationAssertion(Annotation( "Wikipedia:Aortic_arches#Arch_3") "The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010419") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]") AnnotationAssertion( "UBERON:0004352") AnnotationAssertion( "AAO:0010419") AnnotationAssertion( "EHDAA2:0000070") @@ -170395,15 +167706,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery 3") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch artery 4) AnnotationAssertion(Annotation( "MP:0006354") "The vessels formed within the fourth pair of branchial arches in embryogenesis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005008") Annotation( "TAO") Annotation( "ZFIN:curator") "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010420") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia:Aortic_arches#Arch_4") "The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].") -AnnotationAssertion( "Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta") AnnotationAssertion( "UBERON:0004350") AnnotationAssertion( "AAO:0010420") AnnotationAssertion( "EHDAA2:0000087") @@ -170429,14 +167738,12 @@ AnnotationAssertion( "proximal right subclavian") AnnotationAssertion(rdfs:label "pharyngeal arch artery 4") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch artery 5) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The vessels formed within the fifth pair of pharyngeal arches in embryogenesis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005009") Annotation( "TAO") Annotation( "ZFIN:curator") "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]") -AnnotationAssertion(Annotation( "Wikipedia:Aortic_arches#Arch_5") "The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010421") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO]") -AnnotationAssertion( "In humans the 5th arch disappears on both sides") AnnotationAssertion( "AAO:0010421") AnnotationAssertion( "SCTID:308778000") AnnotationAssertion( "TAO:0005009") @@ -170452,14 +167759,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery 5") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch artery 6) AnnotationAssertion(Annotation( "MP:0006355") "The vessels formed within the sixth pair of branchial arches in embryogenesis.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005016") Annotation( "TAO") Annotation( "ZFIN:curator") "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010422") Annotation( "AAO") Annotation( "ISBN:0-02-377110-0") "The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]") -AnnotationAssertion(Annotation( "Wikipedia:Aortic_arches#Arch_6") "The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].") -AnnotationAssertion(Annotation( "http://emedicine.medscape.com/article/899609-overview") "the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries") AnnotationAssertion( "UBERON:0004351") AnnotationAssertion( "AAO:0010422") AnnotationAssertion( "EHDAA2:0000102") @@ -170485,17 +167790,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery 6") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chorion membrane) AnnotationAssertion(Annotation( "MESH:A10.615.284.473") Annotation( "MP:0002836") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/geneontology/go-ontology/issues/22603") "The outermost extraembryonic membrane of amniotes.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000200") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/chorion") "The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]") -AnnotationAssertion(Annotation( "BTO:0000252") "The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000200") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187") Annotation( "http://bgee.unil.ch/") "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]") -AnnotationAssertion( "chorionic") -AnnotationAssertion( "The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584]") -AnnotationAssertion(Annotation( "PMID:19829370") "Extra-embryonic ectoderm") AnnotationAssertion( "BTO:0000252") AnnotationAssertion( "CALOHA:TS-0144") AnnotationAssertion( "EFO:0002780") @@ -170528,6 +167829,7 @@ AnnotationAssertion( "This term refers to the amniote structure. It is distinct from the concept of chorion in insects") AnnotationAssertion(rdfs:label "chorion membrane") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -170539,12 +167841,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0060438") Annotation( "Wikipedia:Vertebrate_trachea") "The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010140") Annotation( "AAO") Annotation( "AAO:BJB") "An elongated tube which carries air to and from the lungs.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000371") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000371") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409") Annotation( "http://bgee.unil.ch/") "In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]") -AnnotationAssertion( "tracheal") -AnnotationAssertion( "In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.") -AnnotationAssertion(Annotation( "ISBN:0123813611") "in mouse 15-18 C-rings, 15-20 in human.") AnnotationAssertion( "AAO:0010140") AnnotationAssertion( "BTO:0001388") AnnotationAssertion( "CALOHA:TS-1060") @@ -170600,6 +167896,7 @@ AnnotationAssertion( "UBERON:0003127") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "open tracheal system trachea") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -170608,19 +167905,13 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cranium) AnnotationAssertion(Annotation( "Wikipedia:Cranium_(anatomy)") Annotation( "http://orcid.org/0000-0002-6601-2165") "Upper portion of the skull that excludes the mandible (when present in the organism).") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "cranial") -AnnotationAssertion(Annotation( "FMA") "the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium") -AnnotationAssertion(Annotation( "WP") "The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton") AnnotationAssertion( "BTO:0001328") AnnotationAssertion( "EFO:0000831") AnnotationAssertion( "EHDAA:6029") -AnnotationAssertion( "EMAPA:17680") AnnotationAssertion( "FMA:71325") AnnotationAssertion( "MA:0000316") AnnotationAssertion( "MAT:0000340") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D012886") AnnotationAssertion( "MIAA:0000340") AnnotationAssertion( "SCTID:181889008") AnnotationAssertion( "VHOG:0000334") @@ -170645,9 +167936,6 @@ SubClassOf(Annotation( "FMA # Class: (skull) AnnotationAssertion(Annotation( "PMID:11523816") Annotation( "Wikipedia:Skull") Annotation( "http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376") "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].") -AnnotationAssertion(Annotation( "FMA") "in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.") -AnnotationAssertion( "in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton") -AnnotationAssertion(Annotation( "WP") "A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates") AnnotationAssertion( "BTO:0001295") AnnotationAssertion( "CALOHA:TS-2344") AnnotationAssertion( "EHDAA2:0000325") @@ -170669,6 +167957,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skull") SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -170678,8 +167967,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (reproductive organ) AnnotationAssertion(Annotation( "UBERON:xp") "An organ involved in reproduction.") -AnnotationAssertion(Annotation( "GO") "GO uses genitalia for the singular organ") -AnnotationAssertion( "EMAPA:17381") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37731") AnnotationAssertion( "MA:0001752") AnnotationAssertion( "MESH:D005835") @@ -170700,7 +167987,8 @@ AnnotationAssertion( "reproductive organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female reproductive organ) @@ -170756,7 +168044,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (blood nerve barrier) AnnotationAssertion(Annotation( "GO:0008065") Annotation( "Wikipedia:Blood-nerve_barrier") "Barrier between the perineurium of peripheral nerves and the vascular endothelium of endoneurial capillaries. The perineurium acts as a diffusion barrier, but ion permeability at the blood-nerve barrier is still higher than at the blood-brain barrier[GO].") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D049428") AnnotationAssertion( "Wikipedia:Blood-nerve_barrier") AnnotationAssertion( "blood-nerve barrier") AnnotationAssertion( "uberon") @@ -170777,7 +168064,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood-cerebrospinal fluid barrier") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -170786,7 +168073,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (gustatory organ) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912).") -AnnotationAssertion(Annotation( ) "FBbt:00005159") AnnotationAssertion( "FMA:77853") AnnotationAssertion(Annotation( "OBOL:automatic") "gustatory organ system organ") AnnotationAssertion(Annotation( "OBOL:automatic") "gustatory system organ") @@ -170801,6 +168087,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland alveolus) @@ -170824,15 +168111,14 @@ AnnotationAssertion( "mammary gland alveolus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (alveolus) AnnotationAssertion(Annotation( "Wikipedia:Alveolus") "Organ part that has the form of a hollow cavity[WP].") -AnnotationAssertion( "alveolar") AnnotationAssertion( "EFO:0002513") -AnnotationAssertion( "EV:0100043") AnnotationAssertion( "FMA:82493") AnnotationAssertion( "NCIT:C12986") AnnotationAssertion(Annotation( "ncithesaurus:Alveolus") "UMLS:C0034051") @@ -170850,12 +168136,12 @@ AnnotationAssertion( "UBERON:0003218") AnnotationAssertion(rdfs:label "ovary septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric mesenchyme) AnnotationAssertion(Annotation( "GO:0072075") Annotation( "Wikipedia:Metanephric_blastema") "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000540") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme") "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000540") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462") Annotation( "http://bgee.unil.ch/") "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0004062") AnnotationAssertion( "EHDAA:4041") AnnotationAssertion( "EHDAA:5021") @@ -170874,16 +168160,17 @@ AnnotationAssertion( "Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 \"Developmental Biology\"]") AnnotationAssertion(rdfs:label "metanephric mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (phalanx) AnnotationAssertion(Annotation( "VSAO:0000199") Annotation( "Wikipedia:Phalanx_bones") "Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.") -AnnotationAssertion( "phalangeal") -AnnotationAssertion(Annotation( "WP") "In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three") AnnotationAssertion( "CALOHA:TS-2211") AnnotationAssertion( "EMAPA:32614") AnnotationAssertion( "FMA:321661") @@ -170904,7 +168191,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phalanx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -170918,8 +168207,9 @@ AnnotationAssertion( "UBERON:0003224") AnnotationAssertion(rdfs:label "chorion syncytiotrophoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "polar trophectoderm syncytiotrophoblast") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of elbow) @@ -170940,6 +168230,8 @@ AnnotationAssertion( "UBERON:0003229") AnnotationAssertion(rdfs:label "epithelium of elbow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of carpal region) @@ -170959,6 +168251,8 @@ AnnotationAssertion( "epithelium of carpal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of hip) @@ -170984,6 +168278,8 @@ AnnotationAssertion( "UBERON:0003231") AnnotationAssertion(rdfs:label "epithelium of hip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of knee) @@ -171001,6 +168297,8 @@ AnnotationAssertion( "UBERON:0003232") AnnotationAssertion(rdfs:label "epithelium of knee") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of shoulder) @@ -171018,6 +168316,8 @@ AnnotationAssertion( "UBERON:0003233") AnnotationAssertion(rdfs:label "epithelium of shoulder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of upper jaw) @@ -171025,7 +168325,6 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a upper jaw [Automatically generated definition].") AnnotationAssertion( "EHDAA2:0002119") AnnotationAssertion( "EHDAA:8027") -AnnotationAssertion( "EMAPA:17943") AnnotationAssertion( "EMAPA:18971") AnnotationAssertion(Annotation( "OBOL:automatic") "epithelial tissue of palatoquadrate arch") AnnotationAssertion(Annotation( "OBOL:automatic") "epithelial tissue of upper jaw") @@ -171038,6 +168337,8 @@ AnnotationAssertion( "UBERON:0003235") AnnotationAssertion(rdfs:label "epithelium of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of lower jaw) @@ -171057,6 +168358,8 @@ AnnotationAssertion( "UBERON:0003236") AnnotationAssertion(rdfs:label "epithelium of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of utricle) @@ -171064,10 +168367,6 @@ AnnotationAssertion(Annotation( "TODO - check relationships w.r.t macula") AnnotationAssertion( "EHDAA:4730") AnnotationAssertion( "EMAPA:17295") -AnnotationAssertion( "EMAPA:17298") -AnnotationAssertion( "EMAPA:17301") -AnnotationAssertion( "EMAPA:17820") -AnnotationAssertion( "EMAPA:17823") AnnotationAssertion( "FMA:75604") AnnotationAssertion( "MA:0001204") AnnotationAssertion( "RETIRED_EHDAA2:0002155") @@ -171093,7 +168392,6 @@ AnnotationAssertion( "epithelium of utricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -171129,7 +168427,8 @@ AnnotationAssertion(Annotation( "UBERON:0003242") AnnotationAssertion(rdfs:label "epithelium of saccule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -171156,6 +168455,8 @@ AnnotationAssertion( "UBERON:0003243") AnnotationAssertion(rdfs:label "epithelium of cochlear duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of mammary gland) @@ -171180,6 +168481,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -171196,6 +168499,8 @@ AnnotationAssertion( "UBERON:0003247") AnnotationAssertion(rdfs:label "epithelium of forearm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of footplate) @@ -171212,6 +168517,9 @@ AnnotationAssertion( "epithelium of footplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (epithelium of otic placode) @@ -171231,11 +168539,14 @@ AnnotationAssertion( "UBERON:0003249") AnnotationAssertion(rdfs:label "epithelium of otic placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic rib cage) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002100") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical cluster that consists of more than one rib in an individual.[TAO]") AnnotationAssertion( "FMA:7480") AnnotationAssertion( "SCTID:361741004") AnnotationAssertion( "Wikipedia:Human_rib_cage") @@ -171251,7 +168562,6 @@ AnnotationAssertion( "thoracic rib cage") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf(Annotation( "check other species") Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -171271,6 +168581,7 @@ AnnotationAssertion( "neck of rib") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "PMID:15906248") ObjectSomeValuesFrom( )) # Class: (amniotic ectoderm) @@ -171292,8 +168603,9 @@ AnnotationAssertion( "amniotic ectoderm") SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2-via-amnioblasts") Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) # Class: (yolk sac endoderm) @@ -171307,6 +168619,9 @@ AnnotationAssertion( "yolk sac endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endoderm of foregut) @@ -171319,6 +168634,9 @@ AnnotationAssertion( "UBERON:0003258") AnnotationAssertion(rdfs:label "endoderm of foregut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (endoderm of midgut) @@ -171333,6 +168651,9 @@ AnnotationAssertion( "UBERON:0003259") AnnotationAssertion(rdfs:label "endoderm of midgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (endoderm of hindgut) @@ -171345,6 +168666,9 @@ AnnotationAssertion( "UBERON:0003260") AnnotationAssertion(rdfs:label "endoderm of hindgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (thyroid primordium endoderm) @@ -171359,6 +168683,9 @@ AnnotationAssertion( "UBERON:0003261") AnnotationAssertion(rdfs:label "thyroid primordium endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA-propagated") ObjectSomeValuesFrom( )) # Class: (amniotic mesoderm) @@ -171385,8 +168712,8 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (chorionic mesenchyme) @@ -171410,8 +168737,9 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (tooth of upper jaw) @@ -171429,13 +168757,15 @@ AnnotationAssertion( "UBERON:0003267") AnnotationAssertion(rdfs:label "tooth of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tooth of lower jaw) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary).") -AnnotationAssertion( "EHDAA2:0001029") AnnotationAssertion( "EHDAA:8009") AnnotationAssertion( "EMAPA:17917") AnnotationAssertion( "FMA:321647") @@ -171453,6 +168783,9 @@ AnnotationAssertion( "UBERON:0003268") AnnotationAssertion(rdfs:label "tooth of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -171470,12 +168803,13 @@ AnnotationAssertion(Annotation( "UBERON:0003269") AnnotationAssertion(rdfs:label "skeletal muscle tissue of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of upper jaw) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000429") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101") Annotation( "http://bgee.unil.ch/") "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102") AnnotationAssertion(Annotation( "MA:0001908") "upper jaw") AnnotationAssertion( "AAO:0000622") AnnotationAssertion( "EHDAA2:0002128") @@ -171491,21 +168825,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeleton of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of lower jaw) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001273") Annotation( "TAO") Annotation( "ZFIN:curator") "The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000428") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101") Annotation( "http://bgee.unil.ch/") "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102") AnnotationAssertion(Annotation( "MA:0001906") Annotation( "ZFA:0001273") "lower jaw") AnnotationAssertion(Annotation( "ZFA:0001273") "mandible") AnnotationAssertion( "AAO:0000274") AnnotationAssertion( "EHDAA2:0004606") AnnotationAssertion( "EHDAA:8005") -AnnotationAssertion( "EMAPA:17906") AnnotationAssertion( "EMAPA:17910") AnnotationAssertion( "FMA:54398") AnnotationAssertion( "MA:0001906") @@ -171521,9 +168854,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeleton of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VHOG-modified") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelium of trachea) @@ -171537,12 +168873,14 @@ AnnotationAssertion( "UBERON:0003279") AnnotationAssertion(rdfs:label "endothelium of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (mesentery of stomach) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/mesogastrium") "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum.") AnnotationAssertion( "TODO - check primitive vs developed") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000358") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/mesogastrium") "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]") AnnotationAssertion( "EHDAA2:0001922") AnnotationAssertion( "EHDAA:2999") AnnotationAssertion( "EMAPA:17024") @@ -171578,11 +168916,12 @@ AnnotationAssertion(Annotation( "UBERON:0003282") AnnotationAssertion(rdfs:label "mesentery of heart") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of oesophagus) AnnotationAssertion(Annotation( "OBOL:automatic") "A mesentery that is part of a esophagus [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000415") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") AnnotationAssertion( "EHDAA2:0001288") AnnotationAssertion( "EHDAA:2943") AnnotationAssertion( "EMAPA:16836") @@ -171598,11 +168937,12 @@ AnnotationAssertion( "UBERON:0003283") AnnotationAssertion(rdfs:label "mesentery of oesophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mesentery of midgut) AnnotationAssertion(Annotation( "OBOL:automatic") "A mesentery that is part of a midgut [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000413") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") AnnotationAssertion( "EHDAA2:0001202") AnnotationAssertion( "EHDAA:3031") AnnotationAssertion( "EMAPA:16721") @@ -171614,13 +168954,13 @@ AnnotationAssertion( "UBERON:0003284") AnnotationAssertion(rdfs:label "mesentery of midgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meninx of midbrain) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a midbrain [Automatically generated definition].") AnnotationAssertion( "consider changing genus to subdivision of meninx") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000012") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the midbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000012") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001174") AnnotationAssertion( "EHDAA:3708") AnnotationAssertion( "EMAPA:17791") @@ -171635,13 +168975,13 @@ AnnotationAssertion(Annotation( "UBERON:0003288") AnnotationAssertion(rdfs:label "meninx of midbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meninx of telencephalon) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a telencephalon [Automatically generated definition].") AnnotationAssertion( "consider changing genus to subdivision of meninx") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000010") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the telencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000010") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001990") AnnotationAssertion( "EHDAA:5476") AnnotationAssertion( "EMAPA:17774") @@ -171654,13 +168994,13 @@ AnnotationAssertion( "UBERON:0003289") AnnotationAssertion(rdfs:label "meninx of telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meninx of diencephalon) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a diencephalon [Automatically generated definition].") AnnotationAssertion( "consider changing genus to subdivision of meninx") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000009") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the diencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000009") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000399") AnnotationAssertion( "EHDAA:5458") AnnotationAssertion( "EMAPA:17764") @@ -171685,13 +169025,13 @@ AnnotationAssertion( "UBERON:0003290") AnnotationAssertion(rdfs:label "meninx of diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meninx of hindbrain) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a hindbrain [Automatically generated definition].") AnnotationAssertion( "consider changing genus to subdivision of meninx") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000011") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the hindbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000011") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000770") AnnotationAssertion( "EHDAA:3688") AnnotationAssertion( "EMAPA:17783") @@ -171705,13 +169045,13 @@ AnnotationAssertion(Annotation( "UBERON:0003291") AnnotationAssertion(rdfs:label "meninx of hindbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meninx of spinal cord) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a spinal cord [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000443") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the spinal cord. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000443") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "CALOHA:TS-2148") AnnotationAssertion( "EHDAA2:0001895") AnnotationAssertion( "EHDAA:2865") @@ -171732,6 +169072,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "meninx of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of foregut) @@ -171745,6 +169088,8 @@ AnnotationAssertion( "UBERON:0003294") AnnotationAssertion(rdfs:label "gland of foregut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal gland) @@ -171760,13 +169105,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (gland of diencephalon) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis.") AnnotationAssertion( "EHDAA2:0000395") -AnnotationAssertion( "EHDAA:4475") AnnotationAssertion( "EMAPA:16897") AnnotationAssertion( "VHOG:0000653") AnnotationAssertion(Annotation( "OBOL:automatic") "diencephalon gland") @@ -171775,12 +169121,14 @@ AnnotationAssertion( "UBERON:0003296") AnnotationAssertion(rdfs:label "gland of diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of integumental system) AnnotationAssertion(Annotation( "OBOL:automatic") "A gland that is part of a integumental system [Automatically generated definition].") AnnotationAssertion( "EHDAA2:0000837") -AnnotationAssertion( "EHDAA:6522") AnnotationAssertion( "EMAPA:17758") AnnotationAssertion( "MA:0000144") AnnotationAssertion( "VHOG:0000654") @@ -171791,24 +169139,27 @@ AnnotationAssertion( "UBERON:0003297") AnnotationAssertion(rdfs:label "gland of integumental system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesoderm blood island) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood island that is part of a mesoderm.") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2, gives rise to blood and dorsal aorta") AnnotationAssertion( "UBERON:0003305") AnnotationAssertion( "EHDAA2:0003241") AnnotationAssertion( "EHDAA:170") -AnnotationAssertion( "EMAPA:16115") AnnotationAssertion(Annotation( "EHDAA2:0003241") Annotation( ) "mesoderm blood islands") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "OBOL:automatic") "mesenchyme blood island") AnnotationAssertion( "UBERON:0003304") AnnotationAssertion(rdfs:label "mesoderm blood island") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (mesenchyme of testis) @@ -171822,6 +169173,8 @@ AnnotationAssertion( "UBERON:0003312") AnnotationAssertion(rdfs:label "mesenchyme of testis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye mesenchyme) @@ -171836,6 +169189,9 @@ AnnotationAssertion( "UBERON:0003314") AnnotationAssertion(rdfs:label "eye mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (mesenchyme of ovary) @@ -171859,6 +169215,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of yolk sac) @@ -171876,6 +169234,8 @@ AnnotationAssertion( "UBERON:0003316") AnnotationAssertion(rdfs:label "mesenchyme of yolk sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of elbow) @@ -171892,13 +169252,14 @@ AnnotationAssertion( "UBERON:0003318") AnnotationAssertion(rdfs:label "mesenchyme of elbow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of carpal region) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Mesenchyme of the carpal region that contributes to the carpal skeleton.") AnnotationAssertion( "EHDAA2:0000220") AnnotationAssertion( "EHDAA:5200") -AnnotationAssertion( "EMAPA:19122") AnnotationAssertion(Annotation( "OBOL:automatic") "carpal region mesenchyme") AnnotationAssertion(Annotation( "OBOL:automatic") "carpus mesenchyme") AnnotationAssertion(Annotation( "OBOL:automatic") "mesenchyme of wrist") @@ -171907,6 +169268,8 @@ AnnotationAssertion( "UBERON:0003319") AnnotationAssertion(rdfs:label "mesenchyme of carpal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of hip) @@ -171925,6 +169288,8 @@ AnnotationAssertion( "UBERON:0003320") AnnotationAssertion(rdfs:label "mesenchyme of hip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of knee) @@ -171939,6 +169304,8 @@ AnnotationAssertion( "UBERON:0003321") AnnotationAssertion(rdfs:label "mesenchyme of knee") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of shoulder) @@ -171953,6 +169320,8 @@ AnnotationAssertion( "UBERON:0003322") AnnotationAssertion(rdfs:label "mesenchyme of shoulder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of upper jaw) @@ -171968,6 +169337,9 @@ AnnotationAssertion( "UBERON:0003323") AnnotationAssertion(rdfs:label "mesenchyme of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (mesenchyme of lower jaw) @@ -171984,12 +169356,13 @@ AnnotationAssertion( "UBERON:0003324") AnnotationAssertion(rdfs:label "mesenchyme of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (mesenchyme of pinna) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a developing pinna [Automatically generated definition].") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation") AnnotationAssertion( "EHDAA2:0001469") AnnotationAssertion( "EHDAA:8981") AnnotationAssertion( "EMAPA:17591") @@ -172011,6 +169384,8 @@ AnnotationAssertion( "UBERON:0003325") AnnotationAssertion(rdfs:label "mesenchyme of pinna") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of mammary gland) @@ -172031,6 +169406,9 @@ AnnotationAssertion( "UBERON:0003326") AnnotationAssertion(rdfs:label "mesenchyme of mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of forearm) @@ -172044,11 +169422,12 @@ AnnotationAssertion( "UBERON:0003327") AnnotationAssertion(rdfs:label "mesenchyme of forearm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of footplate) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a footplate.") -AnnotationAssertion(Annotation( "EMAPA") "We group two EMAPA classes here but these may need to be separated") AnnotationAssertion( "UBERON:0005260") AnnotationAssertion( "EHDAA2:0000549") AnnotationAssertion( "EHDAA:5149") @@ -172061,6 +169440,8 @@ AnnotationAssertion( "UBERON:0003328") AnnotationAssertion(rdfs:label "mesenchyme of footplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (submucosa of anal canal) @@ -172084,6 +169465,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of rectum) @@ -172099,6 +169483,8 @@ AnnotationAssertion( "UBERON:0003330") AnnotationAssertion(rdfs:label "submucosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of colon) @@ -172117,6 +169503,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of duodenum) @@ -172136,6 +169524,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of jejunum) @@ -172151,6 +169541,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of rectum) @@ -172166,6 +169558,8 @@ AnnotationAssertion( "UBERON:0003334") AnnotationAssertion(rdfs:label "serosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of colon) @@ -172189,12 +169583,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serosa of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of duodenum) AnnotationAssertion(Annotation( "OBOL:automatic") "A serous membrane that is part of a duodenum [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion( "1st part serosa, 2nd - 4th adventitia") AnnotationAssertion( "EMAPA:27247") AnnotationAssertion( "FMA:14948") AnnotationAssertion( "MA:0003212") @@ -172210,6 +169605,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serosa of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of jejunum) @@ -172227,11 +169624,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serosa of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ganglion of peripheral nervous system) AnnotationAssertion(Annotation( "BIRNLEX:2548") "A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).") -AnnotationAssertion(Annotation( "MA") "we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS") AnnotationAssertion( "BIRNLEX:2548") AnnotationAssertion( "BTO:0001123") AnnotationAssertion( "EMAPA:32814") @@ -172242,11 +169640,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ganglion of peripheral nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ganglion of central nervous system) AnnotationAssertion(Annotation( "OBOL:automatic") "A ganglion that is part of a central nervous system [Automatically generated definition].") -AnnotationAssertion(Annotation( "FMA") "this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia") AnnotationAssertion( "EHDAA2:0000227") AnnotationAssertion( "EMAPA:16658") AnnotationAssertion( "FMA:83843") @@ -172257,6 +169656,9 @@ AnnotationAssertion( "UBERON:0003339") AnnotationAssertion(rdfs:label "ganglion of central nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of anal canal) @@ -172305,11 +169707,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of oral region) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a oral opening [Automatically generated definition].") -AnnotationAssertion( "EMAPA:26937") AnnotationAssertion( "SCTID:362083000") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of oral opening") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of oral part of face") @@ -172346,6 +169750,8 @@ AnnotationAssertion( "UBERON:0003343") AnnotationAssertion(rdfs:label "mucosa of oral region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of rectum) @@ -172368,6 +169774,8 @@ AnnotationAssertion( "UBERON:0003346") AnnotationAssertion(rdfs:label "mucosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of mucosa) @@ -172380,11 +169788,12 @@ AnnotationAssertion( "lies on top of lamina propria") AnnotationAssertion(rdfs:label "epithelium of mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a pharynx [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001174") Annotation( "TAO") Annotation( "ZFIN:curator") "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]") AnnotationAssertion( "BSA:0000112") AnnotationAssertion( "BTO:0005240") AnnotationAssertion( "EMAPA:16708") @@ -172402,6 +169811,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -172419,6 +169831,7 @@ AnnotationAssertion( "UBERON:0003352") AnnotationAssertion(rdfs:label "epithelium of midgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (epithelium of hindgut) @@ -172434,6 +169847,8 @@ AnnotationAssertion( "UBERON:0003353") AnnotationAssertion(rdfs:label "epithelium of hindgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of rectum) @@ -172452,6 +169867,9 @@ AnnotationAssertion( "UBERON:0003354") AnnotationAssertion(rdfs:label "epithelium of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of tongue) @@ -172474,6 +169892,9 @@ AnnotationAssertion( "examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies.") AnnotationAssertion(rdfs:label "epithelium of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of right lung) @@ -172488,6 +169909,8 @@ AnnotationAssertion( "UBERON:0003364") AnnotationAssertion(rdfs:label "epithelium of right lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of left lung) @@ -172501,6 +169924,8 @@ AnnotationAssertion( "UBERON:0003365") AnnotationAssertion(rdfs:label "epithelium of left lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of vomeronasal organ) @@ -172524,6 +169949,9 @@ AnnotationAssertion( "epithelium of vomeronasal organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pelvic appendage bud ectoderm) @@ -172543,8 +169971,12 @@ AnnotationAssertion(Annotation( "UBERON:0003371") AnnotationAssertion(rdfs:label "pelvic appendage bud ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pectoral appendage bud ectoderm) @@ -172565,8 +169997,12 @@ AnnotationAssertion(Annotation( "UBERON:0003372") AnnotationAssertion(rdfs:label "pectoral appendage bud ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (ectoderm of footplate) @@ -172577,6 +170013,8 @@ AnnotationAssertion( "UBERON:0003373") AnnotationAssertion(rdfs:label "ectoderm of footplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chorionic ectoderm) @@ -172590,6 +170028,8 @@ AnnotationAssertion(Annotation( "UBERON:0003374") AnnotationAssertion(rdfs:label "chorionic ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) # Class: (cardiac muscle of right atrium) @@ -172617,6 +170057,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac muscle of right atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle of left atrium) @@ -172643,6 +170085,8 @@ AnnotationAssertion( "UBERON:0003380") AnnotationAssertion(rdfs:label "cardiac muscle of left atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle of right ventricle) @@ -172657,6 +170101,8 @@ AnnotationAssertion(Annotation( "UBERON:0003381") AnnotationAssertion(rdfs:label "cardiac muscle of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle of left ventricle) @@ -172671,6 +170117,8 @@ AnnotationAssertion(Annotation( "UBERON:0003382") AnnotationAssertion(rdfs:label "cardiac muscle of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of interventricular septum) @@ -172691,6 +170139,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac muscle tissue of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (skeletal muscle tissue of pharynx) @@ -172703,6 +170153,8 @@ AnnotationAssertion( "UBERON:0003384") AnnotationAssertion(rdfs:label "skeletal muscle tissue of pharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle of eye) @@ -172716,6 +170168,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle of trachea) @@ -172737,6 +170192,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelium of pericardial cavity) @@ -172754,6 +170211,8 @@ AnnotationAssertion( "UBERON:0003388") AnnotationAssertion(rdfs:label "mesothelium of pericardial cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelium of diaphragm) @@ -172770,6 +170229,9 @@ AnnotationAssertion( "UBERON:0003389") AnnotationAssertion(rdfs:label "mesothelium of diaphragm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelium of pleural cavity) @@ -172788,6 +170250,8 @@ AnnotationAssertion(Annotation( "UBERON:0003390") AnnotationAssertion(rdfs:label "mesothelium of pleural cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of urinary system) @@ -172805,6 +170269,8 @@ AnnotationAssertion( "UBERON:0003393") AnnotationAssertion(rdfs:label "mesentery of urinary system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of hindgut) @@ -172815,6 +170281,8 @@ AnnotationAssertion( "UBERON:0003394") AnnotationAssertion(rdfs:label "mesentery of hindgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of rectum) @@ -172825,6 +170293,8 @@ AnnotationAssertion( "UBERON:0003395") AnnotationAssertion(rdfs:label "mesentery of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mesentery of colon) @@ -172842,6 +170312,8 @@ AnnotationAssertion( "UBERON:0003396") AnnotationAssertion(rdfs:label "mesentery of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) # Class: (mesentery of duodenum) @@ -172853,6 +170325,8 @@ AnnotationAssertion( "UBERON:0003397") AnnotationAssertion(rdfs:label "mesentery of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mesentery of jejunum) @@ -172867,6 +170341,8 @@ AnnotationAssertion( "UBERON:0003398") AnnotationAssertion(rdfs:label "mesentery of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (skin of forearm) @@ -172886,6 +170362,8 @@ AnnotationAssertion( "UBERON:0003403") AnnotationAssertion(rdfs:label "skin of forearm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobar bronchus of right lung) @@ -172903,6 +170381,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (lobar bronchus of left lung) @@ -172922,6 +170401,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (cartilage of respiratory system) @@ -172936,6 +170416,8 @@ AnnotationAssertion( "UBERON:0003406") AnnotationAssertion(rdfs:label "cartilage of respiratory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of digestive tract) @@ -172951,6 +170433,9 @@ AnnotationAssertion( "UBERON:0003408") AnnotationAssertion(rdfs:label "gland of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of tongue) @@ -172962,11 +170447,12 @@ AnnotationAssertion( "UBERON:0003409") AnnotationAssertion(rdfs:label "gland of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage bud mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a pelvic appendage bud.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001386") Annotation( "TAO") Annotation( "ZFIN:curator") "Mesoderm part of pelvic fin bud.[TAO]") AnnotationAssertion( "EHDAA2:0001035") AnnotationAssertion( "EMAPA:16781") AnnotationAssertion( "TAO:0001386") @@ -172980,12 +170466,13 @@ AnnotationAssertion( "UBERON:0003412") AnnotationAssertion(rdfs:label "pelvic appendage bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage bud mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a pectoral appendage bud.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000789") Annotation( "TAO") Annotation( "ZFIN:curator") "Mesoderm that is part of the pectoral fin bud.[TAO]") AnnotationAssertion( "UBERON:0005703") AnnotationAssertion( "EHDAA2:0002135") AnnotationAssertion( "EHDAA:1703") @@ -173002,6 +170489,8 @@ AnnotationAssertion( "UBERON:0003413") AnnotationAssertion(rdfs:label "pectoral appendage bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of tongue) @@ -173015,6 +170504,8 @@ AnnotationAssertion( "UBERON:0003416") AnnotationAssertion(rdfs:label "mesenchyme of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of vomeronasal organ) @@ -173029,6 +170520,8 @@ AnnotationAssertion( "UBERON:0003421") AnnotationAssertion(rdfs:label "mesenchyme of vomeronasal organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -173048,12 +170541,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of umbilical cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (renal lymph node) AnnotationAssertion(Annotation( "OBOL:automatic") "A lymph node that is located in a kidney [Automatically generated definition].") -AnnotationAssertion(Annotation( "PMID:16624319") Annotation( "NCBITaxon:10090") "Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland") AnnotationAssertion(Annotation( "PMID:22740822") "para-renal lymph node") AnnotationAssertion(Annotation( "PMID:28346247") "pararenal lymph node") AnnotationAssertion(Annotation( "PMID:35764904") "perirenal lymph node") @@ -173067,6 +170563,8 @@ AnnotationAssertion( "UBERON:0003425") AnnotationAssertion(rdfs:label "renal lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermis adipose tissue) @@ -173082,6 +170580,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dermis adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (abdomen nerve) @@ -173092,6 +170592,8 @@ AnnotationAssertion( "UBERON:0003429") AnnotationAssertion(rdfs:label "abdomen nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck nerve) @@ -173105,6 +170607,8 @@ AnnotationAssertion( "UBERON:0003430") AnnotationAssertion(rdfs:label "neck nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (leg nerve) @@ -173116,6 +170620,8 @@ AnnotationAssertion( "UBERON:0003431") AnnotationAssertion(rdfs:label "leg nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest nerve) @@ -173133,6 +170639,8 @@ AnnotationAssertion( "UBERON:0003432") AnnotationAssertion(rdfs:label "chest nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arm nerve) @@ -173146,6 +170654,8 @@ AnnotationAssertion( "UBERON:0003433") AnnotationAssertion(rdfs:label "arm nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wrist nerve) @@ -173159,6 +170669,8 @@ AnnotationAssertion( "UBERON:0003434") AnnotationAssertion(rdfs:label "wrist nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit nerve) @@ -173184,6 +170696,8 @@ AnnotationAssertion( "UBERON:0003435") AnnotationAssertion(rdfs:label "pedal digit nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder nerve) @@ -173195,6 +170709,8 @@ AnnotationAssertion( "UBERON:0003436") AnnotationAssertion(rdfs:label "shoulder nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid nerve) @@ -173209,6 +170725,8 @@ AnnotationAssertion( "UBERON:0003437") AnnotationAssertion(rdfs:label "eyelid nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iris nerve) @@ -173222,6 +170740,8 @@ AnnotationAssertion( "UBERON:0003438") AnnotationAssertion(rdfs:label "iris nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of trunk region) @@ -173238,6 +170758,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nerve of trunk region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb nerve) @@ -173250,6 +170772,8 @@ AnnotationAssertion( "UBERON:0003440") AnnotationAssertion(rdfs:label "limb nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb nerve) @@ -173266,6 +170790,8 @@ AnnotationAssertion( "UBERON:0003441") AnnotationAssertion(rdfs:label "forelimb nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb nerve) @@ -173281,6 +170807,8 @@ AnnotationAssertion( "UBERON:0003442") AnnotationAssertion(rdfs:label "hindlimb nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity nerve) @@ -173301,6 +170829,8 @@ AnnotationAssertion( "UBERON:0003443") AnnotationAssertion(rdfs:label "thoracic cavity nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvis nerve) @@ -173312,6 +170842,8 @@ AnnotationAssertion( "UBERON:0003444") AnnotationAssertion(rdfs:label "pelvis nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes nerve) @@ -173324,11 +170856,12 @@ AnnotationAssertion( "UBERON:0003445") AnnotationAssertion(rdfs:label "pes nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ankle nerve) AnnotationAssertion(Annotation( "OBOL:automatic") "A nerve that is part of an ankle [Automatically generated definition].") -AnnotationAssertion(Annotation( "FMA") "FMA placement dubious") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37346") AnnotationAssertion( "MA:0000640") AnnotationAssertion(Annotation( "OBOL:automatic") "nerve of ankle") @@ -173339,6 +170872,8 @@ AnnotationAssertion( "ankle nerve") AnnotationAssertion(rdfs:seeAlso ) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digit nerve of manus) @@ -173362,6 +170897,8 @@ AnnotationAssertion( "UBERON:0003447") AnnotationAssertion(rdfs:label "digit nerve of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus nerve) @@ -173375,6 +170912,8 @@ AnnotationAssertion( "UBERON:0003448") AnnotationAssertion(rdfs:label "manus nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail intervertebral disc) @@ -173391,6 +170930,8 @@ AnnotationAssertion( "UBERON:0003449") AnnotationAssertion(rdfs:label "tail intervertebral disc") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula carnea cardiac muscle tissue) @@ -173446,6 +170987,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trabecula carnea cardiac muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (large intestine Peyer's patch) @@ -173462,12 +171005,13 @@ AnnotationAssertion(Annotation( "UBERON:0003453") AnnotationAssertion(rdfs:label "large intestine Peyer's patch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (small intestine Peyer's patch) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Nodular lymphoid structures on the serosal surface of the small intestine.") AnnotationAssertion( "add subtypes for jejunum, ileum") -AnnotationAssertion( ) AnnotationAssertion(Annotation( "FMA:15054") "Peyer's patch") AnnotationAssertion( "EMAPA:35782") AnnotationAssertion( "FMA:15054") @@ -173483,6 +171027,7 @@ AnnotationAssertion( "UBERON:0003454") AnnotationAssertion(rdfs:label "small intestine Peyer's patch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ncithesaurus") ObjectSomeValuesFrom( )) # Class: (inner renal medulla loop of Henle) @@ -173496,6 +171041,8 @@ AnnotationAssertion( "UBERON:0003455") AnnotationAssertion(rdfs:label "inner renal medulla loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system lymphatic vessel) @@ -173513,6 +171060,8 @@ AnnotationAssertion( "UBERON:0003456") AnnotationAssertion(rdfs:label "respiratory system lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head bone) @@ -173534,6 +171083,8 @@ AnnotationAssertion( "Different sources vary regarding which bones are craniofacial; e.g. hyoid bone") AnnotationAssertion(rdfs:label "head bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck bone) @@ -173551,6 +171102,8 @@ AnnotationAssertion( "UBERON:0003458") AnnotationAssertion(rdfs:label "neck bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest bone) @@ -173576,6 +171129,8 @@ AnnotationAssertion( "UBERON:0003459") AnnotationAssertion(rdfs:label "chest bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (arm bone) @@ -173583,7 +171138,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37303") AnnotationAssertion( "MA:0000592") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D050280") AnnotationAssertion(Annotation( "OBOL:automatic") "arm bone organ") AnnotationAssertion(Annotation( "OBOL:automatic") "bone of arm") AnnotationAssertion(Annotation( "OBOL:automatic") "bone organ of arm") @@ -173593,12 +171147,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arm bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder bone) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods.") -AnnotationAssertion(Annotation( "MA") "this is a forelimb bone in MA, but this would lead to part-disjointness violations.") AnnotationAssertion( "MA:0000631") AnnotationAssertion(Annotation( "OBOL:automatic") "bone of shoulder") AnnotationAssertion( "shoulder-articulating bone") @@ -173607,9 +171161,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "shoulder bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "UBERONREF:0000003") Annotation( "MA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial bone) @@ -173619,7 +171173,6 @@ AnnotationAssertion( "EMAPA:35924") AnnotationAssertion( "MA:0001482") AnnotationAssertion( "MA:0003159") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005147") AnnotationAssertion( "NCIT:C63706") AnnotationAssertion( "SCTID:181799005") AnnotationAssertion(Annotation( "ncithesaurus:Facial_Bone") "UMLS:C0015455") @@ -173633,6 +171186,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facial bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (trunk bone) @@ -173652,11 +171207,12 @@ AnnotationAssertion( "UBERON:0003463") AnnotationAssertion(rdfs:label "trunk bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindlimb bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle).") -AnnotationAssertion(Annotation( "MA") "the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc") AnnotationAssertion( "EFO:0003842") AnnotationAssertion( "GAID:198") AnnotationAssertion( "NCIT:C12982") @@ -173677,7 +171233,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb zeugopod bone) @@ -173698,6 +171256,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb zeugopod bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteric segment of renal artery) @@ -173715,7 +171274,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureteric segment of renal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (respiratory system artery) @@ -173727,6 +171288,8 @@ AnnotationAssertion( "UBERON:0003469") AnnotationAssertion(rdfs:label "respiratory system artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (artery of upper lip) @@ -173746,7 +171309,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "artery of upper lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (artery of lower lip) @@ -173768,7 +171333,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "artery of lower lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (cerebellar artery) @@ -173787,12 +171354,13 @@ AnnotationAssertion( "cerebellar artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity artery) AnnotationAssertion(Annotation( "https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376") "An artery that is part of a thoracic cavity[cjm].") -AnnotationAssertion(Annotation( "MA") "in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37241") AnnotationAssertion( "MA:0001902") AnnotationAssertion( "MESH:D013895") @@ -173801,6 +171369,8 @@ AnnotationAssertion(Annotation( "UBERON:0003473") AnnotationAssertion(rdfs:label "thoracic cavity artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (meningeal artery) @@ -173814,6 +171384,8 @@ AnnotationAssertion( "UBERON:0003474") AnnotationAssertion(rdfs:label "meningeal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteric vein) @@ -173826,6 +171398,9 @@ AnnotationAssertion( "UBERON:0003475") AnnotationAssertion(rdfs:label "ureteric vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system venous blood vessel) @@ -173841,6 +171416,8 @@ AnnotationAssertion( "UBERON:0003476") AnnotationAssertion(rdfs:label "respiratory system venous blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein of upper lip) @@ -173859,7 +171436,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vein of upper lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein of lower lip) @@ -173880,7 +171458,8 @@ AnnotationAssertion( "vein of lower lip") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity vein) @@ -173900,6 +171479,8 @@ AnnotationAssertion( "UBERON:0003479") AnnotationAssertion(rdfs:label "thoracic cavity vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (vein of clitoris) @@ -173912,6 +171493,9 @@ AnnotationAssertion( "UBERON:0003480") AnnotationAssertion(rdfs:label "vein of clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail vein) @@ -173930,6 +171514,8 @@ AnnotationAssertion(Annotation( "UBERON:0003481") AnnotationAssertion(rdfs:label "tail vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (thymus lymphoid tissue) @@ -173946,6 +171532,9 @@ AnnotationAssertion( "UBERON:0003483") AnnotationAssertion(rdfs:label "thymus lymphoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye sebaceous gland) @@ -173963,6 +171552,7 @@ AnnotationAssertion( "eye sebaceous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) # Class: (vagina sebaceous gland) @@ -173975,6 +171565,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vagina sebaceous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin sebaceous gland) @@ -173988,13 +171582,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin sebaceous gland") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (abdominal mammary gland) AnnotationAssertion(Annotation( "OBOL:automatic") "A lactiferous gland that is part of the abdominal region [Automatically generated definition].") -AnnotationAssertion( "Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml") AnnotationAssertion( "EMAPA:36507") AnnotationAssertion( "MA:0000787") AnnotationAssertion( "SCTID:113191002") @@ -174011,6 +171602,8 @@ AnnotationAssertion( "UBERON:0003488") AnnotationAssertion(rdfs:label "abdominal mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (respiratory system capillary endothelium) @@ -174044,7 +171637,8 @@ AnnotationAssertion( "UBERON:0003489") AnnotationAssertion(rdfs:label "respiratory system capillary endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (respiratory system venule) @@ -174059,6 +171653,8 @@ AnnotationAssertion( "UBERON:0003494") AnnotationAssertion(rdfs:label "respiratory system venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (respiratory system arteriole) @@ -174069,6 +171665,8 @@ AnnotationAssertion( "UBERON:0003495") AnnotationAssertion(rdfs:label "respiratory system arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (head blood vessel) @@ -174084,6 +171682,7 @@ AnnotationAssertion( "UBERON:0003496") AnnotationAssertion(rdfs:label "head blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (abdomen blood vessel) @@ -174094,8 +171693,9 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0003497") AnnotationAssertion(rdfs:label "abdomen blood vessel") -AnnotationAssertion(Annotation( "abdominal aorta artery") rdfs:seeAlso "UBERON:0012254") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart blood vessel) @@ -174109,6 +171709,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heart blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain blood vessel) @@ -174122,6 +171724,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (corneal blood vessel) @@ -174137,6 +171741,9 @@ AnnotationAssertion( "UBERON:0003500") AnnotationAssertion(rdfs:label "corneal blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (retina blood vessel) @@ -174158,6 +171765,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retina blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -174173,6 +171782,8 @@ AnnotationAssertion( "UBERON:0003502") AnnotationAssertion(rdfs:label "neck blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (leg blood vessel) @@ -174184,6 +171795,8 @@ AnnotationAssertion( "UBERON:0003503") AnnotationAssertion(rdfs:label "leg blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system blood vessel) @@ -174198,6 +171811,8 @@ AnnotationAssertion( "UBERON:0003504") AnnotationAssertion(rdfs:label "respiratory system blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trachea blood vessel) @@ -174210,6 +171825,9 @@ AnnotationAssertion( "UBERON:0003505") AnnotationAssertion(rdfs:label "trachea blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest blood vessel) @@ -174227,6 +171845,8 @@ AnnotationAssertion( "UBERON:0003506") AnnotationAssertion(rdfs:label "chest blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arm blood vessel) @@ -174238,6 +171858,8 @@ AnnotationAssertion( "UBERON:0003507") AnnotationAssertion(rdfs:label "arm blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit blood vessel) @@ -174262,6 +171884,8 @@ AnnotationAssertion( "UBERON:0003508") AnnotationAssertion(rdfs:label "pedal digit blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arterial blood vessel) @@ -174274,6 +171898,8 @@ AnnotationAssertion( "only in MA - supertype of artery, arteriole, aorta.") AnnotationAssertion(rdfs:label "arterial blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid blood vessel) @@ -174287,19 +171913,23 @@ AnnotationAssertion( "UBERON:0003510") AnnotationAssertion(rdfs:label "eyelid blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iris blood vessel) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood vessel that is part of a iris [Automatically generated definition].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37387") AnnotationAssertion( "MA:0001290") -AnnotationAssertion( "ZFA:0005568") AnnotationAssertion(Annotation( "OBOL:automatic") "blood vessel of iris") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003511") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "iris blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung blood vessel) @@ -174314,6 +171944,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk blood vessel) @@ -174328,6 +171962,8 @@ AnnotationAssertion( "UBERON:0003513") AnnotationAssertion(rdfs:label "trunk blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb blood vessel) @@ -174339,6 +171975,8 @@ AnnotationAssertion( "UBERON:0003514") AnnotationAssertion(rdfs:label "limb blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb blood vessel) @@ -174356,6 +171994,9 @@ AnnotationAssertion( "UBERON:0003515") AnnotationAssertion(rdfs:label "forelimb blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb blood vessel) @@ -174370,12 +172011,13 @@ AnnotationAssertion( "UBERON:0003516") AnnotationAssertion(rdfs:label "hindlimb blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney blood vessel) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood vessel that is part of a kidney [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion( "EMAPA:28457") AnnotationAssertion( "MA:0001682") AnnotationAssertion( "TAO:0005306") AnnotationAssertion( "ZFA:0005306") @@ -174388,6 +172030,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity blood vessel) @@ -174408,6 +172051,8 @@ AnnotationAssertion( "UBERON:0003519") AnnotationAssertion(rdfs:label "thoracic cavity blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvis blood vessel) @@ -174419,6 +172064,8 @@ AnnotationAssertion( "UBERON:0003520") AnnotationAssertion(rdfs:label "pelvis blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes blood vessel) @@ -174431,6 +172078,8 @@ AnnotationAssertion( "UBERON:0003521") AnnotationAssertion(rdfs:label "pes blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit blood vessel) @@ -174448,6 +172097,8 @@ AnnotationAssertion( "UBERON:0003522") AnnotationAssertion(rdfs:label "manual digit blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus blood vessel) @@ -174461,6 +172112,8 @@ AnnotationAssertion( "UBERON:0003523") AnnotationAssertion(rdfs:label "manus blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail blood vessel) @@ -174474,6 +172127,8 @@ AnnotationAssertion( "UBERON:0003524") AnnotationAssertion(rdfs:label "tail blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system capillary) @@ -174495,6 +172150,8 @@ AnnotationAssertion( "UBERON:0003526") AnnotationAssertion(rdfs:label "respiratory system capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (kidney capillary) @@ -174515,7 +172172,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (brain gray matter) @@ -174533,6 +172191,8 @@ AnnotationAssertion( "UBERON:0003528") AnnotationAssertion(rdfs:label "brain gray matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system lymphatic vessel endothelium) @@ -174557,6 +172217,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system lymphatic vessel endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit skin) @@ -174586,6 +172248,9 @@ AnnotationAssertion( "UBERON:0003530") AnnotationAssertion(rdfs:label "pedal digit skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb skin) @@ -174608,6 +172273,8 @@ AnnotationAssertion( "UBERON:0003531") AnnotationAssertion(rdfs:label "forelimb skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb skin) @@ -174630,6 +172297,8 @@ AnnotationAssertion( "UBERON:0003532") AnnotationAssertion(rdfs:label "hindlimb skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit skin) @@ -174658,6 +172327,9 @@ AnnotationAssertion( "UBERON:0003533") AnnotationAssertion(rdfs:label "manual digit skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail skin) @@ -174673,6 +172345,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tail skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vagus X nerve trunk) @@ -174695,6 +172369,8 @@ AnnotationAssertion( "UBERON:0003535") AnnotationAssertion(rdfs:label "vagus X nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung alveolar duct) @@ -174708,6 +172384,7 @@ AnnotationAssertion( "UBERON:0003536") AnnotationAssertion(rdfs:label "right lung alveolar duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lung alveolar duct) @@ -174723,6 +172400,7 @@ AnnotationAssertion( "Mice have 1 left lobe") AnnotationAssertion(rdfs:label "left lung alveolar duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung bronchiole) @@ -174738,6 +172416,8 @@ AnnotationAssertion( "UBERON:0003538") AnnotationAssertion(rdfs:label "right lung bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lung bronchiole) @@ -174752,6 +172432,8 @@ AnnotationAssertion( "UBERON:0003539") AnnotationAssertion(rdfs:label "left lung bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung terminal bronchiole) @@ -174767,6 +172449,8 @@ AnnotationAssertion( "UBERON:0003540") AnnotationAssertion(rdfs:label "right lung terminal bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (left lung terminal bronchiole) @@ -174782,6 +172466,8 @@ AnnotationAssertion( "UBERON:0003541") AnnotationAssertion(rdfs:label "left lung terminal bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (right lung respiratory bronchiole) @@ -174797,6 +172483,8 @@ AnnotationAssertion( "UBERON:0003542") AnnotationAssertion(rdfs:label "right lung respiratory bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (left lung respiratory bronchiole) @@ -174812,12 +172500,13 @@ AnnotationAssertion( "UBERON:0003543") AnnotationAssertion(rdfs:label "left lung respiratory bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (brain white matter) AnnotationAssertion(Annotation( "MP:0008026") "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.") AnnotationAssertion( "EMAPA:35187") -AnnotationAssertion( "HBA:9218") AnnotationAssertion( "MA:0000820") AnnotationAssertion( "NCIT:C49334") AnnotationAssertion(Annotation( "ncithesaurus:Brain_White_Matter") "UMLS:C1706995") @@ -174831,6 +172520,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal convoluted tubule macula densa) @@ -174841,17 +172532,16 @@ AnnotationAssertion( "UBERON:0003546") AnnotationAssertion(rdfs:label "distal convoluted tubule macula densa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (brain meninx) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a brain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000013") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Meninges that are part of the brain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000013") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "CALOHA:TS-2147") AnnotationAssertion( "EMAPA:32662") -AnnotationAssertion( "EV:0100312") AnnotationAssertion( "MA:0000813") AnnotationAssertion( "SCTID:180949007") AnnotationAssertion( "VHOG:0000013") @@ -174864,12 +172554,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain meninx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain meninges) AnnotationAssertion(Annotation( "OBOL:automatic") "A meninx that is part of a forebrain [Automatically generated definition].") -AnnotationAssertion( "EMAPA:17764") -AnnotationAssertion( "EMAPA:17774") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37543") AnnotationAssertion( "MA:0000883") AnnotationAssertion(Annotation( "OBOL:automatic") "forebrain meninx") @@ -174879,14 +172569,13 @@ AnnotationAssertion( "UBERON:0003548") AnnotationAssertion(rdfs:label "forebrain meninges") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain pia mater) AnnotationAssertion(Annotation( "MP:0009026") "The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000470") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pia+mater") "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000470") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:32667") -AnnotationAssertion( "EV:0100315") AnnotationAssertion( "MA:0000816") AnnotationAssertion( "NCIT:C49335") AnnotationAssertion(Annotation( "ncithesaurus:Brain_Pia_Mater") "UMLS:C1706994") @@ -174899,12 +172588,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (forebrain pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a forebrain [Automatically generated definition].") -AnnotationAssertion( "EMAPA:17767") -AnnotationAssertion( "EMAPA:17777") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37546") AnnotationAssertion( "MA:0000886") AnnotationAssertion(Annotation( "OBOL:automatic") "forebrain pia mater of neuraxis") @@ -174914,12 +172603,12 @@ AnnotationAssertion( "UBERON:0003550") AnnotationAssertion(rdfs:label "forebrain pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (midbrain pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a midbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000467") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Pia mater that is part of the midbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000467") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001175") AnnotationAssertion( "EMAPA:17794") AnnotationAssertion( "MA:0001061") @@ -174933,12 +172622,12 @@ AnnotationAssertion(Annotation( "UBERON:0003551") AnnotationAssertion(rdfs:label "midbrain pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (telencephalon pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a telencephalon [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000476") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Pia mater that is part of the telencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000476") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001992") AnnotationAssertion( "EMAPA:17777") AnnotationAssertion( "MA:0000982") @@ -174950,12 +172639,12 @@ AnnotationAssertion( "UBERON:0003552") AnnotationAssertion(rdfs:label "telencephalon pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (diencephalon pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a diencephalon [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000475") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Pia mater that is part of the diencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000475") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000400") AnnotationAssertion( "EMAPA:17767") AnnotationAssertion( "MA:0000829") @@ -174979,12 +172668,12 @@ AnnotationAssertion( "UBERON:0003553") AnnotationAssertion(rdfs:label "diencephalon pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindbrain pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a hindbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000466") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Pia mater that is part of the hindbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000466") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000772") AnnotationAssertion( "EMAPA:17786") AnnotationAssertion( "MA:0000990") @@ -174997,12 +172686,12 @@ AnnotationAssertion(Annotation( "UBERON:0003554") AnnotationAssertion(rdfs:label "hindbrain pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (spinal cord pia mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A pia mater that is part of a spinal cord [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000468") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/pia+mater") "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000468") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001896") AnnotationAssertion( "EMAPA:17807") AnnotationAssertion( "MA:0001133") @@ -175017,12 +172706,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spinal cord pia mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (forebrain arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that is part of a forebrain [Automatically generated definition].") -AnnotationAssertion( "EMAPA:17765") -AnnotationAssertion( "EMAPA:17775") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37544") AnnotationAssertion( "MA:0000884") AnnotationAssertion(Annotation( "OBOL:automatic") "arachnoid mater of forebrain") @@ -175034,12 +172723,12 @@ AnnotationAssertion( "UBERON:0003556") AnnotationAssertion(rdfs:label "forebrain arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (midbrain arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that is part of a midbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000233") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000233") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17792") AnnotationAssertion( "MA:0001059") AnnotationAssertion( "VHOG:0000233") @@ -175053,12 +172742,12 @@ AnnotationAssertion(Annotation( "UBERON:0003557") AnnotationAssertion(rdfs:label "midbrain arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (diencephalon arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that is part of a diencephalon [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000231") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000231") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17765") AnnotationAssertion( "MA:0000827") AnnotationAssertion( "VHOG:0000231") @@ -175089,12 +172778,12 @@ AnnotationAssertion( "UBERON:0003558") AnnotationAssertion(rdfs:label "diencephalon arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindbrain arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that is part of a hindbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000236") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000236") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17784") AnnotationAssertion( "MA:0000988") AnnotationAssertion( "VHOG:0000236") @@ -175108,12 +172797,12 @@ AnnotationAssertion(Annotation( "UBERON:0003559") AnnotationAssertion(rdfs:label "hindbrain arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (spinal cord arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that is part of a spinal cord [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000234") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/arachnoid+mater") "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000234") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17805") AnnotationAssertion( "MA:0001131") AnnotationAssertion( "VHOG:0000234") @@ -175127,11 +172816,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spinal cord arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (forebrain dura mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A dura mater that is part of a forebrain.") -AnnotationAssertion( "EMAPA:17766") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37545") AnnotationAssertion( "MA:0000885") AnnotationAssertion(Annotation( "OBOL:automatic") "dura mater of forebrain") @@ -175141,12 +172831,12 @@ AnnotationAssertion( "UBERON:0003561") AnnotationAssertion(rdfs:label "forebrain dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (midbrain dura mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A dura mater that is part of a midbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000410") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Dura mater that is part of the midbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000410") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17793") AnnotationAssertion( "MA:0001060") AnnotationAssertion( "VHOG:0000410") @@ -175158,6 +172848,8 @@ AnnotationAssertion(Annotation( "UBERON:0003562") AnnotationAssertion(rdfs:label "midbrain dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (telencephalon dura mater) @@ -175171,12 +172863,12 @@ AnnotationAssertion( "UBERON:0003563") AnnotationAssertion(rdfs:label "telencephalon dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (diencephalon dura mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A dura mater that is part of a diencephalon [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000258") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Dura mater that is part of the diencephalon. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000258") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17766") AnnotationAssertion( "MA:0000828") AnnotationAssertion( "VHOG:0000258") @@ -175199,12 +172891,12 @@ AnnotationAssertion( "UBERON:0003564") AnnotationAssertion(rdfs:label "diencephalon dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindbrain dura mater) AnnotationAssertion(Annotation( "OBOL:automatic") "A dura mater that is part of a hindbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000409") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Dura mater that is part of the hindbrain. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000409") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:17785") AnnotationAssertion( "MA:0000989") AnnotationAssertion( "VHOG:0000409") @@ -175216,11 +172908,12 @@ AnnotationAssertion(Annotation( "UBERON:0003565") AnnotationAssertion(rdfs:label "hindbrain dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (head connective tissue) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of connective tissue that is part of a head [Automatically generated definition].") -AnnotationAssertion( "EMAPA:16098") AnnotationAssertion( "MA:0000577") AnnotationAssertion(Annotation( "OBOL:automatic") "adult head connective tissue") AnnotationAssertion(Annotation( "OBOL:automatic") "adult head portion of connective tissue") @@ -175237,6 +172930,8 @@ AnnotationAssertion( "UBERON:0003566") AnnotationAssertion(rdfs:label "head connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdomen connective tissue) @@ -175252,6 +172947,8 @@ AnnotationAssertion( "UBERON:0003567") AnnotationAssertion(rdfs:label "abdomen connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck connective tissue) @@ -175273,6 +172970,8 @@ AnnotationAssertion( "UBERON:0003568") AnnotationAssertion(rdfs:label "neck connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (leg connective tissue) @@ -175288,6 +172987,8 @@ AnnotationAssertion( "UBERON:0003569") AnnotationAssertion(rdfs:label "leg connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system connective tissue) @@ -175310,6 +173011,8 @@ AnnotationAssertion( "UBERON:0003570") AnnotationAssertion(rdfs:label "respiratory system connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trachea connective tissue) @@ -175324,6 +173027,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trachea connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest connective tissue) @@ -175358,6 +173063,8 @@ AnnotationAssertion( "UBERON:0003572") AnnotationAssertion(rdfs:label "chest connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arm connective tissue) @@ -175368,6 +173075,8 @@ AnnotationAssertion( "UBERON:0003573") AnnotationAssertion(rdfs:label "arm connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (elbow connective tissue) @@ -175381,6 +173090,8 @@ AnnotationAssertion( "UBERON:0003574") AnnotationAssertion(rdfs:label "elbow connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (wrist connective tissue) @@ -175395,6 +173106,8 @@ AnnotationAssertion( "UBERON:0003575") AnnotationAssertion(rdfs:label "wrist connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hip connective tissue) @@ -175409,6 +173122,8 @@ AnnotationAssertion( "UBERON:0003576") AnnotationAssertion(rdfs:label "hip connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (knee connective tissue) @@ -175422,6 +173137,8 @@ AnnotationAssertion( "UBERON:0003577") AnnotationAssertion(rdfs:label "knee connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit connective tissue) @@ -175441,6 +173158,9 @@ AnnotationAssertion( "UBERON:0003578") AnnotationAssertion(rdfs:label "pedal digit connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder connective tissue) @@ -175457,6 +173177,8 @@ AnnotationAssertion( "UBERON:0003579") AnnotationAssertion(rdfs:label "shoulder connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower respiratory tract connective tissue) @@ -175473,6 +173195,9 @@ AnnotationAssertion( "UBERON:0003580") AnnotationAssertion(rdfs:label "lower respiratory tract connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid connective tissue) @@ -175488,6 +173213,9 @@ AnnotationAssertion( "UBERON:0003581") AnnotationAssertion(rdfs:label "eyelid connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasopharynx connective tissue) @@ -175516,6 +173244,9 @@ AnnotationAssertion( "UBERON:0003582") AnnotationAssertion(rdfs:label "nasopharynx connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx connective tissue) @@ -175534,6 +173265,9 @@ AnnotationAssertion(Annotation( "UBERON:0003583") AnnotationAssertion(rdfs:label "larynx connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland connective tissue) @@ -175557,6 +173291,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mammary gland connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -175575,7 +173312,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dermis connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk connective tissue) @@ -175598,6 +173337,8 @@ AnnotationAssertion( "UBERON:0003586") AnnotationAssertion(rdfs:label "trunk connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb connective tissue) @@ -175613,6 +173354,8 @@ AnnotationAssertion( "UBERON:0003587") AnnotationAssertion(rdfs:label "limb connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb connective tissue) @@ -175630,6 +173373,8 @@ AnnotationAssertion( "UBERON:0003588") AnnotationAssertion(rdfs:label "forelimb connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb connective tissue) @@ -175646,6 +173391,8 @@ AnnotationAssertion( "UBERON:0003589") AnnotationAssertion(rdfs:label "hindlimb connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobar bronchus connective tissue) @@ -175661,6 +173408,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lobar bronchus connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchus connective tissue) @@ -175694,6 +173444,8 @@ AnnotationAssertion(Annotation( "UBERON:0003592") AnnotationAssertion(rdfs:label "bronchus connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity connective tissue) @@ -175733,6 +173485,8 @@ AnnotationAssertion( "UBERON:0003593") AnnotationAssertion(rdfs:label "thoracic cavity connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvis connective tissue) @@ -175748,6 +173502,8 @@ AnnotationAssertion( "UBERON:0003594") AnnotationAssertion(rdfs:label "pelvis connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes connective tissue) @@ -175762,6 +173518,9 @@ AnnotationAssertion( "UBERON:0003595") AnnotationAssertion(rdfs:label "pes connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ankle connective tissue) @@ -175775,6 +173534,8 @@ AnnotationAssertion( "UBERON:0003596") AnnotationAssertion(rdfs:label "ankle connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit connective tissue) @@ -175793,6 +173554,9 @@ AnnotationAssertion( "UBERON:0003597") AnnotationAssertion(rdfs:label "manual digit connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus connective tissue) @@ -175807,6 +173571,9 @@ AnnotationAssertion( "UBERON:0003598") AnnotationAssertion(rdfs:label "manus connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail connective tissue) @@ -175829,6 +173596,8 @@ AnnotationAssertion( "UBERON:0003599") AnnotationAssertion(rdfs:label "tail connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck cartilage) @@ -175842,6 +173611,8 @@ AnnotationAssertion( "UBERON:0003601") AnnotationAssertion(rdfs:label "neck cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower respiratory tract cartilage) @@ -175855,13 +173626,15 @@ AnnotationAssertion( "UBERON:0003603") AnnotationAssertion(rdfs:label "lower respiratory tract cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trachea cartilage) AnnotationAssertion(Annotation( "J:97123") Annotation( "MGI:smb") Annotation( "MP:0003120") Annotation( "http://orcid.org/0000-0002-6601-2165") "The ring-shaped cartilaginous structures that support the trachea.") AnnotationAssertion( "check whether to classify as part of splanchoncranium") AnnotationAssertion( ) -AnnotationAssertion( "in mammals the rings are incomplete, in avians the rings are complete.") AnnotationAssertion( "EMAPA:18699") AnnotationAssertion( "EMAPA:35875") AnnotationAssertion( "FMA:7434") @@ -175891,6 +173664,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye skin gland) @@ -175915,6 +173690,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eye skin gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb long bone) @@ -175927,6 +173706,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "limb long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (forelimb long bone) @@ -175947,6 +173728,8 @@ AnnotationAssertion( "UBERON:0003607") AnnotationAssertion(rdfs:label "forelimb long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindlimb long bone) @@ -175964,6 +173747,8 @@ AnnotationAssertion( "UBERON:0003608") AnnotationAssertion(rdfs:label "hindlimb long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (aorta elastic tissue) @@ -175999,6 +173784,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart elastic tissue) @@ -176015,6 +173802,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heart elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system elastic tissue) @@ -176036,6 +173827,8 @@ AnnotationAssertion( "UBERON:0003611") AnnotationAssertion(rdfs:label "respiratory system elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiovascular system elastic tissue) @@ -176057,6 +173850,7 @@ AnnotationAssertion( "UBERON:0003613") AnnotationAssertion(rdfs:label "cardiovascular system elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel elastic tissue) @@ -176079,6 +173873,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung elastic tissue) @@ -176094,6 +173891,8 @@ AnnotationAssertion( "UBERON:0003615") AnnotationAssertion(rdfs:label "lung elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (bronchus elastic tissue) @@ -176122,6 +173921,8 @@ AnnotationAssertion( "UBERON:0003616") AnnotationAssertion(rdfs:label "bronchus elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trachea elastic tissue) @@ -176152,6 +173953,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trachea elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (aorta tunica media) @@ -176173,6 +173976,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta tunica media") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -176196,6 +174000,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta tunica intima") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -176208,6 +174014,8 @@ AnnotationAssertion( "UBERON:0003643") AnnotationAssertion(rdfs:label "respiratory system arterial blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (kidney arterial blood vessel) @@ -176220,11 +174028,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney arterial blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mesopodium bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a mesopodial skeleton.") -AnnotationAssertion(Annotation( "Wikipedia:Carpus_and_tarsus_of_land_vertebrates") "The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost") AnnotationAssertion( "EMAPA:36579") AnnotationAssertion( "MA:0000295") AnnotationAssertion( "Wikipedia:Carpus_and_tarsus_of_land_vertebrates") @@ -176236,8 +174045,9 @@ AnnotationAssertion( "UBERON:0003656") AnnotationAssertion(rdfs:label "mesopodium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "UBERON:cjm") ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb joint) @@ -176256,6 +174066,8 @@ AnnotationAssertion( "Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses") AnnotationAssertion(rdfs:label "limb joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hip muscle) @@ -176271,6 +174083,8 @@ AnnotationAssertion( "UBERON:0003658") AnnotationAssertion(rdfs:label "hip muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (pedal digit muscle) @@ -176297,11 +174111,12 @@ AnnotationAssertion( "UBERON:0003659") AnnotationAssertion(rdfs:label "pedal digit muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid muscle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A muscle that attaches to an eyelid.") -AnnotationAssertion(Annotation( "ncithesaurus:Eyelid_Muscle") "The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle].") AnnotationAssertion( "MA:0000269") AnnotationAssertion( "NCIT:C52803") AnnotationAssertion(Annotation( "ncithesaurus:Eyelid_Muscle") "UMLS:C1707990") @@ -176313,12 +174128,13 @@ AnnotationAssertion( "UBERON:0003660") AnnotationAssertion(rdfs:label "eyelid muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a limb [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion( "EMAPA:32700") AnnotationAssertion( "MA:0000692") AnnotationAssertion(Annotation( "OBOL:accepted") "limb muscle organ") AnnotationAssertion(Annotation( "OBOL:exploratory") "limb skeletal muscle") @@ -176329,14 +174145,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "limb muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation(rdfs:seeAlso "https://purl.obolibrary.org/obo/uberon/tracker/324") ObjectSomeValuesFrom( )) # Class: (forelimb muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a forelimb.") -AnnotationAssertion(Annotation( "FMA") "FMA and MA class actually refer to muscles of entire pectoral complex") AnnotationAssertion( "UBERON:0005634") AnnotationAssertion( "AAO:0000204") AnnotationAssertion( "BTO:0000479") @@ -176356,6 +174171,8 @@ AnnotationAssertion(Annotation( "UBERON:0003662") AnnotationAssertion(rdfs:label "forelimb muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (hindlimb muscle) @@ -176383,6 +174200,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (manual digit muscle) @@ -176409,11 +174228,12 @@ AnnotationAssertion( "UBERON:0003664") AnnotationAssertion(rdfs:label "manual digit muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (post-anal tail muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A muscle organ that attaches to a tail vertebra [Automatically generated definition].") -AnnotationAssertion(Annotation( "BTO") "the BTO class may possibly refer to an invertebrate structure") AnnotationAssertion( "AAO:0000081") AnnotationAssertion( "BTO:0001905") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37759") @@ -176429,14 +174249,13 @@ AnnotationAssertion( "UBERON:0003665") AnnotationAssertion(rdfs:label "post-anal tail muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dentition) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000126") Annotation( "AAO") Annotation( "AAO:LAP") "Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]") -AnnotationAssertion(Annotation( "ncithesaurus:Dentition") "The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition])") -AnnotationAssertion(Annotation( "FMA") "In FMA this is an anatomical set") AnnotationAssertion( "AAO:0000126") AnnotationAssertion( "FMA:75150") AnnotationAssertion( "GAID:1249") @@ -176455,7 +174274,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dentition") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tooth root) @@ -176473,13 +174294,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tooth root") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal cavity) AnnotationAssertion(Annotation( "UBERON:cjm") "The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).") -AnnotationAssertion(Annotation( "FMA") "in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity") AnnotationAssertion( "EFO:0000213") AnnotationAssertion( "EMAPA:36505") AnnotationAssertion( "FMA:12266") @@ -176501,12 +174322,13 @@ AnnotationAssertion( "abdominal cavity") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial suture) AnnotationAssertion(Annotation( "FMA:71385") Annotation( "ISBN:3110148986") Annotation( "Wikipedia:Suture_(joint)") "Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture.") -AnnotationAssertion( ) AnnotationAssertion( "sutura") AnnotationAssertion(Annotation( "FMA:71385") "suture") AnnotationAssertion( "EMAPA:35263") @@ -176526,14 +174348,13 @@ AnnotationAssertion( "cranial suture") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "GO") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (foramen magnum) AnnotationAssertion(Annotation( "Wikipedia:Foramen_magnum") "In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002045") Annotation( "TAO") Annotation( "TAO:wd") "Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]") AnnotationAssertion( "AAO:0010826") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006035") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37868") AnnotationAssertion( "FMA:75306") AnnotationAssertion( "GAID:228") @@ -176552,12 +174373,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "foramen magnum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (omentum) AnnotationAssertion(Annotation( "ncithesaurus:Omentum") "A fold of peritoneum originating at the stomach and supporting the viscera.") -AnnotationAssertion( "omental") AnnotationAssertion( "CALOHA:TS-2004") AnnotationAssertion( "EV:0100084") AnnotationAssertion( "FMA:14650") @@ -176570,16 +174392,13 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003688") AnnotationAssertion(rdfs:label "omentum") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epidural space) AnnotationAssertion(Annotation( "Wikipedia:Epidural_space") "The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater.") -AnnotationAssertion( "epidural") -AnnotationAssertion( "extradural") -AnnotationAssertion( "In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus") -AnnotationAssertion(Annotation( "FMA") "in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail") AnnotationAssertion( "FMA:71228") AnnotationAssertion( "GAID:243") AnnotationAssertion( "MESH:D004824") @@ -176595,11 +174414,13 @@ AnnotationAssertion(Annotation( "UBERON:0003691") AnnotationAssertion(rdfs:label "epidural space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acromioclavicular joint) AnnotationAssertion(Annotation( "Wikipedia:Acromioclavicular_joint") Annotation( "http://orcid.org/0000-0002-6601-2165") "Any joint connecting the acromonion of the scapula and clavicle.") -AnnotationAssertion(Annotation( "MESH:A02.835.583.032") "The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula.") AnnotationAssertion( "FMA:25898") AnnotationAssertion( "GAID:249") AnnotationAssertion( "MESH:D000173") @@ -176616,7 +174437,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (atlanto-axial joint) @@ -176641,13 +174464,15 @@ AnnotationAssertion( "atlanto-axial joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metacarpophalangeal joint) AnnotationAssertion(Annotation( "Wikipedia:Metacarpophalangeal_joint") "The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted].") AnnotationAssertion( "we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part") -AnnotationAssertion( ) AnnotationAssertion(Annotation( "FMA:35246") "metacarpal joint") AnnotationAssertion( "EMAPA:19302") AnnotationAssertion( "FMA:35246") @@ -176673,7 +174498,10 @@ AnnotationAssertion( "metacarpophalangeal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metatarsophalangeal joint) @@ -176700,7 +174528,10 @@ AnnotationAssertion( "metatarsophalangeal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal wall) @@ -176726,12 +174557,13 @@ AnnotationAssertion( "abdominal wall") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extrahepatic bile duct) AnnotationAssertion(Annotation( "MESH:A03.159.183.079") "Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.") AnnotationAssertion( "includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct") -AnnotationAssertion( ) AnnotationAssertion( "FMA:14678") AnnotationAssertion( "GAID:281") AnnotationAssertion( "MA:0002659") @@ -176752,7 +174584,6 @@ SubClassOf( "MESH:A03.159.183.158") "Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.") AnnotationAssertion( "includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005169") Annotation( "TAO") Annotation( "ZFIN:curator") "Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]") AnnotationAssertion( "FMA:15766") AnnotationAssertion( "GAID:287") AnnotationAssertion( "MA:0001630") @@ -176777,7 +174608,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (circle of Willis) AnnotationAssertion(Annotation( "Wikipedia:Circle_of_Willis") "A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle.") -AnnotationAssertion(Annotation( "http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html") "In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis") AnnotationAssertion(Annotation( "Wikipedia:Circle_of_Willis") "arterial circle") AnnotationAssertion( "EHDAA2:0000252") AnnotationAssertion( "EHDAA:9758") @@ -176836,7 +174666,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Cavernous_sinus") "The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MESH:A07.231.908.224.334") "An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334].") AnnotationAssertion( "EMAPA:19059") AnnotationAssertion( "FMA:50772") AnnotationAssertion( "GAID:532") @@ -176889,8 +174718,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (neural tissue) AnnotationAssertion(Annotation( "FMA:9642") "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000325") Annotation( "AAO") Annotation( "AAO:LAP") "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]") -AnnotationAssertion(Annotation( "FMA") "FMA definition includes vasculature") AnnotationAssertion( "AAO:0000325") AnnotationAssertion( "AEO:0000123") AnnotationAssertion( "EHDAA2:0003123") @@ -176907,13 +174734,15 @@ AnnotationAssertion( "UBERON:0003714") AnnotationAssertion(rdfs:label "neural tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (splanchnic nerve) AnnotationAssertion(Annotation( "MP:0008318") "The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.") -AnnotationAssertion( "All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers") AnnotationAssertion( "BAMS:spn") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37959") AnnotationAssertion( "FMA:5883") @@ -176928,13 +174757,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "splanchnic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (recurrent laryngeal nerve) AnnotationAssertion(Annotation( "Wikipedia:Recurrent_laryngeal_nerve") "A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch.") -AnnotationAssertion(Annotation( "AAO:0010754") "Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754].") AnnotationAssertion(Annotation( "Wikipedia:Recurrent_laryngeal_nerve") "recurrent nerve") AnnotationAssertion( "AAO:0010754") AnnotationAssertion( "FMA:6246") @@ -176951,8 +174780,8 @@ AnnotationAssertion(Annotation( "AAO:0010754") "ramus recurrens") AnnotationAssertion( "UBERON:0003716") AnnotationAssertion(rdfs:label "recurrent laryngeal nerve") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -176994,6 +174823,8 @@ AnnotationAssertion( "UBERON:0003721") AnnotationAssertion(rdfs:label "lingual nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic nerve) @@ -177013,6 +174844,8 @@ AnnotationAssertion(Annotation( "UBERON:0003726") AnnotationAssertion(rdfs:label "thoracic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intercostal nerve) @@ -177040,7 +174873,6 @@ SubClassOf( (mediastinum) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Mediastinum") "The central part of the thoracic cavity enclosed by the left and right pleurae.") -AnnotationAssertion( "mediastinal") AnnotationAssertion( "CALOHA:TS-2338") AnnotationAssertion( "EFO:0003057") AnnotationAssertion( "EMAPA:36001") @@ -177066,8 +174898,6 @@ SubClassOf(Annotation( "FMA # Class: (mouth mucosa) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A mucous membrane that lines the mouth.") -AnnotationAssertion( "this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)") -AnnotationAssertion(Annotation( "Wikipedia:Oral_mucosa") "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].") AnnotationAssertion( "BTO:0002860") AnnotationAssertion( "CALOHA:TS-0716") AnnotationAssertion( "EMAPA:26937") @@ -177095,6 +174925,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mouth mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177103,7 +174935,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (prostate bud) AnnotationAssertion(Annotation( "GO:0060513") "A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].") -AnnotationAssertion( "AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204]") AnnotationAssertion( "EMAPA:36141") AnnotationAssertion(Annotation( "PMID:18977204") "prostate ductal progenitor") AnnotationAssertion( "prostatic bud") @@ -177113,8 +174944,11 @@ AnnotationAssertion( "UBERON:0003820") AnnotationAssertion(rdfs:label "prostate bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:18977204") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metapodium bone) @@ -177131,15 +174965,13 @@ AnnotationAssertion( "UBERON:0003821") AnnotationAssertion(rdfs:label "metapodium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA-abduced") ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb stylopod) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the forelimb between pectoral region and the elbow, corresponding to the humerus.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000887") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the hindleg corresponding to the humerus.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000343") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group.") AnnotationAssertion( "AAO:0000199") AnnotationAssertion( "EHDAA2:0002112") AnnotationAssertion( "EHDAA:4186") @@ -177172,6 +175004,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb stylopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177179,10 +175013,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hindlimb zeugopod) AnnotationAssertion(Annotation( "PHENOSCAPE:curators") "The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000348") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") -AnnotationAssertion( "sural") -AnnotationAssertion(Annotation( "FMA") "FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here") AnnotationAssertion( "EFO:0003051") AnnotationAssertion( "EHDAA2:0001030") AnnotationAssertion( "EHDAA:5165") @@ -177195,7 +175025,6 @@ AnnotationAssertion( "SCTID:244015008") AnnotationAssertion(Annotation( "ncithesaurus:Leg") "UMLS:C1140621") AnnotationAssertion( "VHOG:0000348") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "VO:0010971") AnnotationAssertion( "VSAO:0005060") AnnotationAssertion( "Wikipedia:Forearm") AnnotationAssertion( "galen:Leg") @@ -177226,6 +175055,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb zeugopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177245,6 +175076,8 @@ AnnotationAssertion(Annotation( "UBERON:0003824") AnnotationAssertion(rdfs:label "nerve of thoracic segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of abdominal segment) @@ -177256,6 +175089,8 @@ AnnotationAssertion( "UBERON:0003825") AnnotationAssertion(rdfs:label "nerve of abdominal segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper leg bone) @@ -177268,6 +175103,8 @@ AnnotationAssertion( "May be merged into femur. See https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376") AnnotationAssertion(rdfs:label "upper leg bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic segment bone) @@ -177284,6 +175121,8 @@ AnnotationAssertion(Annotation( "UBERON:0003827") AnnotationAssertion(rdfs:label "thoracic segment bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (abdominal segment bone) @@ -177298,6 +175137,8 @@ AnnotationAssertion( "UBERON:0003828") AnnotationAssertion(rdfs:label "abdominal segment bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (urethra muscle tissue) @@ -177309,6 +175150,9 @@ AnnotationAssertion(Annotation( "UBERON:0003829") AnnotationAssertion(rdfs:label "urethra muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic segment muscle) @@ -177321,6 +175165,8 @@ AnnotationAssertion(Annotation( "UBERON:0003830") AnnotationAssertion(rdfs:label "thoracic segment muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (respiratory system muscle) @@ -177336,6 +175182,8 @@ AnnotationAssertion( "UBERON:0003831") AnnotationAssertion(rdfs:label "respiratory system muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus muscle) @@ -177355,6 +175203,9 @@ AnnotationAssertion( "UBERON:0003832") AnnotationAssertion(rdfs:label "esophagus muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (abdominal segment muscle) @@ -177368,6 +175219,8 @@ AnnotationAssertion( "UBERON:0003833") AnnotationAssertion(rdfs:label "abdominal segment muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (thoracic segment blood vessel) @@ -177381,6 +175234,8 @@ AnnotationAssertion(Annotation( "UBERON:0003834") AnnotationAssertion(rdfs:label "thoracic segment blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal segment blood vessel) @@ -177393,6 +175248,8 @@ AnnotationAssertion( "UBERON:0003835") AnnotationAssertion(rdfs:label "abdominal segment blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal segment skin) @@ -177406,6 +175263,8 @@ AnnotationAssertion( "UBERON:0003836") AnnotationAssertion(rdfs:label "abdominal segment skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic segment connective tissue) @@ -177423,6 +175282,8 @@ AnnotationAssertion(Annotation( "UBERON:0003837") AnnotationAssertion(rdfs:label "thoracic segment connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal segment connective tissue) @@ -177439,11 +175300,12 @@ AnnotationAssertion( "UBERON:0003838") AnnotationAssertion(rdfs:label "abdominal segment connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb joint) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb joint that is part of a forelimb [Automatically generated definition].") -AnnotationAssertion( ) AnnotationAssertion( "EMAPA:19204") AnnotationAssertion( "MA:0000614") AnnotationAssertion(Annotation( "OBOL:automatic") "anteriormost limb joint of limb") @@ -177473,11 +175335,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb joint) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb joint that is part of a hindlimb [Automatically generated definition].") -AnnotationAssertion( ) AnnotationAssertion( "EMAPA:32635") AnnotationAssertion( "MA:0000662") AnnotationAssertion( "SCTID:304573000") @@ -177504,6 +175367,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autopod joint) @@ -177523,11 +175388,12 @@ AnnotationAssertion(Annotation( "UBERON:0003841") AnnotationAssertion(rdfs:label "autopod joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural tube lumen) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical space that surrounded_by a neural tube.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001119") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]") AnnotationAssertion( "UBERON:0005713") AnnotationAssertion( "AAO:0011073") AnnotationAssertion( "EHDAA2:0001269") @@ -177547,14 +175413,15 @@ AnnotationAssertion(Annotation( "UBERON:0003842") AnnotationAssertion(rdfs:label "neural tube lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dental epithelium) AnnotationAssertion(Annotation( "ZFA:0005134") Annotation( "https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107") "Epithelium that is part of a developing tooth or dental organ.") AnnotationAssertion( "see comments for dental organ.") AnnotationAssertion( "todo - full developmental relationships") -AnnotationAssertion(Annotation( "PMID:10954731") "In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)") AnnotationAssertion( "AAO:0011027") AnnotationAssertion( "BTO:0001723") AnnotationAssertion( "EMAPA:32903") @@ -177575,7 +175442,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dental epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "epithelium") Annotation( "JB") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thymus epithelium) @@ -177605,6 +175474,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:21293377") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177612,8 +175485,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (thyroid artery) AnnotationAssertion(Annotation( "OBOL:automatic") "An artery that supplies a thyroid gland.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010490") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the external carotid which supplies blood to the thyroid gland.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010490") Annotation( "AAO") "relationship loss: part_of external carotid (AAO:0010218)[AAO]") AnnotationAssertion( "AAO:0010490") AnnotationAssertion( "EHDAA2:0002029") AnnotationAssertion( "EHDAA:7372") @@ -177626,6 +175497,8 @@ AnnotationAssertion( "UBERON:0003847") AnnotationAssertion(rdfs:label "thyroid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gonadal vein) @@ -177644,11 +175517,12 @@ AnnotationAssertion( "gonadal vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesencephalic neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural crest that has_potential_to_developmentally_contribute_to a midbrain.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000796") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EFO:0003591") AnnotationAssertion( "EHDAA2:0001101") AnnotationAssertion( "EHDAA:360") @@ -177663,13 +175537,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesencephalic neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (telencephalon neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural crest that has_potential_to_developmentally_contribute_to a telencephalon.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000812") Annotation( "TAO") Annotation( "ZFIN:curator") "Cranial neural crest that is part of the telencephalon.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000799") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EFO:0003574") AnnotationAssertion( "RETIRED_EHDAA2:0001991") AnnotationAssertion( "TAO:0000812") @@ -177682,11 +175556,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "telencephalon neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diencephalon neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000798") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EFO:0003573") AnnotationAssertion( "EHDAA2:0000603") AnnotationAssertion( "EMAPA:16518") @@ -177702,12 +175577,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diencephalon neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rhombencephalon neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0007063") Annotation( "TAO") Annotation( "ZFIN:curator") "Cranial neural crest that is part of the hindbrain.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001210") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001628") AnnotationAssertion( "EHDAA:362") AnnotationAssertion( "EMAPA:35747") @@ -177722,12 +175597,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rhombencephalon neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001006") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]") AnnotationAssertion( "EHDAA:696") AnnotationAssertion( "EMAPA:16163") AnnotationAssertion( "EMAPA:16881") @@ -177738,12 +175614,12 @@ AnnotationAssertion(Annotation( "UBERON:0003853") AnnotationAssertion(rdfs:label "spinal cord neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord neural plate) AnnotationAssertion(Annotation( "OBOL:automatic") "A neural plate that develops_from a future spinal cord.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000439") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000439") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28") Annotation( "http://bgee.unil.ch/") "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]") AnnotationAssertion( "FMA:312957") AnnotationAssertion( "TAO:0007021") AnnotationAssertion( "VHOG:0000439") @@ -177753,6 +175629,7 @@ AnnotationAssertion( "UBERON:0003854") AnnotationAssertion(rdfs:label "spinal cord neural plate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (gonad mesenchyme) @@ -177770,13 +175647,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gonad mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (uncondensed odontogenic mesenchyme) AnnotationAssertion(Annotation( "https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107") Annotation( "https://orcid.org/0000-0002-6601-2165") "Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla.") AnnotationAssertion( "we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme") -AnnotationAssertion(Annotation( "MP") Annotation( "J:153554") "Mesenchyme enclosed by dental organ.[MP]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005139") Annotation( "TAO") Annotation( "ZFIN:curator") "Mesenchyme enclosed by dental organ.[TAO]") AnnotationAssertion( "EMAPA:32891") AnnotationAssertion( "MA:0003152") AnnotationAssertion( "TAO:0005139") @@ -177792,7 +175670,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "uncondensed odontogenic mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "see comments") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb mesenchyme) @@ -177814,6 +175695,8 @@ AnnotationAssertion( "UBERON:0003859") AnnotationAssertion(rdfs:label "forelimb mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb mesenchyme) @@ -177831,17 +175714,12 @@ AnnotationAssertion( "UBERON:0003860") AnnotationAssertion(rdfs:label "hindlimb mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural arch) AnnotationAssertion(Annotation( "Wikipedia:Vertebral_arch") "Posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001066") Annotation( "TAO") Annotation( "ZFIN:curator") "A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000725") Annotation( "AAO") Annotation( "AAO:Pugener_2002") "Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO]") -AnnotationAssertion(Annotation( "MP:0004599:csmith") "the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process)") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001066") Annotation( "TAO") "relationship loss: develops_from basidorsal (TAO:0001060)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001670") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270") Annotation( "http://bgee.unil.ch/") "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]") -AnnotationAssertion( "tiny neural arches present in Hagfish (which lack a true vertebraal column).") -AnnotationAssertion( "The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone") AnnotationAssertion(Annotation( "MA:0001453") Annotation( ) "vertebra neural arch") AnnotationAssertion( "AAO:0000725") AnnotationAssertion( "EFO:0003618") @@ -177893,7 +175771,7 @@ AnnotationAssertion( "middle phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177922,8 +175800,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "distal phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (middle phalanx of pes) @@ -177944,7 +175822,7 @@ AnnotationAssertion( "middle phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -177973,8 +175851,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "distal phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal phalanx of pes) @@ -178000,7 +175878,7 @@ AnnotationAssertion( "proximal phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive ganglion) @@ -178010,6 +175888,8 @@ AnnotationAssertion( "UBERON:0003869") AnnotationAssertion(rdfs:label "presumptive ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesometrium) @@ -178026,8 +175906,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesometrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (future coelemic cavity lumen) @@ -178041,7 +175921,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future coelemic cavity lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178049,7 +175931,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0012187") "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.") AnnotationAssertion( "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000316") Annotation( "VHOG") Annotation( "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166") Annotation( "http://bgee.unil.ch/") "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]") AnnotationAssertion( "EHDAA:251") AnnotationAssertion( "EMAPA:16088") AnnotationAssertion( "NCIT:C34195") @@ -178069,12 +175950,10 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003574") Annotation( "http://orcid.org/0000-0002-6601-2165") "Initial section of the oviduct through which the ova pass from the ovary to the uterus.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Talk:Fallopian_tube#Homology") "Homologous to appendix testis") AnnotationAssertion(Annotation( ) "salpinges") AnnotationAssertion( "salpinx") AnnotationAssertion( "CALOHA:TS-0732") AnnotationAssertion( "EHDAA2:0000504") -AnnotationAssertion( "EMAPA:18984") AnnotationAssertion( "EMAPA:35660") AnnotationAssertion( "EV:0100112") AnnotationAssertion( "FMA:18245") @@ -178101,19 +175980,19 @@ AnnotationAssertion( "fallopian tube") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Mullerian duct) AnnotationAssertion(Annotation( "GO:0061205") Annotation( "Wikipedia:Paramesonephric_duct") Annotation( "http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html") "Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001199") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/paramesonephric+duct") "Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010141") Annotation( "AAO") Annotation( "AAO:RED") "Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001199") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559") Annotation( "http://bgee.unil.ch/") "In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]") -AnnotationAssertion( "Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct") AnnotationAssertion( "UBERON:0005318") AnnotationAssertion( "AAO:0010141") AnnotationAssertion( "EHDAA2:0004048") @@ -178138,6 +176017,8 @@ AnnotationAssertion( "Mullerian duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -178145,7 +176026,6 @@ SubClassOf(Annotation( "Wik # Class: (stroma) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.") -AnnotationAssertion( "stromal") AnnotationAssertion( "FMA:81494") AnnotationAssertion( "NCIT:C67387") AnnotationAssertion(Annotation( "ncithesaurus:Stroma_Connective_Tissue") "UMLS:C0927195") @@ -178161,7 +176041,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (capsule) AnnotationAssertion(Annotation( "Wikipedia:Capsule_(anatomy)") "A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP].") -AnnotationAssertion( "capsular") AnnotationAssertion( "EHDAA:4739") AnnotationAssertion( "EHDAA:9061") AnnotationAssertion( "FMA:85272") @@ -178174,7 +176053,6 @@ AnnotationAssertion( "see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells") AnnotationAssertion(rdfs:label "capsule") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver primordium) @@ -178207,8 +176085,12 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "XAO") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ventral foregut endoderm") Annotation( "Zaret 1996") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axial muscle) @@ -178223,7 +176105,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "axial muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle tissue of trunk) @@ -178240,6 +176124,7 @@ AnnotationAssertion( "UBERON:0003898") AnnotationAssertion(rdfs:label "skeletal muscle tissue of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178247,7 +176132,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0003407") "The part of the retina that contains neurons and photoreceptor cells[GO].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000535") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "AAO:0011095") AnnotationAssertion( "BTO:0000929") AnnotationAssertion( "CALOHA:TS-0685") @@ -178276,17 +176160,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retinal neural layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (sinusoid) AnnotationAssertion(Annotation( "Wikipedia:Sinusoid_(blood_vessel)") "Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005261") Annotation( "TAO") Annotation( "ZFIN:curator") "Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]") -AnnotationAssertion( "sinusoidal") -AnnotationAssertion(Annotation( "FMA") "some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).") AnnotationAssertion( "FMA:63131") AnnotationAssertion( "SCTID:340163004") AnnotationAssertion( "TAO:0005261") @@ -178301,7 +176182,6 @@ AnnotationAssertion( "UBERON:0003909") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sinusoid") -SubClassOf(Annotation( "Wikipedia-inconsistent") ) SubClassOf(Annotation( "Wikipedia") Annotation( "ZFA") ) # Class: (splenic sinusoid) @@ -178312,7 +176192,6 @@ AnnotationAssertion(Annotation( "http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml") ) AnnotationAssertion(Annotation( "http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml") ) AnnotationAssertion( ) -AnnotationAssertion( "Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml") AnnotationAssertion( "FMA:63199") AnnotationAssertion( "SCTID:9081000") AnnotationAssertion( "Wikipedia:Red_pulp#Sinusoids") @@ -178323,6 +176202,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "splenic sinusoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178331,8 +176211,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (choroid plexus epithelium) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Choroid_plexus") "The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue.") -AnnotationAssertion( "The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006008") AnnotationAssertion( "EMAPA:36608") AnnotationAssertion( "FMA:242811") AnnotationAssertion( "MA:0000824") @@ -178346,6 +176224,8 @@ AnnotationAssertion( "UBERON:0003911") AnnotationAssertion(rdfs:label "choroid plexus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tooth-like structure) @@ -178364,16 +176244,15 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (epithelial tube) AnnotationAssertion(Annotation( "GO:0060562") Annotation( "PMID:12526790") "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.") -AnnotationAssertion( "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers") AnnotationAssertion( "AEO:0000114") AnnotationAssertion( "EHDAA2:0003114") -AnnotationAssertion(Annotation( ) "FBbt:00007474") AnnotationAssertion( "epithelial or endothelial tube") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003914") AnnotationAssertion(rdfs:label "epithelial tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (endothelial tube) @@ -178382,6 +176261,7 @@ AnnotationAssertion( "UBERON:0003915") AnnotationAssertion(rdfs:label "endothelial tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (kidney mesenchyme) @@ -178394,6 +176274,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous blood vessel) @@ -178410,12 +176292,12 @@ AnnotationAssertion( "Compare to: vein") AnnotationAssertion(rdfs:label "venous blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas primordium) AnnotationAssertion(Annotation( "Wikipedia:Pancreas#Embryological_development") "Embryonic structure that develops into pancreatic bud.") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds") -AnnotationAssertion( "revisit after standardizing terms 'primordium', 'anlagen', 'bud'") AnnotationAssertion( "EFO:0002579") AnnotationAssertion( "EFO:0003434") AnnotationAssertion( "EHDAA2:0001382") @@ -178436,9 +176318,11 @@ AnnotationAssertion( "pancreas primordium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreatic epithelial bud) @@ -178461,18 +176345,18 @@ AnnotationAssertion( "pancreatic epithelial bud") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Pancreas#Embryological_development") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "zebrafish") Annotation( "Wikipedia:Pancreatic_bud") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-inferred") ObjectSomeValuesFrom( )) # Class: (dorsal pancreatic bud) AnnotationAssertion(Annotation( "Wikipedia:Pancreatic_bud") "Pancreatic bud that gives rise to the accessory pancreatic duct.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011031") Annotation( "AAO") Annotation( "XAO:curator") "The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001428") Annotation( "VHOG") Annotation( "DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)") Annotation( "http://bgee.unil.ch/") "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]") AnnotationAssertion( "AAO:0011031") AnnotationAssertion( "EFO:0003465") AnnotationAssertion( "EHDAA2:0001385") @@ -178503,9 +176387,6 @@ SubClassOf(Annotation( "XAO # Class: (ventral pancreatic bud) AnnotationAssertion(Annotation( "Wikipedia:Pancreatic_bud") "Pancreatic bud that gives rise to the major pancreatic duct.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001429") Annotation( "VHOG") Annotation( "DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)") Annotation( "http://bgee.unil.ch/") "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]") -AnnotationAssertion( "The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]") -AnnotationAssertion( "the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship.") AnnotationAssertion( "AAO:0011111") AnnotationAssertion( "EFO:0003464") AnnotationAssertion( "EHDAA2:0001389") @@ -178544,16 +176425,15 @@ AnnotationAssertion( "UBERON:0003928") AnnotationAssertion(rdfs:label "digestive system duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive tract epithelium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An epithelium that lines the lumen of the digestive tract.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005123") Annotation( "TAO") Annotation( "ZFIN:curator") "Epithelium lining the lumen of the gut.[TAO]") -AnnotationAssertion( "") AnnotationAssertion( "BTO:0000956") AnnotationAssertion( "EHDAA2:0004567") AnnotationAssertion( "EMAPA:32928") -AnnotationAssertion(Annotation( ) "FBbt:00047166") AnnotationAssertion( "MA:0003201") AnnotationAssertion( "NCIT:C12963") AnnotationAssertion( "TAO:0005123") @@ -178573,6 +176453,8 @@ AnnotationAssertion(Annotation( "UBERON:0003929") AnnotationAssertion(rdfs:label "digestive tract epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diencephalic white matter) @@ -178591,6 +176473,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diencephalic white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilage element of chondrocranium) @@ -178607,11 +176491,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cartilage element of chondrocranium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial cartilage) AnnotationAssertion(Annotation( "ZFA:0001458") Annotation( "https://orcid.org/0000-0002-6601-2165") "A cartilage element that is part of the cranial skeleton.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001458") Annotation( "TAO") Annotation( "ZFIN:curator") "Cartilage which is part of the cranium.[TAO]") AnnotationAssertion( "TAO:0001458") AnnotationAssertion( "ZFA:0001458") AnnotationAssertion(Annotation( "OBOL:automatic") "cartilage of cranium") @@ -178621,11 +176506,12 @@ AnnotationAssertion(Annotation( "UBERON:0003933") AnnotationAssertion(rdfs:label "cranial cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (reproductive gland) AnnotationAssertion(Annotation( "MP:0000653") "Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006162") AnnotationAssertion( "MA:0001751") AnnotationAssertion(Annotation( "OBOL:automatic") "genitalia gland") AnnotationAssertion(Annotation( "MP:0000653") "gland of genitalia") @@ -178639,12 +176525,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (somatosensory system) AnnotationAssertion(Annotation( "NLXANAT:090818") "The sensory system for the sense of touch and pain.") -AnnotationAssertion(Annotation( "MP:0000959") "The neural tissue involved in the transmission of sensory signals") -AnnotationAssertion(Annotation( "MP") "MP defines this in a may more appropriate to somatosensory cortex") AnnotationAssertion( "UBERON:0014511") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37954") AnnotationAssertion( "NLXANAT:090818") @@ -178664,7 +176550,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0001716") "The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood.") AnnotationAssertion(Annotation( "http://placentation.ucsd.edu") ) -AnnotationAssertion( "Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ]") AnnotationAssertion(Annotation( "GO:0060713") "labyrinthine layer") AnnotationAssertion(Annotation( "GO:0060713") "labyrinthine layer of placenta") AnnotationAssertion( "placental labyrinth") @@ -178673,7 +176558,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "placenta labyrinth") AnnotationAssertion(rdfs:seeAlso "http://placentation.ucsd.edu/placenta.html"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178687,6 +176573,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain ventricle/choroid plexus") EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178704,7 +176591,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anterior stroma of cornea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) @@ -178719,7 +176609,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "posterior stroma of cornea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (aqueous drainage system) @@ -178731,6 +176624,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aqueous drainage system") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (rete testis) @@ -178753,6 +176647,8 @@ AnnotationAssertion( "rete testis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -178770,6 +176666,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cutaneous elastic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental labyrinth vasculature) @@ -178783,7 +176682,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "placental labyrinth vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (internal female genitalia) @@ -178804,10 +176704,11 @@ AnnotationAssertion( "TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547") AnnotationAssertion(rdfs:label "internal female genitalia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (valve) -AnnotationAssertion( "valvular") AnnotationAssertion( "EHDAA2:0004046") AnnotationAssertion( "EHDAA:1892") AnnotationAssertion( "EHDAA:4406") @@ -178826,7 +176727,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cerebellum fissure) AnnotationAssertion(Annotation( "MP:0009267") "One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows.") -AnnotationAssertion( ) AnnotationAssertion( "BAMS:CBf") AnnotationAssertion( "DHBA:12828") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37818") @@ -178847,6 +176747,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cerebellum fissure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (primordial ovarian follicle) @@ -178868,9 +176770,6 @@ SubClassOf( (conus arteriosus) AnnotationAssertion(Annotation( "MP:0009464") Annotation( "Wikipedia:Conus_arteriosus") "A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010250") Annotation( "AAO") Annotation( "AAO:BJB") "Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]") -AnnotationAssertion( "Kardong says absent in adult tetrapods, check AAO") -AnnotationAssertion(Annotation( "ISBN:0073040584") "we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally") AnnotationAssertion( "AAO:0010250") AnnotationAssertion( "Wikipedia:Conus_arteriosus") AnnotationAssertion( "uberon") @@ -178885,8 +176784,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0009466") Annotation( "Wikipedia:Infundibulum_of_uterine_tube") "The funnel-like expansion of the abdominal extremity of the uterine tube[MP].") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Infundibulum_of_uterine_tube") "The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube].") -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-2825-0621") "In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct.") AnnotationAssertion(Annotation( ) "infundibulum") AnnotationAssertion( "EMAPA:29897") AnnotationAssertion( "FMA:18307") @@ -178924,11 +176821,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus corticomedullary boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord motor column) @@ -178954,6 +176856,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory bulb layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic-extraembryonic boundary) @@ -178964,14 +176869,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic-extraembryonic boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermatome) AnnotationAssertion(Annotation( "AEO:0001017") Annotation( "AEO:JB") "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.") -AnnotationAssertion( "Not to be confused with 'dermatome segment of skin'.") AnnotationAssertion( "AAO:0011028") AnnotationAssertion( "AEO:0001017") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006248") AnnotationAssertion( "EHDAA2_RETIRED:0003428") AnnotationAssertion( "EHDAA:1719") AnnotationAssertion( "EHDAA:1725") @@ -178993,15 +176899,11 @@ AnnotationAssertion( "dermatome") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png"^^xsd:anyURI) SubClassOf(Annotation( "AEO") ) -SubClassOf(Annotation( "AEO-text") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) # Class: (spongiotrophoblast layer) AnnotationAssertion(Annotation( "MP:0004255") Annotation( "PMID:19829370") "The structure of the outer structural layer of the rodent placenta[MP].") -AnnotationAssertion( "restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition") -AnnotationAssertion( "Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells") -AnnotationAssertion(Annotation( "PMID:19829370") "In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone") AnnotationAssertion( "spongiotrophoblast") AnnotationAssertion( "BTO:0005402") AnnotationAssertion( "EMAPA:31876") @@ -179011,6 +176913,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spongiotrophoblast layer") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP:0004255") Annotation( "PMID:11433360") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:19829370") ObjectSomeValuesFrom( )) @@ -179019,7 +176924,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (germinal neuroepithelium) AnnotationAssertion(Annotation( "MP:0004261") Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK10047") "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.") -AnnotationAssertion( "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "germinal neuroepithelial layer") AnnotationAssertion(Annotation( "NCBIBook:NBK10047") "germinal neuroepithelium") AnnotationAssertion(Annotation( "NCBIBook:NBK10047") "original neural tube") @@ -179027,6 +176931,8 @@ AnnotationAssertion( "UBERON:0004022") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "germinal neuroepithelium") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK10047") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179036,7 +176942,6 @@ DisjointClasses( (ganglionic eminence) AnnotationAssertion(Annotation( "MP:0004274") "The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP].") -AnnotationAssertion( "contributes significantly in building up the GABAergic cortical cell population[WP]") AnnotationAssertion(Annotation( ) "GE") AnnotationAssertion(Annotation( "MP:0004274") Annotation( ) "SVZ") AnnotationAssertion(Annotation( ) "embryonic GE") @@ -179054,8 +176959,7 @@ AnnotationAssertion( "UBERON:0004023") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ganglionic eminence") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (medial ganglionic eminence) @@ -179069,7 +176973,7 @@ AnnotationAssertion( "UBERON:0004024") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "medial ganglionic eminence") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) @@ -179085,7 +176989,7 @@ AnnotationAssertion( "UBERON:0004025") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lateral ganglionic eminence") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179102,7 +177006,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "caudal ganglionic eminence") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179121,7 +177025,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chorionic plate") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179129,12 +177035,10 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cortical subplate) AnnotationAssertion(Annotation( "MP:0008440") Annotation( "Wikipedia:Subplate") Annotation( "https://github.com/obophenotype/mouse-anatomy-ontology/issues/1") "The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate.") -AnnotationAssertion(Annotation( "WP") "The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects") AnnotationAssertion(Annotation( "BRAINSPAN:BRAINSPAN") Annotation( ) "SP") AnnotationAssertion( "DHBA:10522") AnnotationAssertion( "EMAPA:32703") AnnotationAssertion( "PBA:294021932") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "VO:0011276") AnnotationAssertion( "Wikipedia:Subplate") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png") AnnotationAssertion( "neuronames:3233") @@ -179146,7 +177050,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortical subplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortical intermediate zone) @@ -179169,7 +177076,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0008471") "The nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA:15843 is classified as primary follicle so it belongs here") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37960") AnnotationAssertion( "FMA:15843") AnnotationAssertion(Annotation( "CL:tm") "primary spleen B cell follicle") @@ -179179,6 +177085,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen primary B follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (spleen secondary B follicle) @@ -179193,6 +177101,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen secondary B follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) # Class: (semicircular canal ampulla) @@ -179211,8 +177121,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "semicircular canal ampulla") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (anterior visceral endoderm) @@ -179246,6 +177156,8 @@ AnnotationAssertion( "TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547") AnnotationAssertion(rdfs:label "external male genitalia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -179267,13 +177179,14 @@ AnnotationAssertion( "TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547") AnnotationAssertion(rdfs:label "internal male genitalia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (biliary ductule) AnnotationAssertion(Annotation( "BTO:0002840") Annotation( "MP:0009494") "One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ZFA") "In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)") AnnotationAssertion( "BTO:0002840") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37440") AnnotationAssertion( "TAO:0005164") @@ -179291,6 +177204,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "biliary ductule") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179308,7 +177222,6 @@ SubClassOf( "MP:0009689") Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK10047") "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.") AnnotationAssertion( "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure") -AnnotationAssertion(Annotation( "MP:0009689") "The layer of undifferentiated, proliferating cells that line the neural tube lumen") AnnotationAssertion(Annotation( "NCBIBook:NBK10047") "ependymal layer") AnnotationAssertion( "EMAPA:17152") AnnotationAssertion( "EMAPA:35362") @@ -179322,6 +177235,8 @@ AnnotationAssertion( "UBERON:0004060") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural tube ventricular layer") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK10047") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179339,9 +177254,11 @@ AnnotationAssertion(Annotation( "UBERON:0004061") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural tube mantle layer") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK10047") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "by division") Annotation( "NCBIBook:NBK10047") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179356,9 +177273,10 @@ AnnotationAssertion( "UBERON:0004062") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural tube marginal layer") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "forms from axons") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord alar plate) @@ -179376,6 +177294,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spinal cord alar plate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural tube basal plate) @@ -179397,11 +177317,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural tube basal plate") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Shh") Annotation( "Swenson") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontonasal prominence) @@ -179456,7 +177377,6 @@ DisjointClasses(Annotation( # Class: (medial nasal prominence) AnnotationAssertion(Annotation( "MP:0009903") Annotation( "Wikipedia:Medial_nasal_prominence") "The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it.") -AnnotationAssertion( "Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.") AnnotationAssertion( "EHDAA2:0001076") AnnotationAssertion( "EHDAA:4792") AnnotationAssertion( "EMAPA:16808") @@ -179483,8 +177403,6 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/300") "One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BIRNLEX:1356") "Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356].") -AnnotationAssertion(Annotation( "FMA") "FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies.") AnnotationAssertion( "BIRNLEX:1356") AnnotationAssertion( "BTO:0001442") AnnotationAssertion( "EFO:0001914") @@ -179506,6 +177424,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain ventricle") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -179533,15 +177452,13 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (orbital region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.") AnnotationAssertion( "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye") -AnnotationAssertion(Annotation( "HP:0000284") "in HP covers eyelid, eyebrow.") AnnotationAssertion( "FMA:260119") AnnotationAssertion(Annotation( "FMA:260119") "content of orbital part of eye") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "eye region") @@ -179561,8 +177478,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "HP:0000309") Annotation( "http://www.merriam-webster.com/medical/midface") "The middle of the face including the nose and its associated bony structures[MW].") AnnotationAssertion( "this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.") -AnnotationAssertion( "midfacial") -AnnotationAssertion( "EMAPA:32806") AnnotationAssertion( "FMA:285406") AnnotationAssertion( "MA:0001910") AnnotationAssertion( "uberon") @@ -179587,7 +177502,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "joint space of elbow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal collecting system) @@ -179611,7 +177528,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (alveolar ridge) AnnotationAssertion(Annotation( "HP:0006477") Annotation( "Wikipedia:Alveolar_ridge") "One of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP].") -AnnotationAssertion(Annotation( "BTO") "in BTO, this is part of an embryo") AnnotationAssertion( "BTO:0001383") AnnotationAssertion( "EMAPA:35118") AnnotationAssertion( "FMA:313923") @@ -179632,6 +177548,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alveolar ridge") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:19767574") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -179648,6 +177565,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortex of humerus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical conduit) @@ -179655,7 +177577,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature") AnnotationAssertion( "AEO:0000080") AnnotationAssertion( "EHDAA2:0003080") AnnotationAssertion( "FMA:242873") @@ -179671,12 +177592,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical conduit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectExactCardinality(2 )) # Class: (muscle of auditory ossicle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A muscle of the tympanic cavity that attaches to an auditory ossicle.") -AnnotationAssertion( "attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter") AnnotationAssertion( "UBERON:0004112") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37776") AnnotationAssertion( "FMA:49026") @@ -179698,6 +177621,7 @@ EquivalentClasses( ObjectIntersec SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tympanic cavity) @@ -179720,11 +177644,14 @@ AnnotationAssertion( "tympanic cavity") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel of tympanic cavity) @@ -179745,8 +177672,9 @@ AnnotationAssertion( "UBERON:0004115") AnnotationAssertion(rdfs:label "blood vessel of tympanic cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of tympanic cavity) @@ -179767,15 +177695,13 @@ AnnotationAssertion( "UBERON:0004116") AnnotationAssertion(rdfs:label "nerve of tympanic cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal pouch) AnnotationAssertion(Annotation( "PMID:23020903") Annotation( "ZFA:0001106") Annotation( "http://orcid.org/0000-0002-6601-2165") "An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001106") Annotation( "TAO") Annotation( "ZFIN:curator") "Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001203") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA also includes a distinct pouch endoderm") AnnotationAssertion( "AAO:0011113") AnnotationAssertion( "EFO:0003627") AnnotationAssertion( "EHDAA:1086") @@ -179803,9 +177729,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389]") AnnotationAssertion(rdfs:label "pharyngeal pouch") -SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://tolweb.org/Chordata/2499") ObjectSomeValuesFrom( )) @@ -179824,48 +177750,47 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of iris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endoderm-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops (entirely or partially) from the endoderm.") -AnnotationAssertion( "Grouping term for query purposes") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004119") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endoderm-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesoderm-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops (entirely or partially) from the mesoderm.") -AnnotationAssertion( "Grouping term for query purposes") AnnotationAssertion(Annotation( "FBbt:00025998") "mesodermal derivative") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004120") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesoderm-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectoderm-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops (entirely or partially) from the ectoderm.") -AnnotationAssertion( "Grouping term for query purposes") AnnotationAssertion(Annotation( "FBbt:00025990") "ectodermal deriviative") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004121") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ectoderm-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (genitourinary system) AnnotationAssertion(Annotation( "VHOG:0000286") "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000624") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000624") Annotation( "AAO") "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000286") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633") Annotation( "http://bgee.unil.ch/") "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]") -AnnotationAssertion( "genitourinary") -AnnotationAssertion( "urogenital") AnnotationAssertion( "AAO:0000624") AnnotationAssertion( "BILA:0000122") AnnotationAssertion( "BTO:0003091") @@ -179896,6 +177821,8 @@ AnnotationAssertion( "genitourinary system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocardial layer) @@ -179911,12 +177838,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myocardial layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocardium trabecular layer) AnnotationAssertion(Annotation( "ZFA:0005059") "The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005059") Annotation( "TAO") Annotation( "ZFIN:curator") "The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]") AnnotationAssertion( "EFO:0003706") AnnotationAssertion( "MA:0002866") AnnotationAssertion( "TAO:0005059") @@ -179934,6 +177862,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myocardium trabecular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecular layer of ventricle) @@ -179950,13 +177881,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trabecular layer of ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (optic vesicle) AnnotationAssertion(Annotation( "GO:0003404") Annotation( "Wikipedia:Optic_vesicles") "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000165") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]") AnnotationAssertion( "AAO:0011039") AnnotationAssertion( "EHDAA2:0001320") AnnotationAssertion( "EMAPA:16540") @@ -179981,6 +177911,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "optic vesicle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO-def") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -180019,6 +177950,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cerebellar layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -180029,7 +177962,8 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0004133") AnnotationAssertion(rdfs:label "salivatory nucleus") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal tubule) @@ -180049,16 +177983,13 @@ AnnotationAssertion( "UBERON:0004134") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal tubule") -SubClassOf( ) -SubClassOf(Annotation( "checkme") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "multiple") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) # Class: (distal tubule) AnnotationAssertion(Annotation( "GO:0072017") "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0000482") AnnotationAssertion( "CALOHA:TS-0504") AnnotationAssertion( "EMAPA:28387") @@ -180088,7 +178019,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "GO:0003142") "The first recognizable structure derived from the heart field.") AnnotationAssertion( "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000975") Annotation( "VHOG") Annotation( "PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)") Annotation( "http://bgee.unil.ch/") "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000215") AnnotationAssertion( "EMAPA:16106") AnnotationAssertion( "VHOG:0000975") @@ -180100,14 +178030,12 @@ AnnotationAssertion( "UBERON:0004139") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiogenic plate") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (primary heart field) AnnotationAssertion(Annotation( "GO:0003138") Annotation( "GOC:mtg_heart") Annotation( "GOC:rl") "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.") -AnnotationAssertion(Annotation( "GO") "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]") AnnotationAssertion( "XAO:0004185") AnnotationAssertion(Annotation( "XAO:0004185") "first heart field") AnnotationAssertion(Annotation( "PMID:17276708") Annotation( "XAO:0004185") "primary heart field") @@ -180117,6 +178045,9 @@ AnnotationAssertion(Annotation( "XAO:0004185") "heart field") AnnotationAssertion( "UBERON:0004140") AnnotationAssertion(rdfs:label "primary heart field") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "GO:0003128") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://orcid.org/0000-0003-3308-6245") ObjectSomeValuesFrom( )) @@ -180124,7 +178055,6 @@ SubClassOf(Annotation( "htt # Class: (heart tube) AnnotationAssertion(Annotation( "GO:0003143") Annotation( "GOC:mtg_heart") "An epithelial tube that will give rise to the mature heart.") -AnnotationAssertion(Annotation( "MP:0012700") "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.") AnnotationAssertion( "AAO:0010411") AnnotationAssertion( "EFO:0003526") AnnotationAssertion( "EMAPA:32685") @@ -180142,7 +178072,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heart tube") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA-modified") ObjectSomeValuesFrom( )) # Class: (outflow tract septum) @@ -180153,11 +178084,12 @@ AnnotationAssertion( "UBERON:0004142") AnnotationAssertion(rdfs:label "outflow tract septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract) AnnotationAssertion(Annotation( "GO:0003151") "The outflow tract is the portion of the heart through which blood flows into the arteries.") -AnnotationAssertion( "Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]") AnnotationAssertion( "EHDAA2:0001351") AnnotationAssertion( "EHDAA:464") AnnotationAssertion( "EHDAA:798") @@ -180173,6 +178105,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outflow tract") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -180181,7 +178114,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (His-Purkinje system) AnnotationAssertion(Annotation( "GO:0003164") Annotation( "https://github.com/geneontology/go-ontology/issues/12451") "The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.") -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/His-Purkinje+system") "the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles.") AnnotationAssertion(Annotation( ) "HPS") AnnotationAssertion( "His-Purkinji network") AnnotationAssertion( "VCS") @@ -180190,7 +178122,7 @@ AnnotationAssertion( "UBERON:0004146") AnnotationAssertion(rdfs:label "His-Purkinje system") SubClassOf(Annotation( "cjm") ) -SubClassOf(Annotation( "GO-def") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:12626327") Annotation( "PMID:21234997") Annotation( "github:michaelerice") ObjectSomeValuesFrom( )) @@ -180220,7 +178152,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac chamber) @@ -180234,13 +178169,12 @@ AnnotationAssertion( "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus") AnnotationAssertion(rdfs:label "cardiac chamber") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proepicardium) AnnotationAssertion(Annotation( "GO:0003342") Annotation( "http://en.wiktionary.org/wiki/proepicardium") "An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium.") -AnnotationAssertion( "propepicardial") -AnnotationAssertion( "Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]") AnnotationAssertion( "EMAPA:36025") AnnotationAssertion( "ZFA:0005808") AnnotationAssertion(Annotation( "ZFA:0005808") "proepicardial cluster") @@ -180249,16 +178183,12 @@ AnnotationAssertion( "UBERON:0004160") AnnotationAssertion(rdfs:label "proepicardium") SubClassOf( ) -SubClassOf(Annotation( "todo check other taxa") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (septum transversum) AnnotationAssertion(Annotation( "VHOG:0000019") Annotation( "Wikipedia:Septum_transversum") "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000019") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/transverse+septum") "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000019") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206") Annotation( "http://bgee.unil.ch/") "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]") -AnnotationAssertion( "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum") AnnotationAssertion( "EHDAA2:0001829") AnnotationAssertion( "EHDAA:736") AnnotationAssertion( "EMAPA:16318") @@ -180280,8 +178210,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (branchiomeric muscle) AnnotationAssertion(Annotation( "ISBN:0073040584") "A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves.") -AnnotationAssertion(Annotation( "GO:0014707") "The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707].") -AnnotationAssertion( "It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]") AnnotationAssertion( "Wikipedia:Branchiomeric_musculature") AnnotationAssertion( "XAO:0004325") AnnotationAssertion(Annotation( "XAO:0004325") "branchial head muscle") @@ -180290,6 +178218,7 @@ AnnotationAssertion( "UBERON:0004164") AnnotationAssertion(rdfs:label "branchiomeric muscle") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:21610022") ObjectSomeValuesFrom( )) @@ -180328,14 +178257,11 @@ AnnotationAssertion( "TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547") AnnotationAssertion(rdfs:label "external genitalia") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hemopoietic organ) AnnotationAssertion(Annotation( "GOC:Obol") "Organ that is part of the hematopoietic system.") AnnotationAssertion( "consider splitting out lymph organ, compare with lymph node") -AnnotationAssertion(Annotation( "http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs") "the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].") -AnnotationAssertion(Annotation( "FMA") "the FMA class 'lymphoid organ' is a general anatomical term") AnnotationAssertion( "BTO:0004605") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37665") AnnotationAssertion( "FMA:7143") @@ -180359,6 +178285,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hemopoietic organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (aorta smooth muscle tissue) @@ -180379,13 +178308,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate glandular acinus) AnnotationAssertion(Annotation( "GO:0060525") Annotation( "PMID:18977204") "A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells.") AnnotationAssertion( "the muscle layer is implicitly treated as outside the acinus") AnnotationAssertion( ) -AnnotationAssertion( "Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]") AnnotationAssertion( "FMA:66808") AnnotationAssertion(Annotation( "FMA:66808") "prostatic acinus") AnnotationAssertion(Annotation( "FMA:66808") "prostatic follicle") @@ -180393,9 +178324,10 @@ AnnotationAssertion( "UBERON:0004179") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prostate glandular acinus") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:18977204") ObjectSomeValuesFrom( )) # Class: (mammary gland fat) @@ -180429,11 +178361,12 @@ AnnotationAssertion( "UBERON:0004180") AnnotationAssertion(rdfs:label "mammary gland fat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mammary gland cord) AnnotationAssertion(Annotation( "MP:0013725") "The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis.") -AnnotationAssertion( "in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree") AnnotationAssertion( "lactiferous gland cord") AnnotationAssertion( "mammary cord") AnnotationAssertion( "uberon") @@ -180441,6 +178374,10 @@ AnnotationAssertion( "UBERON:0004182") AnnotationAssertion(rdfs:label "mammary gland cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental labyrinth blood vessel) @@ -180456,6 +178393,7 @@ AnnotationAssertion( "UBERON:0004183") AnnotationAssertion(rdfs:label "placental labyrinth blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate gland stroma) @@ -180479,6 +178417,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prostate gland stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endodermal part of digestive tract) @@ -180490,11 +178432,12 @@ AnnotationAssertion( "UBERON:0004185") AnnotationAssertion(rdfs:label "endodermal part of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (olfactory bulb mitral cell layer) AnnotationAssertion(Annotation( "GO:0061034") "The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer.") -AnnotationAssertion(Annotation( "NIF") "NIF divides this into main and accessory") AnnotationAssertion( "BAMS:Mi") AnnotationAssertion( "BTO:0001108") AnnotationAssertion( "DHBA:11329") @@ -180531,6 +178474,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular endothelium) @@ -180543,6 +178489,7 @@ AnnotationAssertion( "glomerular endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal glomerulus vasculature) @@ -180559,6 +178506,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal glomerulus vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (loop of Henle ascending limb thin segment) @@ -180626,7 +178575,6 @@ SubClassOf(Annotation( "ZFA AnnotationAssertion(Annotation( "GO:0072050") "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.") AnnotationAssertion( "TODO") AnnotationAssertion( "EMAPA:27756") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "VO:0010896") AnnotationAssertion( "ZFA:0005589") AnnotationAssertion(Annotation( ) "SSB") AnnotationAssertion(Annotation( "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html") "stage II nephron") @@ -180642,8 +178590,6 @@ SubClassOf(Annotation( "GO" AnnotationAssertion(Annotation( "GO:0072056") Annotation( "http://anatomy.uams.edu/anatomyhtml/kidney.html") "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)") -AnnotationAssertion( ) AnnotationAssertion( "UBERON:0002449") AnnotationAssertion( "UBERON:0005098") AnnotationAssertion(Annotation( "GO:0072056") "pyramid") @@ -180739,6 +178685,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortical collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer medullary collecting duct) @@ -180754,6 +178703,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outer medullary collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner medullary collecting duct) @@ -180771,6 +178722,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inner medullary collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nephrogenic mesenchyme) @@ -180782,6 +178735,8 @@ AnnotationAssertion( "The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]") AnnotationAssertion(rdfs:label "nephrogenic mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal vesicle) @@ -180807,12 +178762,13 @@ AnnotationAssertion( "UBERON:0004211") AnnotationAssertion(rdfs:label "nephron epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular capillary) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0011320") "The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005284") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-000824-1") Annotation( "ZFIN:curator") "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]") AnnotationAssertion( "EMAPA:28245") AnnotationAssertion( "FMA:274259") AnnotationAssertion( "MA:0002587") @@ -180836,6 +178792,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -180853,6 +178810,8 @@ AnnotationAssertion( "UBERON:0004214") AnnotationAssertion(rdfs:label "upper leg nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (back nerve) @@ -180864,6 +178823,8 @@ AnnotationAssertion( "UBERON:0004215") AnnotationAssertion(rdfs:label "back nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower arm nerve) @@ -180874,6 +178835,8 @@ AnnotationAssertion( "UBERON:0004216") AnnotationAssertion(rdfs:label "lower arm nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm nerve) @@ -180884,6 +178847,8 @@ AnnotationAssertion( "UBERON:0004217") AnnotationAssertion(rdfs:label "upper arm nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower leg nerve) @@ -180894,6 +178859,8 @@ AnnotationAssertion( "UBERON:0004218") AnnotationAssertion(rdfs:label "lower leg nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethra smooth muscle layer) @@ -180913,11 +178880,12 @@ AnnotationAssertion(Annotation( "UBERON:0004219") AnnotationAssertion(rdfs:label "urethra smooth muscle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (large intestine smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].") -AnnotationAssertion(Annotation( "MA") "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa") AnnotationAssertion( "EMAPA:35469") AnnotationAssertion( "MA:0001547") AnnotationAssertion(Annotation( "OBOL:automatic") "involuntary muscle of large intestine") @@ -180931,13 +178899,13 @@ AnnotationAssertion( "UBERON:0004220") AnnotationAssertion(rdfs:label "large intestine smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "consider merging") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestine smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition].") -AnnotationAssertion(Annotation( "MA") "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa") AnnotationAssertion( "BTO:0000643") AnnotationAssertion( "EMAPA:35441") AnnotationAssertion( "EMAPA:35443") @@ -180966,8 +178934,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intestine smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "consider merging") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach smooth muscle) @@ -180998,13 +178967,13 @@ AnnotationAssertion(Annotation( "UBERON:0004222") AnnotationAssertion(rdfs:label "stomach smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vagina smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition].") AnnotationAssertion( "BTO:0004999") -AnnotationAssertion( "EMAPA:30997") AnnotationAssertion( "MA:0001733") AnnotationAssertion(Annotation( "OBOL:automatic") "involuntary muscle of vagina") AnnotationAssertion(Annotation( "OBOL:automatic") "non-striated muscle of vagina") @@ -181019,6 +178988,9 @@ AnnotationAssertion(Annotation( "UBERON:0004223") AnnotationAssertion(rdfs:label "vagina smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscular coat of vas deferens) @@ -181040,7 +179012,10 @@ AnnotationAssertion( "UBERON:0004224") AnnotationAssertion(rdfs:label "muscular coat of vas deferens") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system smooth muscle) @@ -181056,6 +179031,8 @@ AnnotationAssertion(Annotation( "UBERON:0004225") AnnotationAssertion(rdfs:label "respiratory system smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrointestinal system smooth muscle) @@ -181067,6 +179044,8 @@ AnnotationAssertion( "UBERON:0004226") AnnotationAssertion(rdfs:label "gastrointestinal system smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney pelvis smooth muscle) @@ -181083,6 +179062,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney pelvis smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder smooth muscle) @@ -181113,6 +179094,8 @@ AnnotationAssertion( "UBERON:0004228") AnnotationAssertion(rdfs:label "urinary bladder smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder trigone smooth muscle) @@ -181173,6 +179156,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urinary bladder trigone smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder neck smooth muscle) @@ -181228,6 +179213,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anal region smooth muscle) @@ -181261,6 +179248,8 @@ AnnotationAssertion( "UBERON:0004231") AnnotationAssertion(rdfs:label "anal region smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic vessel smooth muscle) @@ -181290,6 +179279,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphatic vessel smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower respiratory tract smooth muscle) @@ -181308,6 +179299,9 @@ AnnotationAssertion( "UBERON:0004233") AnnotationAssertion(rdfs:label "lower respiratory tract smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iris smooth muscle) @@ -181342,6 +179336,9 @@ AnnotationAssertion( "UBERON:0004235") AnnotationAssertion(rdfs:label "mammary gland smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole smooth muscle) @@ -181353,12 +179350,14 @@ AnnotationAssertion( "UBERON:0004236") AnnotationAssertion(rdfs:label "arteriole smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel smooth muscle) AnnotationAssertion(Annotation( "Wikipedia:Vascular_smooth_muscle") "Smooth muscle found within, and composing the majority of the wall of blood vessels.") AnnotationAssertion( ) -AnnotationAssertion( "Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.") AnnotationAssertion( "UBERON:0010508") AnnotationAssertion( "BTO:0001431") AnnotationAssertion( "CALOHA:TS-1107") @@ -181385,6 +179384,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spleen smooth muscle) @@ -181402,11 +179403,12 @@ AnnotationAssertion( "UBERON:0004238") AnnotationAssertion(rdfs:label "spleen smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (small intestine smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition].") -AnnotationAssertion(Annotation( "MA") "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa") AnnotationAssertion( "EMAPA:35783") AnnotationAssertion( "MA:0001559") AnnotationAssertion(Annotation( "OBOL:automatic") "involuntary muscle of small bowel") @@ -181429,8 +179431,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "small intestine smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "consider merging") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gallbladder smooth muscle) @@ -181459,6 +179462,9 @@ AnnotationAssertion(Annotation( "UBERON:0004240") AnnotationAssertion(rdfs:label "gallbladder smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchus smooth muscle) @@ -181499,6 +179505,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bronchus smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate gland smooth muscle) @@ -181531,12 +179539,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prostate gland smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (oviduct smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition].") -AnnotationAssertion( "EMAPA:29046") AnnotationAssertion( "MA:0001721") AnnotationAssertion(Annotation( "OBOL:automatic") "fallopian tube involuntary muscle") AnnotationAssertion(Annotation( "OBOL:automatic") "fallopian tube non-striated muscle") @@ -181550,6 +179559,9 @@ AnnotationAssertion( "UBERON:0004245") AnnotationAssertion(rdfs:label "oviduct smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract smooth muscle) @@ -181567,12 +179579,12 @@ AnnotationAssertion( "UBERON:0004246") AnnotationAssertion(rdfs:label "outflow tract smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of dorsum) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A bone that is part of the dorsal region of an animal.") -AnnotationAssertion( "this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37248") AnnotationAssertion( "MA:0000494") AnnotationAssertion( "uberon") @@ -181583,11 +179595,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of dorsum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (pedal digit bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37309") AnnotationAssertion( "MA:0000646") AnnotationAssertion(Annotation( "OBOL:automatic") "bone of digit of foot") @@ -181606,12 +179619,13 @@ AnnotationAssertion( "UBERON:0004248") AnnotationAssertion(rdfs:label "pedal digit bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37305") AnnotationAssertion( "MA:0000622") AnnotationAssertion( "digital bone of hand") @@ -181624,12 +179638,13 @@ AnnotationAssertion( "UBERON:0004249") AnnotationAssertion(rdfs:label "manual digit bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm bone) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376") "A bone that is part of a forelimb stylopod [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:35892") AnnotationAssertion( "MA:0000604") AnnotationAssertion(Annotation( "https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376") "humerus") @@ -181638,11 +179653,12 @@ AnnotationAssertion( "May be merged into humerus. See: https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376") AnnotationAssertion(rdfs:label "upper arm bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb zeugopod bone) AnnotationAssertion(Annotation( "OBOL:automatic") "A bone that is part of a lower leg [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:35519") AnnotationAssertion( "MA:0000676") AnnotationAssertion(Annotation( "OBOL:automatic") "bone of hind limb middle limb segment") @@ -181724,6 +179740,8 @@ AnnotationAssertion( "UBERON:0004251") AnnotationAssertion(rdfs:label "hindlimb zeugopod bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb stylopod muscle) @@ -181742,13 +179760,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb stylopod muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (skin muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a skin of body [Automatically generated definition].") AnnotationAssertion( "review as part of general integumentary system review - part of skin, or more generally, integumental system") -AnnotationAssertion(Annotation( "MA") "in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only") AnnotationAssertion( "UBERON:0015797") AnnotationAssertion( "EMAPA:18187") AnnotationAssertion( "EMAPA:35776") @@ -181762,6 +179780,8 @@ AnnotationAssertion( "UBERON:0004253") AnnotationAssertion(rdfs:label "skin muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb zeugopod muscle) @@ -181779,13 +179799,13 @@ AnnotationAssertion( "UBERON:0004254") AnnotationAssertion(rdfs:label "forelimb zeugopod muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (forelimb stylopod muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition].") AnnotationAssertion( "the FMA class 'muscle of arm' belongs here, do not move") -AnnotationAssertion( "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'") AnnotationAssertion( "EMAPA:19107") AnnotationAssertion( "FMA:37370") AnnotationAssertion( "MA:0000606") @@ -181800,6 +179820,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb stylopod muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (hindlimb zeugopod muscle) @@ -181807,7 +179828,6 @@ SubClassOf(Annotation( "pro AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition].") AnnotationAssertion( "the FMA class 'muscle of leg' belongs here, do not move[cjm]") AnnotationAssertion( ) -AnnotationAssertion( "See notes on UBERON:0000978 for possible terminological confusion over term 'leg'") AnnotationAssertion( "EMAPA:19318") AnnotationAssertion( "FMA:22471") AnnotationAssertion( "MA:0000678") @@ -181821,6 +179841,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hindlimb zeugopod muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (upper leg blood vessel) @@ -181839,6 +179860,8 @@ AnnotationAssertion( "UBERON:0004257") AnnotationAssertion(rdfs:label "upper leg blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (back blood vessel) @@ -181850,6 +179873,8 @@ AnnotationAssertion( "UBERON:0004258") AnnotationAssertion(rdfs:label "back blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower arm blood vessel) @@ -181861,6 +179886,8 @@ AnnotationAssertion( "UBERON:0004259") AnnotationAssertion(rdfs:label "lower arm blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm blood vessel) @@ -181872,6 +179899,8 @@ AnnotationAssertion( "UBERON:0004260") AnnotationAssertion(rdfs:label "upper arm blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower leg blood vessel) @@ -181883,6 +179912,8 @@ AnnotationAssertion( "UBERON:0004261") AnnotationAssertion(rdfs:label "lower leg blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper leg skin) @@ -181900,6 +179931,8 @@ AnnotationAssertion(Annotation( "UBERON:0004262") AnnotationAssertion(rdfs:label "upper leg skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm skin) @@ -181915,6 +179948,8 @@ AnnotationAssertion( "UBERON:0004263") AnnotationAssertion(rdfs:label "upper arm skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower leg skin) @@ -181928,11 +179963,12 @@ AnnotationAssertion( "UBERON:0004264") AnnotationAssertion(rdfs:label "lower leg skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract myocardium) AnnotationAssertion(Annotation( "OBOL:automatic") "A myocardium that is part of a outflow tract [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000603") Annotation( "VHOG") Annotation( "PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)") Annotation( "http://bgee.unil.ch/") "(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]") AnnotationAssertion( "EHDAA2:0001358") AnnotationAssertion( "EMAPA:35623") AnnotationAssertion( "MA:0000489") @@ -181950,6 +179986,8 @@ AnnotationAssertion( "UBERON:0004265") AnnotationAssertion(rdfs:label "outflow tract myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper leg connective tissue) @@ -181960,6 +179998,8 @@ AnnotationAssertion( "UBERON:0004266") AnnotationAssertion(rdfs:label "upper leg connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (back connective tissue) @@ -181972,6 +180012,8 @@ AnnotationAssertion(Annotation( "UBERON:0004267") AnnotationAssertion(rdfs:label "back connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower arm connective tissue) @@ -181982,6 +180024,8 @@ AnnotationAssertion( "UBERON:0004268") AnnotationAssertion(rdfs:label "lower arm connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm connective tissue) @@ -181993,6 +180037,8 @@ AnnotationAssertion( "UBERON:0004269") AnnotationAssertion(rdfs:label "upper arm connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower leg connective tissue) @@ -182004,6 +180050,8 @@ AnnotationAssertion( "UBERON:0004270") AnnotationAssertion(rdfs:label "lower leg connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract pericardium) @@ -182016,6 +180064,9 @@ AnnotationAssertion( "UBERON:0004271") AnnotationAssertion(rdfs:label "outflow tract pericardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilaginous joint suture) @@ -182046,6 +180097,8 @@ AnnotationAssertion( "UBERON:0004273") AnnotationAssertion(rdfs:label "cartilaginous joint suture") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral ventricle choroid plexus epithelium) @@ -182074,6 +180127,8 @@ AnnotationAssertion( "UBERON:0004274") AnnotationAssertion(rdfs:label "lateral ventricle choroid plexus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fourth ventricle choroid plexus epithelium) @@ -182101,6 +180156,7 @@ AnnotationAssertion( "UBERON:0004276") AnnotationAssertion(rdfs:label "fourth ventricle choroid plexus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye muscle) @@ -182114,16 +180170,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eye muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton) AnnotationAssertion(Annotation( "VSAO:0000026") "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.") -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000026") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]") -AnnotationAssertion( "skeletal") AnnotationAssertion( "AEO:0000168") AnnotationAssertion( "EHDAA2:0001843") AnnotationAssertion( "EHDAA:5047") @@ -182157,11 +180212,6 @@ DisjointClasses( (dermomyotome) AnnotationAssertion(Annotation( "AEO:0000214") "The bilaminar epithelium formed from the myotome and dermatome.") -AnnotationAssertion(Annotation( "http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768") "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001513") Annotation( "TAO") Annotation( "ZFIN:curator") "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010572") Annotation( "AAO") Annotation( "AAO:EJS") "Portion of somites that gives rise to dermis and muscles.[AAO]") -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/dermomyotome") "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000676") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)") Annotation( "http://bgee.unil.ch/") "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]") AnnotationAssertion( "AAO:0010572") AnnotationAssertion( "AEO:0000214") AnnotationAssertion( "EHDAA2:0003259") @@ -182185,7 +180235,6 @@ SubClassOf(Annotation( "EHD # Class: (heart rudiment) AnnotationAssertion(Annotation( "GO:0003313") "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000115") Annotation( "TAO") Annotation( "ZFIN:curator") "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]") AnnotationAssertion( "TAO:0000115") AnnotationAssertion( "ZFA:0000115") AnnotationAssertion(Annotation( "GO:0003313") "heart cone") @@ -182193,14 +180242,12 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0004291") AnnotationAssertion(rdfs:label "heart rudiment") -SubClassOf( ) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac skeleton) AnnotationAssertion(Annotation( "GO:0003204") Annotation( "Wikipedia:Cardiac_skeleton") "Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.") -AnnotationAssertion( "It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]") AnnotationAssertion( "EMAPA:36645") AnnotationAssertion( "FMA:9496") AnnotationAssertion( "Wikipedia:Cardiac_skeleton") @@ -182217,7 +180264,8 @@ AnnotationAssertion(Annotation( "UBERON:0004292") AnnotationAssertion(rdfs:label "cardiac skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -182235,6 +180283,8 @@ AnnotationAssertion( "UBERON:0004293") AnnotationAssertion(rdfs:label "parasympathetic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK10065") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK10065") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -182254,6 +180304,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular capillary endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sympathetic nerve trunk) @@ -182270,6 +180323,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sympathetic nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system lymphatic vessel smooth muscle) @@ -182281,6 +180336,8 @@ AnnotationAssertion( "UBERON:0004296") AnnotationAssertion(rdfs:label "respiratory system lymphatic vessel smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system blood vessel smooth muscle) @@ -182293,11 +180350,13 @@ AnnotationAssertion( "UBERON:0004297") AnnotationAssertion(rdfs:label "respiratory system blood vessel smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal phalanx) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/120") "Distal-most phalanx within a digit.") -AnnotationAssertion( "In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.") AnnotationAssertion( "AAO:0010676") AnnotationAssertion( "EMAPA:35287") AnnotationAssertion( "MA:0002914") @@ -182313,14 +180372,14 @@ AnnotationAssertion( "distal phalanx") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (middle phalanx) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A phalanx located between proximal and distal phalanges.") AnnotationAssertion( "consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit") -AnnotationAssertion(Annotation( "WP") "Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin") -AnnotationAssertion( "in some groups such as whales, there are multiple intermediate phalanges") AnnotationAssertion( "AAO:0010677") AnnotationAssertion( "EMAPA:35572") AnnotationAssertion( "MA:0002915") @@ -182335,14 +180394,13 @@ AnnotationAssertion( "UBERON:0004301") AnnotationAssertion(rdfs:label "middle phalanx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal phalanx) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Proximal-most phalanx within a digit.") -AnnotationAssertion(Annotation( "WP") "Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)") -AnnotationAssertion( "1"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010680") AnnotationAssertion( "EMAPA:35716") AnnotationAssertion( "MA:0002916") @@ -182355,15 +180413,12 @@ AnnotationAssertion( "UBERON:0004302") AnnotationAssertion(rdfs:label "proximal phalanx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (allantois) AnnotationAssertion(Annotation( "VHOG:0000738") Annotation( "Wikipedia:Allantois") "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000738") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/allantois") "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000738") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187") Annotation( "http://bgee.unil.ch/") "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]") -AnnotationAssertion( "allantoic") -AnnotationAssertion( "a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]") -AnnotationAssertion(Annotation( "EHDAA2") "part_of embryo in EHDAA2 - note differences in humans") AnnotationAssertion( "BTO:0000474") AnnotationAssertion( "EHDAA2:0001504") AnnotationAssertion( "EMAPA:16107") @@ -182385,20 +180440,16 @@ SubClassOf( "EHDAA2-modified") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Hymans") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Hymans") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "hindgut diverticulum endoderm") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) # Class: (primitive streak) AnnotationAssertion(Annotation( "MP:0002231") Annotation( "Wikipedia:Primitive_streak") "The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001202") Annotation( "VHOG") Annotation( "PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139") Annotation( "http://bgee.unil.ch/") "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "VHOG") "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826") AnnotationAssertion( "EHDAA2:0001525") AnnotationAssertion( "EHDAA:185") AnnotationAssertion( "EMAPA:16072") AnnotationAssertion( "FMA:293110") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054240") AnnotationAssertion( "NCIT:C28402") AnnotationAssertion( "SCTID:361438007") AnnotationAssertion(Annotation( "ncithesaurus:Primitive_Streak") "UMLS:C0033153") @@ -182412,7 +180463,7 @@ AnnotationAssertion( "primitive streak") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png"^^xsd:anyURI) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -182420,10 +180471,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0005028") "Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition.") AnnotationAssertion( "distinction between trophectoderm and trophoblast unclear/inconsistent in many sources") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000979") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000979") Annotation( "VHOG") Annotation( "ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106") Annotation( "http://bgee.unil.ch/") "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]") -AnnotationAssertion( "trophectodermal") -AnnotationAssertion(Annotation( "BTO") "BTO has this has part of the trophoblast") AnnotationAssertion( "BTO:0001840") AnnotationAssertion( "EHDAA2:0002091") AnnotationAssertion( "EHDAA:56") @@ -182435,6 +180482,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trophectoderm") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -182442,7 +180490,6 @@ SubClassOf(Annotation( "EHD # Class: (limb bud) AnnotationAssertion(Annotation( "ISBN:9780878932504") Annotation( "MP:0005650") Annotation( "Wikipedia:Limb_bud") Annotation( "https://orcid.org/0000-0002-6601-2165") "An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010375") Annotation( "AAO") Annotation( "AAO:EJS") "Early outgrowth of presumptive limb.[AAO]") AnnotationAssertion( "AAO:0010375") AnnotationAssertion( "BTO:0001640") AnnotationAssertion( "EMAPA:35944") @@ -182478,18 +180525,12 @@ AnnotationAssertion( "UBERON:0004348") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "optic eminence") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (apical ectodermal ridge) AnnotationAssertion(Annotation( "MP:0001676") Annotation( "Wikipedia:Apical_ectodermal_ridge") "Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].") -AnnotationAssertion( "note that media, dorsal fins etc have AERs.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010760") Annotation( "AAO") Annotation( "AAO:EJS") "Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002146") Annotation( "TAO") Annotation( "ZFIN:curator") "Proliferative region that is part of the developing fin fold or fin.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002146") Annotation( "TAO") "relationship loss: subclass proliferative region (TAO:0000098)[TAO]") -AnnotationAssertion(Annotation( "PMID:20574421") "The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold") -AnnotationAssertion( "maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop") AnnotationAssertion( "AAO:0010760") AnnotationAssertion( "EMAPA:32744") AnnotationAssertion( "NCIT:C34109") @@ -182517,7 +180558,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (paired limb/fin bud) AnnotationAssertion(Annotation( "ISBN:9780878932504") Annotation( "MP:0005650") Annotation( "https://orcid.org/0000-0002-6601-2165") "An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001258") Annotation( "VHOG") Annotation( "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)") Annotation( "http://bgee.unil.ch/") "The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]") AnnotationAssertion( "VHOG:0001258") AnnotationAssertion(Annotation( "VHOG:0001258") "limb - fin bud") AnnotationAssertion( "paired appendage bud") @@ -182528,8 +180568,7 @@ AnnotationAssertion( "Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]") AnnotationAssertion(rdfs:label "paired limb/fin bud") SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -182537,10 +180576,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pharyngeal arch 1) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010364") Annotation( "AAO") Annotation( "XAO:EJS") "The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]") -AnnotationAssertion(Annotation( "MP:0006337,MGI:smb") "the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000296") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion( "1"^^xsd:nonNegativeInteger) AnnotationAssertion( "AAO:0010364") AnnotationAssertion( "CALOHA:TS-2089") AnnotationAssertion( "EHDAA2:0000006") @@ -182579,11 +180614,6 @@ SubClassOf( "MP:0002672") "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP].") AnnotationAssertion( "add specific artery derivatives") -AnnotationAssertion( "Do not confuse with arch of aorta.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000122") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/aortic+arches") "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000122") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]") -AnnotationAssertion( "Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods") -AnnotationAssertion( "The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches") AnnotationAssertion( "UBERON:0004342") AnnotationAssertion( "AAO:0010414") AnnotationAssertion( "EFO:0003695") @@ -182619,19 +180649,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png"^^xsd:anyURI) -SubClassOf(Annotation( "ZFA") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "abduced from EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectoplacental cone) AnnotationAssertion(Annotation( "MP:0001717") Annotation( "PMID:19829370") "Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta.") -AnnotationAssertion(Annotation( "PMID:19829370") "derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast.") AnnotationAssertion( "BTO:0001715") AnnotationAssertion( "EMAPA:16059") AnnotationAssertion( "epamniotic cone") @@ -182640,9 +180669,8 @@ AnnotationAssertion( "UBERON:0004364") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ectoplacental cone") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitelline blood vessel) @@ -182653,12 +180681,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vitelline blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Descemet's membrane) AnnotationAssertion(Annotation( "MP:0004285") Annotation( "https://github.com/obophenotype/uberon/issues/15") "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].") -AnnotationAssertion(Annotation( "2016-05-01") Annotation( "TAO:0002157") Annotation( "ZFIN") Annotation( "ZFIN:ZDB-PUB-061010-3") Annotation( "https://orcid.org/0000-0001-9114-8737") "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]") AnnotationAssertion( "EMAPA:18804") AnnotationAssertion( "FMA:58309") AnnotationAssertion( "GAID:894") @@ -182685,15 +180714,18 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "Descemet's membrane") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/15"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Cline et al") ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (anterior limiting lamina of cornea) AnnotationAssertion(Annotation( "ncithesaurus:Bowman_s_Membrane") "A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002155") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-061010-3") "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]") -AnnotationAssertion( "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals") AnnotationAssertion( "FMA:58273") AnnotationAssertion( "MA:0001240") AnnotationAssertion( "NCIT:C32226") @@ -182718,6 +180750,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anterior limiting lamina of cornea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitelline vasculature) @@ -182731,6 +180767,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vitelline vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of free limb or fin) @@ -182743,6 +180781,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of free limb or fin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal metaphysis) @@ -182754,6 +180794,8 @@ AnnotationAssertion( "UBERON:0004378") AnnotationAssertion(rdfs:label "proximal metaphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal epiphysis) @@ -182765,13 +180807,13 @@ AnnotationAssertion( "UBERON:0004380") AnnotationAssertion(rdfs:label "proximal epiphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of limb) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in an individual limb.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000300") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal subdivision that is part of the limb.[VSAO]") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 considers hip and shoulder joints part of limb skeleton.") AnnotationAssertion( "EHDAA2:0002221") AnnotationAssertion( "EMAPA:32702") AnnotationAssertion( "VSAO:0000300") @@ -182782,7 +180824,9 @@ AnnotationAssertion( "UBERON:0004381") AnnotationAssertion(rdfs:label "skeleton of limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of humerus) @@ -182795,6 +180839,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of humerus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of tibia) @@ -182809,6 +180856,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of tibia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of femur) @@ -182823,6 +180873,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of femur") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of phalanx of manus) @@ -182836,6 +180889,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of fibula) @@ -182847,6 +180902,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of fibula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of metatarsal bone) @@ -182861,6 +180919,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of metatarsal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of metacarpal bone) @@ -182875,6 +180936,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of metacarpal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone tissue of epiphysis) @@ -182884,6 +180948,8 @@ AnnotationAssertion( "UBERON:0004400") AnnotationAssertion(rdfs:label "bone tissue of epiphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone tissue of proximal epiphysis) @@ -182893,6 +180959,8 @@ AnnotationAssertion( "UBERON:0004402") AnnotationAssertion(rdfs:label "bone tissue of proximal epiphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (periosteum of epiphysis) @@ -182903,6 +180971,8 @@ AnnotationAssertion( "UBERON:0004403") AnnotationAssertion(rdfs:label "periosteum of epiphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal epiphysis of humerus) @@ -182923,6 +180993,8 @@ AnnotationAssertion( "proximal epiphysis of humerus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal epiphysis of femur) @@ -182936,6 +181008,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal epiphysis of femur") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal epiphysis of phalanx of manus) @@ -182951,6 +181025,8 @@ AnnotationAssertion(Annotation( "UBERON:0004414") AnnotationAssertion(rdfs:label "proximal epiphysis of phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal epiphysis of metatarsal bone) @@ -182965,6 +181041,8 @@ AnnotationAssertion( "UBERON:0004415") AnnotationAssertion(rdfs:label "proximal epiphysis of metatarsal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal epiphysis of metacarpal bone) @@ -182980,6 +181058,8 @@ AnnotationAssertion( "UBERON:0004416") AnnotationAssertion(rdfs:label "proximal epiphysis of metacarpal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (epiphysis of phalanx) @@ -182990,6 +181070,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of phalanx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal epiphysis of phalanx) @@ -182998,13 +181081,12 @@ AnnotationAssertion( "UBERON:0004447") AnnotationAssertion(rdfs:label "proximal epiphysis of phalanx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cerebral artery) AnnotationAssertion(Annotation( "Wikipedia:Cerebral_artery") "One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010493") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010493") Annotation( "AAO") "relationship loss: part_of internal carotid (AAO:0010219)[AAO]") -AnnotationAssertion(Annotation( "AAO") "in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required") AnnotationAssertion( "AAO:0010493") AnnotationAssertion( "BTO:0005205") AnnotationAssertion( "CALOHA:TS-0126") @@ -183024,13 +181106,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cerebral artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk or cervical vertebra) AnnotationAssertion(Annotation( "UBERONREF:0000006") "A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra.") -AnnotationAssertion( "In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)") -AnnotationAssertion(Annotation( "XAO") "it's not clear if the XAO class belongs here or below") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37722") AnnotationAssertion( "MA:0002869") AnnotationAssertion( "XAO:0003077") @@ -183041,6 +181123,8 @@ AnnotationAssertion( "trunk or cervical vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carpal region) @@ -183078,7 +181162,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png"^^xsd:anyURI) AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -183087,8 +181173,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "OBOL:automatic") "A metapodium region that is part of a manus.") AnnotationAssertion( "Note that along with FMA we treat this as a limb segment rather than a purely skeletal element") -AnnotationAssertion( "metacarpal") -AnnotationAssertion( "Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton") AnnotationAssertion( "CALOHA:TS-2218") AnnotationAssertion( "EMAPA:32654") AnnotationAssertion( "FMA:24925") @@ -183108,14 +181192,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsal region) AnnotationAssertion(Annotation( "Wikipedia:Ankle") Annotation( "https://orcid.org/0000-0002-6601-2165") "Mesopodial segment of the pes, including the tarsal skeleton and associated tissues.") -AnnotationAssertion( "this term refers to the limb segment. See also: tarsal bones and tarsal skeleton") -AnnotationAssertion(Annotation( "MA") "MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin).") AnnotationAssertion( "UBERON:0002388") AnnotationAssertion( "CALOHA:TS-2219") AnnotationAssertion( "EFO:0001409") @@ -183142,7 +181225,9 @@ AnnotationAssertion( "tarsal region") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -183162,11 +181247,11 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire sense organ system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Sum of all sensory systems in an organism.") -AnnotationAssertion( "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs") AnnotationAssertion( "FMA:78499") AnnotationAssertion(Annotation( "FMA:78499") "sense organ system") AnnotationAssertion( "uberon") @@ -183196,13 +181281,15 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/4"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/1405"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of body wall) AnnotationAssertion(Annotation( "OBOL:automatic") "Any collection of muscles that is part of a body wall [Automatically generated definition].") -AnnotationAssertion( "define generically to encompass both vertebrates and invertebrates") AnnotationAssertion( "BSA:0000058") AnnotationAssertion( "BTO:0001863") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37853") @@ -183214,6 +181301,8 @@ AnnotationAssertion( "UBERON:0004462") AnnotationAssertion(rdfs:label "musculature of body wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of hindlimb stylopod) @@ -183228,11 +181317,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of hindlimb stylopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of thorax) AnnotationAssertion(Annotation( "OBOL:automatic") "Any collection of muscles that is part of a thorax [Automatically generated definition].") -AnnotationAssertion(Annotation( "BTO") "BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm") AnnotationAssertion( "BTO:0000508") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37260") AnnotationAssertion( "FMA:71293") @@ -183246,6 +181336,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of thorax") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of neck) @@ -183266,11 +181358,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of neck") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of leg) AnnotationAssertion(Annotation( "OBOL:automatic") "Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition].") -AnnotationAssertion( "see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)") AnnotationAssertion( "UBERON:0005632") AnnotationAssertion( "EHDAA2:0000973") AnnotationAssertion(Annotation( "EHDAA2:0000973") "leg muscle system") @@ -183278,6 +181371,8 @@ AnnotationAssertion( "UBERON:0004466") AnnotationAssertion(rdfs:label "musculature of leg") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pharynx) @@ -183303,6 +181398,8 @@ AnnotationAssertion( "UBERON:0004468") AnnotationAssertion(rdfs:label "set of muscles of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of back) @@ -183316,11 +181413,12 @@ AnnotationAssertion( "UBERON:0004469") AnnotationAssertion(rdfs:label "musculature of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pelvic girdle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any collection of muscles that is part of a pelvic girdle [Automatically generated definition].") -AnnotationAssertion(Annotation( "FMA") "we merge two FMA classes here") AnnotationAssertion( "UBERON:0004485") AnnotationAssertion( "UBERON:0005633") AnnotationAssertion( "AAO:0000427") @@ -183341,6 +181439,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of pelvic girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pectoral girdle) @@ -183357,6 +181458,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of pectoral girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of face) @@ -183374,6 +181477,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of face") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of arm) @@ -183388,6 +181493,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of arm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of hip) @@ -183401,7 +181508,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of hip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of shoulder) @@ -183414,7 +181523,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of shoulder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of larynx) @@ -183433,6 +181544,9 @@ AnnotationAssertion( "UBERON:0004478") AnnotationAssertion(rdfs:label "musculature of larynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of trunk) @@ -183450,6 +181564,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of limb) @@ -183468,6 +181584,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of upper limb) @@ -183483,6 +181601,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of upper limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of lower limb) @@ -183498,6 +181619,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of lower limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of forelimb zeugopod) @@ -183510,6 +181634,8 @@ AnnotationAssertion( "UBERON:0004487") AnnotationAssertion(rdfs:label "musculature of forelimb zeugopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pes) @@ -183525,6 +181651,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of manus) @@ -183540,11 +181668,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of atrium) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].") -AnnotationAssertion(Annotation( "GO") "in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.") AnnotationAssertion( "FMA:7283") AnnotationAssertion(Annotation( "GO:0055009") "atrial cardiac muscle tissue") AnnotationAssertion(Annotation( "GO:0055009") "atrial heart muscle") @@ -183554,6 +181683,7 @@ AnnotationAssertion(Annotation( "UBERON:0004490") AnnotationAssertion(rdfs:label "cardiac muscle tissue of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of interatrial septum) @@ -183568,6 +181698,8 @@ AnnotationAssertion( "UBERON:0004491") AnnotationAssertion(rdfs:label "cardiac muscle tissue of interatrial septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of cardiac septum) @@ -183581,12 +181713,13 @@ AnnotationAssertion( "UBERON:0004492") AnnotationAssertion(rdfs:label "cardiac muscle tissue of cardiac septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of myocardium) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].") AnnotationAssertion( "Note placement of MA class based on parthood relationship") -AnnotationAssertion( "EMAPA:32688") AnnotationAssertion( "FMA:261726") AnnotationAssertion( "MA:0002441") AnnotationAssertion( "uberon") @@ -183594,6 +181727,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac muscle tissue of myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (skeletal muscle tissue of diaphragm) @@ -183604,6 +181738,9 @@ AnnotationAssertion( "UBERON:0004495") AnnotationAssertion(rdfs:label "skeletal muscle tissue of diaphragm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle tissue of deltoid) @@ -183614,6 +181751,8 @@ AnnotationAssertion(Annotation( "UBERON:0004500") AnnotationAssertion(rdfs:label "skeletal muscle tissue of deltoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle tissue of trapezius) @@ -183624,6 +181763,9 @@ AnnotationAssertion(Annotation( "UBERON:0004509") AnnotationAssertion(rdfs:label "skeletal muscle tissue of trapezius") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle tissue of pectoralis major) @@ -183634,6 +181776,8 @@ AnnotationAssertion(Annotation( "UBERON:0004510") AnnotationAssertion(rdfs:label "skeletal muscle tissue of pectoralis major") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue of bronchiole) @@ -183645,6 +181789,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle tissue of bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue of terminal bronchiole) @@ -183657,6 +181803,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle tissue of terminal bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue of respiratory bronchiole) @@ -183670,6 +181818,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle tissue of respiratory bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of vertebral column) @@ -183681,6 +181831,8 @@ AnnotationAssertion( "UBERON:0004518") AnnotationAssertion(rdfs:label "muscle of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated muscle tissue of prostate) @@ -183691,6 +181843,7 @@ AnnotationAssertion( "striated muscle tissue of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (vasculature of muscle organ) @@ -183701,6 +181854,8 @@ AnnotationAssertion( "UBERON:0004521") AnnotationAssertion(rdfs:label "vasculature of muscle organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of musculoskeletal system) @@ -183710,6 +181865,8 @@ AnnotationAssertion( "UBERON:0004522") AnnotationAssertion(rdfs:label "vasculature of musculoskeletal system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of trabecula carnea of right ventricle) @@ -183719,6 +181876,8 @@ AnnotationAssertion( "UBERON:0004525") AnnotationAssertion(rdfs:label "cardiac muscle tissue of trabecula carnea of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of trabecula carnea of left ventricle) @@ -183729,6 +181888,8 @@ AnnotationAssertion( "UBERON:0004526") AnnotationAssertion(rdfs:label "cardiac muscle tissue of trabecula carnea of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (anatomical projection) @@ -183738,9 +181899,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010278") Annotation( "AAO") Annotation( "AAO:BJB") "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001834") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000180") Annotation( "VSAO") Annotation( "TAO:curator") "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]") AnnotationAssertion( "anatomical process") AnnotationAssertion(Annotation( "VSAO:0000180") "process") AnnotationAssertion( "AAO:0010278") @@ -183794,12 +181952,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bony projection") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left testis) AnnotationAssertion(Annotation( "OBOL:automatic") "A testis that is in the left side of the genitalia [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37370") AnnotationAssertion( "FMA:7212") AnnotationAssertion( "MA:0001746") @@ -183811,11 +181970,13 @@ AnnotationAssertion( "UBERON:0004533") AnnotationAssertion(rdfs:label "left testis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right testis) AnnotationAssertion(Annotation( "OBOL:automatic") "A testis that is in the right side of the genitalia [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37371") AnnotationAssertion( "FMA:7211") AnnotationAssertion( "MA:0001747") @@ -183827,22 +181988,21 @@ AnnotationAssertion( "UBERON:0004534") AnnotationAssertion(rdfs:label "right testis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiovascular system) AnnotationAssertion(Annotation( "BTO:0000088") "Anatomical system that has as its parts the heart and blood vessels.") -AnnotationAssertion( "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000302") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451") Annotation( "http://bgee.unil.ch/") "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]") AnnotationAssertion( "AAO:0011001") AnnotationAssertion( "BILA:0000016") AnnotationAssertion( "BTO:0000088") AnnotationAssertion( "CALOHA:TS-1297") AnnotationAssertion( "EFO:0000791") -AnnotationAssertion( "EHDAA2:0000216") AnnotationAssertion( "EHDAA:394") AnnotationAssertion( "EMAPA:16104") -AnnotationAssertion( "EMAPA:16370") AnnotationAssertion( "EV:0100017") AnnotationAssertion( "FMA:7161") AnnotationAssertion( "GAID:467") @@ -183870,15 +182030,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiovascular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph vasculature) AnnotationAssertion(Annotation( "ZFA:0005105") "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.") AnnotationAssertion( "consider merging with parent") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005105") Annotation( "TAO") Annotation( "ZFIN:curator") "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]") AnnotationAssertion( "FMA:63815") -AnnotationAssertion( "TAO:0005105") AnnotationAssertion( "ZFA:0005105") AnnotationAssertion(Annotation( "FMA:63815") "lymphatic trunks and ducts") AnnotationAssertion( "lymphatic vasculature") @@ -183895,7 +182058,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vasculature) @@ -183915,12 +182080,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left kidney) AnnotationAssertion(Annotation( "OBOL:automatic") "A kidney that is part of a left side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:36589") AnnotationAssertion( "FMA:7205") AnnotationAssertion( "MA:0001655") @@ -183935,11 +182101,12 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right kidney) AnnotationAssertion(Annotation( "OBOL:automatic") "A kidney that is part of a right side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:36590") AnnotationAssertion( "FMA:7204") AnnotationAssertion( "MA:0001683") @@ -183954,6 +182121,8 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epididymis epithelium) @@ -183970,12 +182139,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epididymis epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left eye) AnnotationAssertion(Annotation( "OBOL:automatic") "An eye that is part of a left side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37362") AnnotationAssertion( "FMA:12515") AnnotationAssertion( "MA:0002949") @@ -183991,11 +182164,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right eye) AnnotationAssertion(Annotation( "OBOL:automatic") "An eye that is part of a right side of organism [Automatically generated definition].") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "MA:th") "EMAPA:37363") AnnotationAssertion( "FMA:12514") AnnotationAssertion( "MA:0002950") @@ -184011,6 +182186,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastroesophageal sphincter) @@ -184019,7 +182197,6 @@ AnnotationAssertion( "EMAPA:18267") AnnotationAssertion( "FMA:14915") AnnotationAssertion( "MA:0002951") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D049630") AnnotationAssertion( "NCIT:C33009") AnnotationAssertion( "SCTID:267809009") AnnotationAssertion(Annotation( "ncithesaurus:Lower_Esophageal_Sphincter") "UMLS:C0227192") @@ -184046,6 +182223,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastroesophageal sphincter") EquivalentClasses(Annotation( "MA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digital artery) @@ -184059,6 +182238,9 @@ AnnotationAssertion( "UBERON:0004552") AnnotationAssertion(rdfs:label "digital artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb digital artery) @@ -184073,7 +182255,8 @@ AnnotationAssertion( "UBERON:0004553") AnnotationAssertion(rdfs:label "forelimb digital artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (hindlimb digital artery) @@ -184087,6 +182270,8 @@ AnnotationAssertion( "UBERON:0004554") AnnotationAssertion(rdfs:label "hindlimb digital artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (systemic arterial system) @@ -184105,7 +182290,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The part of the cardiovascular system consisting of all arteries.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000273") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") AnnotationAssertion( "BTO:0004690") AnnotationAssertion( "EHDAA2:0000143") AnnotationAssertion( "EHDAA:396") @@ -184119,8 +182303,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") +SubClassOf( ) SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (systemic artery) @@ -184137,13 +182321,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "systemic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (systemic venous system) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Systemic_venous_system") "The part of the venous system that drains the general body tissues[Kardong].") -AnnotationAssertion(Annotation( "Wikipedia:Systemic_venous_system") "In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]") -AnnotationAssertion(Annotation( "FMA") Annotation( "FMA:45626") "Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000277") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") AnnotationAssertion( "FMA:45626") AnnotationAssertion( "Wikipedia:Systemic_venous_system") AnnotationAssertion(Annotation( "FMA:45626") "systemic venous circulatory system") @@ -184157,7 +182340,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000277") Annotation( "VHOG") Annotation( "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)") Annotation( "http://bgee.unil.ch/") "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]") AnnotationAssertion( "BTO:0004692") AnnotationAssertion( "EHDAA2:0002171") AnnotationAssertion( "EHDAA:486") @@ -184172,13 +182354,13 @@ AnnotationAssertion( "UBERON:0004582") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphincter muscle) AnnotationAssertion(Annotation( "Wikipedia:Sphincter") "A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.") -AnnotationAssertion(Annotation( "FMA") "FMA class is not a subtype of muscle") AnnotationAssertion( "FMA:75004") AnnotationAssertion( "NCIT:C28381") AnnotationAssertion(Annotation( "ncithesaurus:Sphincter") "UMLS:C1409894") @@ -184194,15 +182376,9 @@ SubClassOf( "http://www.biology-online.org/dictionary/Otic_capsule") "The capsule surrounding the inner ear mechanism.") AnnotationAssertion( "developmental relationships need to be checked") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010143") Annotation( "AAO") Annotation( "AAO:EJS") "Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000854") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010143") Annotation( "AAO") "relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010143") Annotation( "AAO") "relationship loss: part_of otic and occipital (AAO:0000993)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000854") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)") Annotation( "http://bgee.unil.ch/") "Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG]") -AnnotationAssertion(Annotation( "Biology-Online") "in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern") "otic capsule skeletal element") AnnotationAssertion( "AAO:0010143") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0005981") +AnnotationAssertion( "EMAPA:17596") AnnotationAssertion( "SCTID:361515007") AnnotationAssertion( "VHOG:0000854") AnnotationAssertion(Annotation( "ZFA:0001500") "otic capsule") @@ -184215,8 +182391,8 @@ AnnotationAssertion( "VHOG:0000854") "periotic capsule") AnnotationAssertion( "UBERON:0004637") AnnotationAssertion(rdfs:label "otic capsule") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -184239,6 +182415,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal afferent arteriole) @@ -184265,7 +182443,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal afferent arteriole") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -184298,6 +182478,7 @@ AnnotationAssertion( "renal efferent arteriole") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -184327,6 +182508,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral ventricle ependyma) @@ -184343,6 +182527,8 @@ AnnotationAssertion( "UBERON:0004643") AnnotationAssertion(rdfs:label "lateral ventricle ependyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fourth ventricle ependyma) @@ -184359,19 +182545,19 @@ AnnotationAssertion(Annotation( "UBERON:0004644") AnnotationAssertion(rdfs:label "fourth ventricle ependyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder urothelium) AnnotationAssertion(Annotation( "MP:0000540") "The epithelial lining of the luminal space of the urinary bladder.") AnnotationAssertion( ) -AnnotationAssertion( "5-7 cell layers thick in contracted bladder, 2-3 cells thick in distended bladder; lines renal pelvis, ureters, bladder, most of urethra but not distal urethra") AnnotationAssertion(Annotation( "BTO:0001245") "urothelium") AnnotationAssertion( "BTO:0001694") AnnotationAssertion( "CALOHA:TS-1088") AnnotationAssertion( "EMAPA:28601") AnnotationAssertion( "FMA:15936") AnnotationAssertion( "MA:0001693") -AnnotationAssertion( "NCIT:C13318") AnnotationAssertion( "SCTID:25631003") AnnotationAssertion(Annotation( "ncithesaurus:Transitional_Epithelium") "UMLS:C0225339") AnnotationAssertion(Annotation( "FMA:15936") "bladder transitional cell epithelium") @@ -184386,13 +182572,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urinary bladder urothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver lobule) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0008987") "The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein.") -AnnotationAssertion( "should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]") AnnotationAssertion( ) AnnotationAssertion( "EMAPA:35499") AnnotationAssertion( "FMA:14471") @@ -184412,6 +182601,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "liver lobule") SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -184426,6 +182616,8 @@ AnnotationAssertion( "UBERON:0004650") AnnotationAssertion(rdfs:label "tongue keratinized epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (humerus diaphysis) @@ -184449,6 +182641,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "humerus diaphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (aorta wall) @@ -184463,6 +182658,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (aorta tunica adventitia) @@ -184478,6 +182675,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta tunica adventitia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -184496,11 +182694,14 @@ AnnotationAssertion( "UBERON:0004665") AnnotationAssertion(rdfs:label "muscular coat of seminal vesicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interventricular septum membranous part) AnnotationAssertion(Annotation( "MP:0008823") "The membranous portion of the wall between the two lower chambers of the heart.") -AnnotationAssertion(Annotation( "GO:0003149") "The membranous septum is the upper part of ventricular septum[GO:0003149].") AnnotationAssertion( "UBERON:0004143") AnnotationAssertion(Annotation( "GO:0003149") "membranous septum") AnnotationAssertion(Annotation( "VT:0000018") "ventricle membranous septum") @@ -184524,13 +182725,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interventricular septum membranous part") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (interventricular septum muscular part) AnnotationAssertion(Annotation( "Wikipedia:Interventricular_septum#Portions") Annotation( "http://orcid.org/0000-0002-6601-2165") "The muscular portion of the wall between the two lower chambers of the heart.") -AnnotationAssertion(Annotation( "GO:0003150") "The muscular septum is the lower part of the ventricular septum[GO]") AnnotationAssertion( "UBERON:0004144") AnnotationAssertion(Annotation( "GO:0003150") "muscular septum") AnnotationAssertion( "EHDAA2:0000885") @@ -184553,6 +182757,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interventricular septum muscular part") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fourth ventricle aperture) @@ -184566,14 +182772,13 @@ AnnotationAssertion( "UBERON:0004668") AnnotationAssertion(rdfs:label "fourth ventricle aperture") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ependyma) AnnotationAssertion(Annotation( "ISBN:0387949542") Annotation( "Wikipedia:Ependyma") Annotation( "http://orcid.org/0000-0002-6601-2165") "The thin epithelium-like membrane composed of ependymal cells that lines the ventricular system of the brain and the spinal cord.") -AnnotationAssertion( ) -AnnotationAssertion( "ependymal") -AnnotationAssertion( "unlike other epithelia, there is no basement membrane under the ependymal epithelium[ISBN:0387949542]") -AnnotationAssertion(Annotation( "FMA") "FMA breaks ependyma into ependyma proper (a subdivsion of epithelium) and epithelium of choroid plexus") AnnotationAssertion( "BTO:0000401") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37865") AnnotationAssertion( "FMA:242791") @@ -184593,9 +182798,12 @@ AnnotationAssertion( "ependyma") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray667.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal nerve root) @@ -184620,6 +182828,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial nerve root) @@ -184646,6 +182855,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypoglossal nerve root) @@ -184677,6 +182887,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dentate gyrus molecular layer) @@ -184697,15 +182908,15 @@ AnnotationAssertion(Annotation( "UBERON:0004679") AnnotationAssertion(rdfs:label "dentate gyrus molecular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibular system) AnnotationAssertion(Annotation( "NLXANAT:090819") "The sensory system for the sense of balance.") -AnnotationAssertion(Annotation( "Wikipedia:Vestibular_system") "The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system].") -AnnotationAssertion(Annotation( "FMA") "FMA and NIF have no part information for this class. This is a GAT in FMA") AnnotationAssertion( "BTO:0003381") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37986") AnnotationAssertion( "FMA:7193") @@ -184721,7 +182932,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vestibular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (raphe nuclei) @@ -184786,6 +182999,9 @@ AnnotationAssertion( "UBERON:0004692") AnnotationAssertion(rdfs:label "external naris epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Peyer's patch epithelium) @@ -184798,6 +183014,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Peyer's patch epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arterial system smooth muscle) @@ -184809,6 +183027,8 @@ AnnotationAssertion( "UBERON:0004695") AnnotationAssertion(rdfs:label "arterial system smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous system smooth muscle) @@ -184819,7 +183039,9 @@ AnnotationAssertion( "UBERON:0004696") AnnotationAssertion(rdfs:label "venous system smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Peyer's patch germinal center) @@ -184833,6 +183055,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Peyer's patch germinal center") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -184847,17 +183071,20 @@ AnnotationAssertion( "UBERON:0004698") AnnotationAssertion(rdfs:label "vena cava endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract endothelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An endothelium that is part of a outflow tract [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001524") Annotation( "VHOG") Annotation( "DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)") Annotation( "http://bgee.unil.ch/") "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]") AnnotationAssertion( "MA:0000490") AnnotationAssertion( "VHOG:0001524") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004699") AnnotationAssertion(rdfs:label "outflow tract endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arterial system endothelium) @@ -184870,6 +183097,8 @@ AnnotationAssertion( "UBERON:0004700") AnnotationAssertion(rdfs:label "arterial system endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous system endothelium) @@ -184882,6 +183111,8 @@ AnnotationAssertion( "UBERON:0004701") AnnotationAssertion(rdfs:label "venous system endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system blood vessel endothelium) @@ -184892,6 +183123,8 @@ AnnotationAssertion( "UBERON:0004702") AnnotationAssertion(rdfs:label "respiratory system blood vessel endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal thalamus) @@ -184899,7 +183132,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion( "TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659") AnnotationAssertion(Annotation( "Ariens, p. 1192") ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Category_talk:Thalamus") Annotation( "PMID:8167659") ) AnnotationAssertion( ) AnnotationAssertion( "BAMS:DOR") AnnotationAssertion( "BAMS:Dorsal_thalamus") @@ -184934,8 +183166,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (bone fossa) AnnotationAssertion(Annotation( "Wikipedia:Fossa#Anatomy") "A depression or hollow in a bone[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001743") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO]") -AnnotationAssertion(Annotation( "FMA") "General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here") AnnotationAssertion( "fossa") AnnotationAssertion( "AAO:0010439") AnnotationAssertion( "FMA:45791") @@ -184961,7 +183191,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010568") "A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches.") AnnotationAssertion( "TODO - check relationship to bulbus arteriosus") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000173") Annotation( "TAO") Annotation( "ZFIN:curator") "A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]") AnnotationAssertion( "EHDAA2:0000197") AnnotationAssertion( "EHDAA:438") AnnotationAssertion( "EHDAA:768") @@ -184984,7 +183213,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pharyngula stage) AnnotationAssertion(Annotation( "Wikipedia:Pharyngula") "A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.") -AnnotationAssertion( "Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)") AnnotationAssertion( "DrerDO:0000052") AnnotationAssertion( "EFO:0001310") AnnotationAssertion( "OGES:000006") @@ -184996,6 +183224,7 @@ AnnotationAssertion( "UBERON:0004707") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngula stage") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -185004,7 +183233,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (paired limb/fin) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "https://github.com/geneontology/go-ontology/issues/9029") "An appendage that is part of an appendage girdle complex.") -AnnotationAssertion( "this class is the union of the classes limb, pectoral fin and pelvic fin.") AnnotationAssertion( "UBERON:0009872") AnnotationAssertion( "VSAO:0000067") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "girdle-associated appendage") @@ -185019,6 +183247,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -185026,7 +183255,7 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage) @@ -185045,15 +183274,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic appendage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (pectoral appendage) AnnotationAssertion(Annotation( "VSAO:0000150-modified") "Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001753") Annotation( "VHOG") Annotation( "DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)") Annotation( "http://bgee.unil.ch/") "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]") AnnotationAssertion( "UBERON:0009875") AnnotationAssertion( "anterior appendage") AnnotationAssertion( "VHOG:0001753") @@ -185069,8 +183299,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral appendage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (jugular vein) @@ -185113,6 +183345,8 @@ AnnotationAssertion( "annulus fibrosus disci intervertebralis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (conceptus) @@ -185142,7 +183376,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0011325") "Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins.") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(Annotation( "MA:0002593") "arcuate vein") AnnotationAssertion( "EMAPA:28221") AnnotationAssertion( "FMA:272193") @@ -185160,8 +183393,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney arcuate vein") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (crista ampullaris) @@ -185184,6 +183417,7 @@ AnnotationAssertion( "crista ampullaris") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -185219,7 +183453,6 @@ DisjointClasses(Annotation( AnnotationAssertion(Annotation( "MP:0010009") Annotation( "PMID:17714095") "The subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract; it is located bilaterally in the ventrolateral forebrain and is commonly divided into anterior and posterior regions.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "WP") "Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion") AnnotationAssertion( "BAMS:PIR") AnnotationAssertion( "BAMS:Pir") AnnotationAssertion( "BIRNLEX:1097") @@ -185323,12 +183556,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cochlear nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuromere) AnnotationAssertion(Annotation( "DOI:10.1016/j.tins.2013.06.004") Annotation( "https://github.com/obophenotype/uberon/issues/318") "A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).") AnnotationAssertion( "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001328") Annotation( "TAO") Annotation( "ZFIN:curator") "A metameric segment of the central nervous system.[ZFA]") AnnotationAssertion( ) AnnotationAssertion( "2009-06-18T09:00:04Z") AnnotationAssertion( "NLX:147842") @@ -185346,6 +183583,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuromere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (segmental subdivision of nervous system) @@ -185357,6 +183597,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "segmental subdivision of nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (segmental subdivision of hindbrain) @@ -185369,15 +183611,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "segmental subdivision of hindbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrula) AnnotationAssertion(Annotation( "Wikipedia:Gastrula") Annotation( "Wikipedia:Trilaminar_blastocyst") "Organism at the gastrula stage.") -AnnotationAssertion(Annotation( "NCIT") "We explicitly merge the NCITA terms here") AnnotationAssertion( "UBERON:0007012") AnnotationAssertion( "BILA:0000060") AnnotationAssertion( "BTO:0001403") -AnnotationAssertion(Annotation( ) "FBbt:00005317") AnnotationAssertion( "FMA:293108") AnnotationAssertion( "GAID:1302") AnnotationAssertion( "MESH:D005775") @@ -185404,6 +183647,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric glomerulus) @@ -185414,6 +183658,8 @@ AnnotationAssertion( "UBERON:0004736") AnnotationAssertion(rdfs:label "metanephric glomerulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric collecting duct) @@ -185425,6 +183671,8 @@ AnnotationAssertion(Annotation( "UBERON:0004737") AnnotationAssertion(rdfs:label "metanephric collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -185437,15 +183685,13 @@ AnnotationAssertion( "UBERON:0004738") AnnotationAssertion(rdfs:label "metanephric juxtaglomerular apparatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (pronephric glomerulus) AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0099864") Annotation( "GO:0072013") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:10572058") Annotation( "PMID:15647339") Annotation( "PMID:9268568") Annotation( "XAO:0000318") "The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment.") -AnnotationAssertion(Annotation( "ISBN:0073040584") "a glomus differs from a glomerulus in that each vascular glomus services several tubules") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001557") Annotation( "TAO") Annotation( "ZFIN:curator") "Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001237") Annotation( "VHOG") Annotation( "PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636") Annotation( "http://bgee.unil.ch/") "The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "GO") "GO treats glomus and pronephric glomerulus differently") AnnotationAssertion( "UBERON:0004191") AnnotationAssertion( "AAO:0011049") AnnotationAssertion( "SCTID:360548001") @@ -185464,17 +183710,13 @@ AnnotationAssertion(Annotation( "UBERON:0004739") AnnotationAssertion(rdfs:label "pronephric glomerulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) # Class: (dentary) AnnotationAssertion(Annotation( "VHOG:0001022") "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000191") Annotation( "TAO") Annotation( "TAO:GA_TG") "Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000124") Annotation( "AAO") Annotation( "AAO:LAP") "Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001022") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000191") Annotation( "TAO") "relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001022") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248") Annotation( "http://bgee.unil.ch/") "Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]") -AnnotationAssertion( "In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.") AnnotationAssertion( "AAO:0000124") AnnotationAssertion( "EFO:0003508") AnnotationAssertion( "TAO:0000191") @@ -185490,9 +183732,10 @@ AnnotationAssertion(Annotation( "UBERON:0004742") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dentary") +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) -SubClassOf(Annotation( "mandibular series") Annotation( "ISBN:0073040584") Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-modified") ObjectSomeValuesFrom( )) @@ -185501,11 +183744,6 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "VSAO:0005002") Annotation( "Wikipedia:Scapulocoracoid") Annotation( "https://github.com/obophenotype/uberon/issues/125") Annotation( "https://github.com/obophenotype/uberon/issues/66") "Skeletal element that consists of the scapula and the coracoid[VSAO, modified].") AnnotationAssertion( "todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000781") Annotation( "AAO") Annotation( "AAO:LAP") "Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001455") Annotation( "TAO") Annotation( "TAO:GA_TG") Annotation( "ZFIN:curator") "Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO]") -AnnotationAssertion(Annotation( "2012-09-10") Annotation( "http://palaeos.com/vertebrates/glossary/glossaryS.html") "either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000781") Annotation( "AAO") "relationship loss: part_of scapular area (AAO:0000935)[AAO]") -AnnotationAssertion(Annotation( "ZFA") "ZFA defines as precursor to scapula and coracoid. Cartilage in TAO") AnnotationAssertion( "AAO:0000781") AnnotationAssertion( "TAO:0001455") AnnotationAssertion( "VSAO:0005002") @@ -185524,7 +183762,6 @@ SubClassOf(Annotation( "VSA # Class: (skeletal tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000015") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/134") "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000015") Annotation( "taken from version of VSAO used in TAO and used directly in Uberon") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37744") AnnotationAssertion( "MA:0003047") AnnotationAssertion( "SCTID:309311006") @@ -185537,8 +183774,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "skeletal tissue") SubClassOf(Annotation( "VSAO") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "2012-08-14") Annotation( "VSAO:0000015") Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermal skeletal element) @@ -185548,6 +183784,10 @@ AnnotationAssertion( "UBERON:0004756") AnnotationAssertion(rdfs:label "dermal skeletal element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of anal canal) @@ -185562,10 +183802,10 @@ AnnotationAssertion( "SCTID:245448005") AnnotationAssertion(Annotation( "ncithesaurus:Anal_Gland") "UMLS:C0162322") AnnotationAssertion( "Wikipedia:Anal_gland") -AnnotationAssertion(Annotation( "OBOL:automatic") "gland of anal canal") AnnotationAssertion( "uberon") AnnotationAssertion( "anal gland") AnnotationAssertion(Annotation( "Wikipedia:Anal_gland") Annotation( ) "anal sac") +AnnotationAssertion( "gland of anal sac") AnnotationAssertion( "gland of anus") AnnotationAssertion( "rectal gland") AnnotationAssertion( "UBERON:0004760") @@ -185573,13 +183813,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gland of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilaginous neurocranium) AnnotationAssertion(Annotation( "Wikipedia:Chondrocranium") "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].") -AnnotationAssertion(Annotation( "FMA") "in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)") AnnotationAssertion( "AAO:0000094") -AnnotationAssertion( "AAO:0010153") AnnotationAssertion( "EHDAA:6031") AnnotationAssertion( "FMA:76621") AnnotationAssertion( "NCIT:C34121") @@ -185604,7 +183845,6 @@ SubClassOf(Annotation( "PMC # Class: (endochondral bone tissue) AnnotationAssertion(Annotation( "GO:0001958") Annotation( "VSAO:0000145") Annotation( "Wikipedia:Endochondral_ossification") "Replacement bone tissue that forms within cartilage[VSAO, modified].") -AnnotationAssertion(Annotation( "MA") "the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type") AnnotationAssertion( "EMAPA:35304") AnnotationAssertion( "MA:0002836") AnnotationAssertion( "Wikipedia:Endochondral_ossification") @@ -185614,28 +183854,29 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endochondral bone tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (intramembranous bone tissue) AnnotationAssertion(Annotation( "GO:0001957") Annotation( "Wikipedia:Intramembranous_ossification") "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].") -AnnotationAssertion(Annotation( "MA") "note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)") AnnotationAssertion( "MA:0002837") AnnotationAssertion( "Wikipedia:Intramembranous_ossification") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004764") AnnotationAssertion(rdfs:label "intramembranous bone tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal element) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000128") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001890") Annotation( "TAO") Annotation( "TAO:VSAO_workshop") "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]") AnnotationAssertion( "AAO:0011129") AnnotationAssertion( "TAO:0001890") AnnotationAssertion( "VSAO:0000128") @@ -185653,7 +183894,6 @@ SubClassOf(Annotation( "VSA # Class: (cranial bone) AnnotationAssertion(Annotation( "UBERON:automatic") "A bone that is part of a cranium.") -AnnotationAssertion( "here cranium = skull - mandible") AnnotationAssertion( ) AnnotationAssertion( "SCTID:181792001") AnnotationAssertion(Annotation( "UBERON:automatic") "cranium bone") @@ -185662,19 +183902,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cranial bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vomerine tooth) AnnotationAssertion(Annotation( "http://www.encyclo.co.uk/define/Vomerine%20teeth") "A tooth that is on the vomer.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001631") Annotation( "TAO") Annotation( "TAO:wd") "Tooth that is attached to the vomer.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001631") Annotation( "TAO") "relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO]") -AnnotationAssertion( "AAO:0000635") AnnotationAssertion( "TAO:0001631") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004767") AnnotationAssertion(rdfs:label "vomerine tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of lower jaw) @@ -185686,14 +183927,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) # Class: (diaphysis) AnnotationAssertion(Annotation( "FMA:24013") Annotation( "Wikipedia:Diaphysis") "Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified].") -AnnotationAssertion(Annotation( "FMA:24013") "Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA].") -AnnotationAssertion(Annotation( "FMA:24013, Wikipedia:Diaphysis") "The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis].") AnnotationAssertion( "EMAPA:35504") AnnotationAssertion( "FMA:24013") AnnotationAssertion( "GAID:189") @@ -185727,19 +183966,16 @@ AnnotationAssertion(Annotation( "UBERON:0004770") AnnotationAssertion(rdfs:label "articular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior nasal aperture) AnnotationAssertion(Annotation( "AAO:0000093") Annotation( "Wikipedia:Posterior_nasal_apertures") "Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000545") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000093") Annotation( "AAO") Annotation( "AAO:LAP") "Opening between the nasal cavity and the nasopharynx.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000545") Annotation( "VHOG") Annotation( "DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)") Annotation( "http://bgee.unil.ch/") "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "Fish don't have choanae, instead they have two pairs of external nostrils") -AnnotationAssertion( "In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity.") AnnotationAssertion(Annotation( "Wikipedia:Choane") Annotation( "XAO:0000277") "choana") AnnotationAssertion(Annotation( "MA:0001323") "internal naris") AnnotationAssertion( "AAO:0000093") @@ -185763,7 +183999,9 @@ AnnotationAssertion( "posterior nasal aperture") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer renal medulla vasa recta) @@ -185784,6 +184022,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outer renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner renal medulla vasa recta) @@ -185805,6 +184047,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inner renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system submucosa) @@ -185819,6 +184065,7 @@ AnnotationAssertion( "UBERON:0004777") AnnotationAssertion(rdfs:label "respiratory system submucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx submucosa) @@ -185834,6 +184081,9 @@ AnnotationAssertion(Annotation( "UBERON:0004778") AnnotationAssertion(rdfs:label "larynx submucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system lamina propria) @@ -185851,6 +184101,7 @@ AnnotationAssertion( "UBERON:0004779") AnnotationAssertion(rdfs:label "respiratory system lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -185864,6 +184115,7 @@ AnnotationAssertion( "UBERON:0004780") AnnotationAssertion(rdfs:label "gastrointestinal system lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (gallbladder lamina propria) @@ -185886,6 +184138,8 @@ AnnotationAssertion(Annotation( "UBERON:0004781") AnnotationAssertion(rdfs:label "gallbladder lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (gastrointestinal system serosa) @@ -185904,6 +184158,7 @@ AnnotationAssertion( "UBERON:0004782") AnnotationAssertion(rdfs:label "gastrointestinal system serosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gallbladder serosa) @@ -185928,6 +184183,9 @@ AnnotationAssertion(Annotation( "UBERON:0004783") AnnotationAssertion(rdfs:label "gallbladder serosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart ventricle wall) @@ -185957,13 +184215,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heart ventricle wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system mucosa) AnnotationAssertion(Annotation( "MESH:A04.760") Annotation( "MGI:cwg") Annotation( "MP:0002277") "The mucous membrane lining the respiratory tract.") AnnotationAssertion( "TODO - split respiratory tract mucosa from respiratory system mucosa") AnnotationAssertion( "BTO:0000973") -AnnotationAssertion( "EMAPA:18334") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37577") AnnotationAssertion( "FMA:302092") AnnotationAssertion( "GAID:304") @@ -185988,6 +184247,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrointestinal system mucosa) @@ -186006,7 +184267,9 @@ AnnotationAssertion( "The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468") AnnotationAssertion(rdfs:label "gastrointestinal system mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectSomeValuesFrom( )) @@ -186027,6 +184290,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urethra urothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney pelvis urothelium) @@ -186058,6 +184323,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney pelvis urothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx mucous gland) @@ -186070,6 +184338,9 @@ AnnotationAssertion( "UBERON:0004789") AnnotationAssertion(rdfs:label "larynx mucous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin mucous gland) @@ -186087,8 +184358,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin mucous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (thymus trabecula) @@ -186108,6 +184380,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus trabecula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -186125,6 +184399,8 @@ AnnotationAssertion( "UBERON:0004792") AnnotationAssertion(rdfs:label "secretion of endocrine pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretion of exocrine pancreas) @@ -186140,6 +184416,8 @@ AnnotationAssertion( "UBERON:0004793") AnnotationAssertion(rdfs:label "secretion of exocrine pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus secretion) @@ -186158,6 +184436,8 @@ AnnotationAssertion( "UBERON:0004794") AnnotationAssertion(rdfs:label "esophagus secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas secretion) @@ -186171,12 +184451,12 @@ AnnotationAssertion( "UBERON:0004795") AnnotationAssertion(rdfs:label "pancreas secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate gland secretion) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A bodily secretion that is produced by the prostate gland.") -AnnotationAssertion( "Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline.") -AnnotationAssertion( "A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions]") AnnotationAssertion( "UBERON:0010142") AnnotationAssertion( "EMAPA:36545") AnnotationAssertion( "FMA:66884") @@ -186194,6 +184474,7 @@ AnnotationAssertion( "prostate gland secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel layer) @@ -186205,13 +184486,14 @@ AnnotationAssertion( "blood vessel layer") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervix epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a uterine cervix [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia:Cervix#Histology") "The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium") AnnotationAssertion( "BTO:0000241") AnnotationAssertion( "CALOHA:TS-0137") AnnotationAssertion( "EFO:0001913") @@ -186231,6 +184513,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervix epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory tract epithelium) @@ -186241,7 +184525,6 @@ AnnotationAssertion( "EMAPA:32827") AnnotationAssertion( "MA:0001480") AnnotationAssertion( "SCTID:321764001") -AnnotationAssertion( "VHOG:0000981") AnnotationAssertion(Annotation( "OBOL:automatic") "epithelial tissue of respiratory tract") AnnotationAssertion(Annotation( "OBOL:automatic") "epithelium of respiratory tract") AnnotationAssertion(Annotation( "OBOL:automatic") "respiratory tract epithelial tissue") @@ -186252,6 +184535,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory tract epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -186269,12 +184554,14 @@ AnnotationAssertion( "UBERON:0004803") AnnotationAssertion(rdfs:label "penis epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (oviduct epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a oviduct [Automatically generated definition].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label") AnnotationAssertion( "BTO:0002402") AnnotationAssertion( "CALOHA:TS-1316") AnnotationAssertion( "EMAPA:29043") @@ -186292,6 +184579,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oviduct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminal vesicle epithelium) @@ -186313,6 +184602,10 @@ AnnotationAssertion( "UBERON:0004805") AnnotationAssertion(rdfs:label "seminal vesicle epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vas deferens epithelium) @@ -186345,6 +184638,9 @@ AnnotationAssertion( "UBERON:0004806") AnnotationAssertion(rdfs:label "vas deferens epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system epithelium) @@ -186352,7 +184648,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-0023") AnnotationAssertion( "EMAPA:32826") AnnotationAssertion( "MA:0001823") -AnnotationAssertion( "VHOG:0000981") AnnotationAssertion(Annotation( "OBOL:automatic") "apparatus respiratorius epithelial tissue") AnnotationAssertion(Annotation( "OBOL:automatic") "apparatus respiratorius epithelium") AnnotationAssertion(Annotation( "OBOL:automatic") "epithelial tissue of apparatus respiratorius") @@ -186365,6 +184660,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrointestinal system epithelium) @@ -186382,6 +184679,8 @@ AnnotationAssertion( "UBERON:0004808") AnnotationAssertion(rdfs:label "gastrointestinal system epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (salivary gland epithelium) @@ -186398,6 +184697,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "salivary gland epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nephron tubule epithelium) @@ -186414,13 +184715,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nephron tubule epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endometrium epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of an endometrium [Automatically generated definition].") -AnnotationAssertion(Annotation( "PMID:19829370") "In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)") AnnotationAssertion( "EMAPA:35307") AnnotationAssertion( "MA:0002731") AnnotationAssertion( "SCTID:253526009") @@ -186434,6 +184736,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endometrium epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male prepuce epithelium) @@ -186463,6 +184768,8 @@ AnnotationAssertion( "UBERON:0004812") AnnotationAssertion(rdfs:label "male prepuce epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminiferous tubule epithelium) @@ -186496,6 +184803,9 @@ AnnotationAssertion( "seminiferous tubule epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -186512,6 +184822,8 @@ AnnotationAssertion( "UBERON:0004814") AnnotationAssertion(rdfs:label "upper respiratory tract epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower respiratory tract epithelium) @@ -186525,11 +184837,12 @@ AnnotationAssertion( "UBERON:0004815") AnnotationAssertion(rdfs:label "lower respiratory tract epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a larynx [Automatically generated definition].") -AnnotationAssertion( "composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]") AnnotationAssertion( "EHDAA2:0004065") AnnotationAssertion( "EMAPA:35472") AnnotationAssertion( "MA:0001765") @@ -186544,6 +184857,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "larynx epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal gland epithelium) @@ -186558,6 +184873,8 @@ AnnotationAssertion( "UBERON:0004817") AnnotationAssertion(rdfs:label "lacrimal gland epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney epithelium) @@ -186575,12 +184892,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bile duct epithelium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any epithelium that lines one of the bile ducts.") -AnnotationAssertion(Annotation( "BTO:0000417") "The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium.") AnnotationAssertion( "BTO:0000417") AnnotationAssertion( "MA:0001629") AnnotationAssertion( "NCIT:C43616") @@ -186593,6 +184911,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bile duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary alveolus epithelium) @@ -186616,6 +184938,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary alveolus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -186637,6 +184960,8 @@ AnnotationAssertion( "UBERON:0004822") AnnotationAssertion(rdfs:label "extrahepatic bile duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intrahepatic bile duct epithelium) @@ -186653,6 +184978,8 @@ AnnotationAssertion( "UBERON:0004823") AnnotationAssertion(rdfs:label "intrahepatic bile duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thyroid gland medulla) @@ -186670,6 +184997,9 @@ AnnotationAssertion( "UBERON:0004827") AnnotationAssertion(rdfs:label "thyroid gland medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethra skeletal muscle tissue) @@ -186685,6 +185015,7 @@ AnnotationAssertion(Annotation( "UBERON:0004829") AnnotationAssertion(rdfs:label "urethra skeletal muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system skeletal muscle) @@ -186701,6 +185032,8 @@ AnnotationAssertion( "UBERON:0004830") AnnotationAssertion(rdfs:label "respiratory system skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus skeletal muscle) @@ -186714,6 +185047,7 @@ AnnotationAssertion( "Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal") AnnotationAssertion(rdfs:label "esophagus skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anal region skeletal muscle) @@ -186736,6 +185070,8 @@ AnnotationAssertion( "UBERON:0004832") AnnotationAssertion(rdfs:label "anal region skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lip skeletal muscle) @@ -186750,6 +185086,8 @@ AnnotationAssertion( "UBERON:0004833") AnnotationAssertion(rdfs:label "lip skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic duct smooth muscle) @@ -186760,11 +185098,13 @@ AnnotationAssertion( "UBERON:0004834") AnnotationAssertion(rdfs:label "hepatic duct smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epididymis smooth muscle) AnnotationAssertion(Annotation( "OBOL:automatic") "A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition].") -AnnotationAssertion( "EMAPA:30747") AnnotationAssertion( "MA:0001736") AnnotationAssertion(Annotation( "OBOL:automatic") "epididymis involuntary muscle") AnnotationAssertion(Annotation( "OBOL:automatic") "epididymis non-striated muscle") @@ -186777,6 +185117,9 @@ AnnotationAssertion( "UBERON:0004835") AnnotationAssertion(rdfs:label "epididymis smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system arterial endothelium) @@ -186800,9 +185143,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system arterial endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system venous endothelium) @@ -186826,8 +185169,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system venous endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (lymph node endothelium) @@ -186839,6 +185183,8 @@ AnnotationAssertion( "UBERON:0004850") AnnotationAssertion(rdfs:label "lymph node endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (aorta endothelium) @@ -186864,12 +185210,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiovascular system endothelium) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An endothelium that is part of the cardiovascular system.") AnnotationAssertion( "consider merging with 'endothelium'") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001217") Annotation( "VHOG") Annotation( "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207") Annotation( "http://bgee.unil.ch/") "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]") AnnotationAssertion( "BTO:0001853") AnnotationAssertion( "EMAPA:35201") AnnotationAssertion( "GAID:519") @@ -186888,6 +185236,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiovascular system endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrointestinal system mesentery) @@ -186902,6 +185252,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastrointestinal system mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (skeletal muscle connective tissue) @@ -186925,6 +185277,8 @@ AnnotationAssertion(Annotation( "UBERON:0004857") AnnotationAssertion(rdfs:label "skeletal muscle connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye gland) @@ -186939,6 +185293,8 @@ AnnotationAssertion( "Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands") AnnotationAssertion(rdfs:label "eye gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung alveolus) @@ -186952,6 +185308,7 @@ AnnotationAssertion( "UBERON:0004861") AnnotationAssertion(rdfs:label "right lung alveolus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lung alveolus) @@ -186967,6 +185324,7 @@ AnnotationAssertion( "UBERON:0004862") AnnotationAssertion(rdfs:label "left lung alveolus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic sympathetic nerve trunk) @@ -186992,15 +185350,15 @@ AnnotationAssertion(Annotation( "UBERON:0004863") AnnotationAssertion(rdfs:label "thoracic sympathetic nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of retina) AnnotationAssertion(Annotation( "OBOL:automatic") "A vasculature that is part of a retina [Automatically generated definition].") -AnnotationAssertion(Annotation( "PMID:21622558") Annotation( "PMID:2772405") Annotation( "michaelerice") ) AnnotationAssertion( ) AnnotationAssertion( "FMA:76552") AnnotationAssertion( "MESH:D012171") -AnnotationAssertion( "XAO:0004153") AnnotationAssertion(Annotation( "GO:0061298") "retina vasculature") AnnotationAssertion(Annotation( "GO:0061298") "retina vasculature of camera-type eye") AnnotationAssertion(Annotation( "FMA:76552") "retinal blood vessels") @@ -187015,12 +185373,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of retina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (orbital cavity) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye.") -AnnotationAssertion(Annotation( "AAO") Annotation(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/462") "note that the AAO and ZFA class is a cavity") AnnotationAssertion( "AAO:0000343") AnnotationAssertion( "FMA:84961") AnnotationAssertion( "SCTID:280541000") @@ -187031,6 +185390,8 @@ AnnotationAssertion(Annotation( "UBERON:0004867") AnnotationAssertion(rdfs:label "orbital cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parietal organ) @@ -187044,6 +185405,7 @@ AnnotationAssertion(Annotation( "UBERON:0004869") AnnotationAssertion(rdfs:label "parietal organ") SubClassOf(Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (somatic layer of lateral plate mesoderm) @@ -187062,14 +185424,12 @@ AnnotationAssertion(Annotation( "UBERON:0004871") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "somatic layer of lateral plate mesoderm") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (splanchnic layer of lateral plate mesoderm) AnnotationAssertion(Annotation( "Wikipedia:Lateral_plate_mesoderm#Division_into_layers") "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].") -AnnotationAssertion(Annotation( "BILA") "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors") AnnotationAssertion(Annotation( "BILA:0000044") Annotation( "http://www.drugs.com/dict/visceral-mesoderm.html") Annotation( "http://www.stedmans.com/") "visceral mesoderm") AnnotationAssertion( "AAO:0011102") AnnotationAssertion( "BILA:0000044") @@ -187082,8 +185442,7 @@ AnnotationAssertion(Annotation( "UBERON:0004872") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "splanchnic layer of lateral plate mesoderm") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (splanchnopleure) @@ -187103,16 +185462,13 @@ AnnotationAssertion(Annotation( "UBERON:0004873") AnnotationAssertion(rdfs:label "splanchnopleure") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatopleure) AnnotationAssertion(Annotation( "Wikipedia:Somatopleure") "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].") -AnnotationAssertion( "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/") -AnnotationAssertion( "sources differ as to whether this is part-of or develops-from the LPM") AnnotationAssertion( "EHDAA2:0001847") AnnotationAssertion( "EHDAA:381") AnnotationAssertion( "EMAPA:16180") @@ -187125,8 +185481,7 @@ AnnotationAssertion( "UBERON:0004874") AnnotationAssertion(rdfs:label "somatopleure") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -187143,14 +185498,12 @@ AnnotationAssertion(Annotation( "UBERON:0004875") AnnotationAssertion(rdfs:comment "part_of or develops_from urogenital ridge?") AnnotationAssertion(rdfs:label "nephrogenic cord") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urogenital fold) AnnotationAssertion(Annotation( "MP:0011835") Annotation( "MP:anna") Annotation( "Wikipedia:Urogenital_folds") "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].") -AnnotationAssertion( "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]") AnnotationAssertion( "EHDAA2:0004022") AnnotationAssertion( "EMAPA:30888") AnnotationAssertion( "FMA:321919") @@ -187162,8 +185515,7 @@ AnnotationAssertion(Annotation( "UBERON:0004876") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urogenital fold") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -187172,21 +185524,18 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (visceral endoderm) AnnotationAssertion(Annotation( "MP:0011186") Annotation( "PMID:15905405") "Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP].") -AnnotationAssertion( "Gilbert uses visceral endoderm as a synonym for primitive endoderm/hypoblast") AnnotationAssertion( "BTO:0003487") AnnotationAssertion( "EMAPA:16058") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004877") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visceral endoderm") +SubClassOf( ) SubClassOf(Annotation( "BTO") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (chordamesoderm) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The central region of trunk mesoderm. This tissue forms the notochord.") -AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-961014-576") "Notochord rudiment[ZFIN:ZDB-PUB-961014-576].") -AnnotationAssertion( "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.") AnnotationAssertion( "AAO:0000478") AnnotationAssertion( "EFO:0003426") AnnotationAssertion( "TAO:0000091") @@ -187200,8 +185549,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chordamesoderm") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -187219,6 +185567,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobar bronchus mesenchyme) @@ -187233,6 +185584,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lobar bronchus mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobar bronchus vasculature) @@ -187242,6 +185595,8 @@ AnnotationAssertion( "UBERON:0004889") AnnotationAssertion(rdfs:label "lobar bronchus vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interalveolar septum) @@ -187259,12 +185614,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interalveolar septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alveolar wall) AnnotationAssertion(Annotation( "LG:0012626") Annotation( "MP:0010903") "A wall that contains the alveoli.") -AnnotationAssertion(Annotation( "FMA") "part of wall in FMA") AnnotationAssertion( "UBERON:0008872") AnnotationAssertion( "BTO:0002543") AnnotationAssertion( "EMAPA:35120") @@ -187282,6 +185639,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alveolar wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (alveolar smooth muscle) @@ -187293,6 +185653,8 @@ AnnotationAssertion( "UBERON:0004895") AnnotationAssertion(rdfs:label "alveolar smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung lobar bronchus mesenchyme) @@ -187302,11 +185664,12 @@ AnnotationAssertion( "UBERON:0004901") AnnotationAssertion(rdfs:label "right lung lobar bronchus mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (urogenital sinus epithelium) AnnotationAssertion(Annotation( "PMID:18977204") "The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra.") -AnnotationAssertion(Annotation( "EHDAA2") "we follow EHDAA2 in dividing the UGS into epithelium and lumen") AnnotationAssertion( "EHDAA2:0004061") AnnotationAssertion( "EMAPA:31509") AnnotationAssertion(Annotation( "PMID:18977204") "UGE") @@ -187315,7 +185678,10 @@ AnnotationAssertion( "UBERON:0004902") AnnotationAssertion(rdfs:label "urogenital sinus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "PMID:18977204") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (neuron projection bundle connecting eye with brain) @@ -187325,7 +185691,6 @@ AnnotationAssertion( "BTO:0000966") "optic nerve") AnnotationAssertion( "BTO:0000966") AnnotationAssertion( "EV:0100351") -AnnotationAssertion(Annotation( ) "FBbt:00001956") AnnotationAssertion( "TADS:0000232") AnnotationAssertion( "optic nerve (generic)") AnnotationAssertion( "uberon") @@ -187336,12 +185701,14 @@ AnnotationAssertion( "for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)") AnnotationAssertion(rdfs:label "neuron projection bundle connecting eye with brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (articulation) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.") -AnnotationAssertion(Annotation( ) "FBbt:00005811") AnnotationAssertion( "joint") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004905") @@ -187359,12 +185726,12 @@ AnnotationAssertion( "UBERON:0004906") AnnotationAssertion(rdfs:label "ectodermal part of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (lower digestive tract) AnnotationAssertion(Annotation( "Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract") "The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].") -AnnotationAssertion(Annotation( "MA") "MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509") -AnnotationAssertion(Annotation( "FMA") "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L") AnnotationAssertion(Annotation( "GO:0048565") "gut") AnnotationAssertion( "FMA:49179") AnnotationAssertion( "NCIT:C33010") @@ -187385,7 +185752,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (upper digestive tract) AnnotationAssertion(Annotation( "Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract") "The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.") -AnnotationAssertion(Annotation( "FMA") "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus") AnnotationAssertion( "FMA:49177") AnnotationAssertion( "NCIT:C33837") AnnotationAssertion( "SCTID:181244000") @@ -187416,6 +185782,9 @@ AnnotationAssertion(Annotation( "UBERON:0004909") AnnotationAssertion(rdfs:label "epithelium of gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of male gonad) @@ -187428,6 +185797,8 @@ AnnotationAssertion( "UBERON:0004910") AnnotationAssertion(rdfs:label "epithelium of male gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of female gonad) @@ -187441,6 +185812,8 @@ AnnotationAssertion( "UBERON:0004911") AnnotationAssertion(rdfs:label "epithelium of female gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (biliary bud) @@ -187453,16 +185826,17 @@ AnnotationAssertion(Annotation( "UBERON:0004912") AnnotationAssertion(rdfs:label "biliary bud") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-modified") ObjectSomeValuesFrom( )) # Class: (hepatopancreatic ampulla) AnnotationAssertion(Annotation( "Wikipedia:Ampulla_of_Vater") "A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005167") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-070212-11") Annotation( "ZFIN:ZDB-PUB-080414-12") "Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]") AnnotationAssertion( "CALOHA:TS-2348") AnnotationAssertion( "FMA:15076") AnnotationAssertion( "GAID:283") @@ -187490,6 +185864,9 @@ AnnotationAssertion( "hepatopancreatic ampulla") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duodenal papilla) @@ -187534,6 +185911,9 @@ AnnotationAssertion( "sphincter of hepatopancreatic ampulla") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anal sphincter) @@ -187545,6 +185925,8 @@ AnnotationAssertion( "UBERON:0004916") AnnotationAssertion(rdfs:label "anal sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethral sphincter) @@ -187563,14 +185945,13 @@ AnnotationAssertion( "UBERON:0004917") AnnotationAssertion(rdfs:label "urethral sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (subdivision of digestive tract) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A proximal-distal subdivision of the digestive tract.") -AnnotationAssertion( "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "FBbt:00100315") AnnotationAssertion( "FMA:71131") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FMA:71131") "alimentary system subdivision") @@ -187583,7 +185964,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subdivision of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (organ component layer) @@ -187614,6 +185997,9 @@ AnnotationAssertion(Annotation( "UBERON:0004924") AnnotationAssertion(rdfs:label "submucosa of pharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of cystic duct) @@ -187625,6 +186011,8 @@ AnnotationAssertion( "UBERON:0004926") AnnotationAssertion(rdfs:label "submucosa of cystic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of cecum) @@ -187641,6 +186029,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of cecum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of appendix) @@ -187661,6 +186051,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of ascending colon) @@ -187671,6 +186063,8 @@ AnnotationAssertion( "UBERON:0004929") AnnotationAssertion(rdfs:label "submucosa of ascending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of transverse colon) @@ -187681,6 +186075,8 @@ AnnotationAssertion( "UBERON:0004930") AnnotationAssertion(rdfs:label "submucosa of transverse colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of descending colon) @@ -187691,6 +186087,8 @@ AnnotationAssertion( "UBERON:0004931") AnnotationAssertion(rdfs:label "submucosa of descending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of sigmoid colon) @@ -187701,6 +186099,8 @@ AnnotationAssertion( "UBERON:0004932") AnnotationAssertion(rdfs:label "submucosa of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of fundus of stomach) @@ -187716,6 +186116,8 @@ AnnotationAssertion( "UBERON:0004933") AnnotationAssertion(rdfs:label "submucosa of fundus of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of body of stomach) @@ -187732,6 +186134,8 @@ AnnotationAssertion( "UBERON:0004934") AnnotationAssertion(rdfs:label "submucosa of body of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of cardia of stomach) @@ -187750,6 +186154,8 @@ AnnotationAssertion( "UBERON:0004935") AnnotationAssertion(rdfs:label "submucosa of cardia of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of pyloric antrum) @@ -187764,6 +186170,8 @@ AnnotationAssertion( "UBERON:0004936") AnnotationAssertion(rdfs:label "submucosa of pyloric antrum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of pylorus) @@ -187780,6 +186188,8 @@ AnnotationAssertion( "UBERON:0004937") AnnotationAssertion(rdfs:label "submucosa of pylorus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of biliary tree) @@ -187792,6 +186202,9 @@ AnnotationAssertion( "UBERON:0004938") AnnotationAssertion(rdfs:label "submucosa of biliary tree") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of common bile duct) @@ -187805,6 +186218,8 @@ AnnotationAssertion( "UBERON:0004939") AnnotationAssertion(rdfs:label "submucosa of common bile duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of common hepatic duct) @@ -187818,6 +186233,8 @@ AnnotationAssertion( "UBERON:0004940") AnnotationAssertion(rdfs:label "submucosa of common hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of right hepatic duct) @@ -187829,6 +186246,8 @@ AnnotationAssertion( "UBERON:0004941") AnnotationAssertion(rdfs:label "submucosa of right hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of left hepatic duct) @@ -187840,6 +186259,8 @@ AnnotationAssertion( "UBERON:0004942") AnnotationAssertion(rdfs:label "submucosa of left hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of urinary bladder) @@ -187861,6 +186282,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (submucosa of trigone of urinary bladder) @@ -187885,6 +186308,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of trigone of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of neck of urinary bladder) @@ -187904,6 +186329,8 @@ AnnotationAssertion( "UBERON:0004945") AnnotationAssertion(rdfs:label "submucosa of neck of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of ileum) @@ -187918,6 +186345,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosa of ileum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of lobar bronchus) @@ -187931,6 +186360,8 @@ AnnotationAssertion( "UBERON:0004950") AnnotationAssertion(rdfs:label "submucosa of lobar bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of segmental bronchus) @@ -187944,6 +186375,8 @@ AnnotationAssertion( "UBERON:0004951") AnnotationAssertion(rdfs:label "submucosa of segmental bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of bronchiole) @@ -187954,6 +186387,9 @@ AnnotationAssertion( "UBERON:0004952") AnnotationAssertion(rdfs:label "submucosa of bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of ureter) @@ -187977,6 +186413,8 @@ AnnotationAssertion( "UBERON:0004980") AnnotationAssertion(rdfs:label "mucosa of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mucosa of vagina) @@ -187998,6 +186436,9 @@ AnnotationAssertion( "UBERON:0004983") AnnotationAssertion(rdfs:label "mucosa of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of seminal vesicle) @@ -188024,6 +186465,9 @@ AnnotationAssertion( "UBERON:0004984") AnnotationAssertion(rdfs:label "mucosa of seminal vesicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of ejaculatory duct) @@ -188041,6 +186485,8 @@ AnnotationAssertion( "UBERON:0004985") AnnotationAssertion(rdfs:label "mucosa of ejaculatory duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of deferent duct) @@ -188093,6 +186539,8 @@ AnnotationAssertion( "UBERON:0004986") AnnotationAssertion(rdfs:label "mucosa of deferent duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of cystic duct) @@ -188110,6 +186558,8 @@ AnnotationAssertion( "UBERON:0004988") AnnotationAssertion(rdfs:label "mucosa of cystic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of appendix) @@ -188155,6 +186605,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of ascending colon) @@ -188171,6 +186623,8 @@ AnnotationAssertion( "UBERON:0004990") AnnotationAssertion(rdfs:label "mucosa of ascending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of transverse colon) @@ -188187,6 +186641,8 @@ AnnotationAssertion( "UBERON:0004991") AnnotationAssertion(rdfs:label "mucosa of transverse colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of descending colon) @@ -188203,6 +186659,8 @@ AnnotationAssertion( "UBERON:0004992") AnnotationAssertion(rdfs:label "mucosa of descending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of sigmoid colon) @@ -188219,6 +186677,8 @@ AnnotationAssertion( "UBERON:0004993") AnnotationAssertion(rdfs:label "mucosa of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of fundus of stomach) @@ -188252,6 +186712,8 @@ AnnotationAssertion( "UBERON:0004994") AnnotationAssertion(rdfs:label "mucosa of fundus of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of body of stomach) @@ -188292,6 +186754,8 @@ AnnotationAssertion( "UBERON:0004995") AnnotationAssertion(rdfs:label "mucosa of body of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of cardia of stomach) @@ -188340,6 +186804,8 @@ AnnotationAssertion( "UBERON:0004996") AnnotationAssertion(rdfs:label "mucosa of cardia of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of pyloric antrum) @@ -188375,6 +186841,8 @@ AnnotationAssertion(Annotation( "UBERON:0004997") AnnotationAssertion(rdfs:label "mucosa of pyloric antrum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (mucosa of pylorus) @@ -188411,6 +186879,8 @@ AnnotationAssertion(Annotation( "UBERON:0004998") AnnotationAssertion(rdfs:label "mucosa of pylorus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of biliary tree) @@ -188435,6 +186905,9 @@ AnnotationAssertion( "UBERON:0004999") AnnotationAssertion(rdfs:label "mucosa of biliary tree") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of common bile duct) @@ -188460,6 +186933,8 @@ AnnotationAssertion( "UBERON:0005000") AnnotationAssertion(rdfs:label "mucosa of common bile duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of common hepatic duct) @@ -188485,6 +186960,8 @@ AnnotationAssertion( "UBERON:0005001") AnnotationAssertion(rdfs:label "mucosa of common hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of right hepatic duct) @@ -188502,6 +186979,8 @@ AnnotationAssertion( "UBERON:0005002") AnnotationAssertion(rdfs:label "mucosa of right hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of left hepatic duct) @@ -188519,6 +186998,8 @@ AnnotationAssertion( "UBERON:0005003") AnnotationAssertion(rdfs:label "mucosa of left hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of right ureter) @@ -188536,6 +187017,8 @@ AnnotationAssertion( "UBERON:0005004") AnnotationAssertion(rdfs:label "mucosa of right ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of left ureter) @@ -188555,6 +187038,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of left ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of renal pelvis) @@ -188590,6 +187075,8 @@ AnnotationAssertion( "UBERON:0005006") AnnotationAssertion(rdfs:label "mucosa of renal pelvis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of trigone of urinary bladder) @@ -188648,6 +187135,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of trigone of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of neck of urinary bladder) @@ -188695,6 +187184,8 @@ AnnotationAssertion( "UBERON:0005010") AnnotationAssertion(rdfs:label "mucosa of neck of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of right uterine tube) @@ -188727,6 +187218,8 @@ AnnotationAssertion( "UBERON:0005011") AnnotationAssertion(rdfs:label "mucosa of right uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of left uterine tube) @@ -188759,6 +187252,8 @@ AnnotationAssertion( "UBERON:0005012") AnnotationAssertion(rdfs:label "mucosa of left uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of male urethra) @@ -188775,6 +187270,8 @@ AnnotationAssertion( "UBERON:0005013") AnnotationAssertion(rdfs:label "mucosa of male urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of female urethra) @@ -188791,6 +187288,8 @@ AnnotationAssertion( "UBERON:0005014") AnnotationAssertion(rdfs:label "mucosa of female urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of prostatic urethra) @@ -188817,6 +187316,8 @@ AnnotationAssertion( "UBERON:0005015") AnnotationAssertion(rdfs:label "mucosa of prostatic urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lacrimal sac) @@ -188833,6 +187334,8 @@ AnnotationAssertion( "UBERON:0005017") AnnotationAssertion(rdfs:label "mucosa of lacrimal sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of tongue) @@ -188854,6 +187357,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of nasopharynx) @@ -188887,6 +187392,10 @@ AnnotationAssertion( "UBERON:0005022") AnnotationAssertion(rdfs:label "mucosa of nasopharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of middle ear) @@ -188906,6 +187415,8 @@ AnnotationAssertion( "UBERON:0005026") AnnotationAssertion(rdfs:label "mucosa of middle ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lacrimal canaliculus) @@ -188923,6 +187434,9 @@ AnnotationAssertion( "UBERON:0005029") AnnotationAssertion(rdfs:label "mucosa of lacrimal canaliculus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of upper lip) @@ -188943,6 +187457,8 @@ AnnotationAssertion( "UBERON:0005031") AnnotationAssertion(rdfs:label "mucosa of upper lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lower lip) @@ -188963,6 +187479,8 @@ AnnotationAssertion( "UBERON:0005032") AnnotationAssertion(rdfs:label "mucosa of lower lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of gallbladder) @@ -188990,6 +187508,9 @@ AnnotationAssertion( "UBERON:0005033") AnnotationAssertion(rdfs:label "mucosa of gallbladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lobar bronchus) @@ -189015,6 +187536,8 @@ AnnotationAssertion( "UBERON:0005037") AnnotationAssertion(rdfs:label "mucosa of lobar bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of segmental bronchus) @@ -189040,6 +187563,8 @@ AnnotationAssertion( "UBERON:0005038") AnnotationAssertion(rdfs:label "mucosa of segmental bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of bronchiole) @@ -189057,6 +187582,9 @@ AnnotationAssertion( "UBERON:0005039") AnnotationAssertion(rdfs:label "mucosa of bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of terminal bronchiole) @@ -189081,6 +187609,8 @@ AnnotationAssertion( "UBERON:0005040") AnnotationAssertion(rdfs:label "mucosa of terminal bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of respiratory bronchiole) @@ -189105,11 +187635,12 @@ AnnotationAssertion( "UBERON:0005041") AnnotationAssertion(rdfs:label "mucosa of respiratory bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner epithelial layer of tympanic membrane) AnnotationAssertion(Annotation( "PMID:11237469") Annotation( "https://orcid.org/0000-0002-6601-2165") "A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane.") -AnnotationAssertion(Annotation( "FMA") "in FMA this is classified as a mucosa") AnnotationAssertion( "FMA:56844") AnnotationAssertion( "SCTID:36411006") AnnotationAssertion(Annotation( "FMA:56844") "mucosa of tympanic membrane") @@ -189121,6 +187652,9 @@ AnnotationAssertion( "UBERON:0005042") AnnotationAssertion(rdfs:label "inner epithelial layer of tympanic membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of nasolacrimal duct) @@ -189138,6 +187672,9 @@ AnnotationAssertion( "UBERON:0005043") AnnotationAssertion(rdfs:label "mucosa of nasolacrimal duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of uterine tube) @@ -189165,6 +187702,9 @@ AnnotationAssertion( "UBERON:0005048") AnnotationAssertion(rdfs:label "mucosa of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of infundibulum of uterine tube) @@ -189184,6 +187724,8 @@ AnnotationAssertion( "UBERON:0005049") AnnotationAssertion(rdfs:label "mucosa of infundibulum of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mediastinum testis) @@ -189201,9 +187743,8 @@ AnnotationAssertion( "UBERON:0005051") AnnotationAssertion(rdfs:label "mediastinum testis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189217,11 +187758,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "zone of long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (external female genitalia) AnnotationAssertion(Annotation( "OBOL:automatic") "An external genitalia that is part of a female reproductive system [Automatically generated definition].") -AnnotationAssertion( "in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]") AnnotationAssertion( "BTO:0003100") AnnotationAssertion( "EMAPA:30984") AnnotationAssertion( "FMA:45649") @@ -189238,6 +187780,8 @@ AnnotationAssertion( "TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547") AnnotationAssertion(rdfs:label "external female genitalia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) DisjointClasses( ) # Class: (immune organ) @@ -189250,6 +187794,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immune organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hemolymphoid system gland) @@ -189264,11 +187810,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hemolymphoid system gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural groove) AnnotationAssertion(Annotation( "GO:0001842") Annotation( "Wikipedia:Neural_groove") Annotation( "http://orcid.org/0000-0002-6601-2165") "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.") -AnnotationAssertion(Annotation( "Wikipedia:Neural_groove") "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].") AnnotationAssertion( "AAO:0011071") AnnotationAssertion( "EMAPA:35594") AnnotationAssertion( "FMA:295624") @@ -189281,13 +187828,12 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005061") AnnotationAssertion(rdfs:label "neural groove") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural fold) AnnotationAssertion(Annotation( "GO:0001842") Annotation( "MP:0011256") Annotation( "Wikipedia:Neural_fold") "One of the two elevated edges of the neural groove[GO,MP].") -AnnotationAssertion(Annotation( "Wikipedia:Neural_fold") "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].") AnnotationAssertion( "EHDAA2:0001249") AnnotationAssertion( "FMA:295618") AnnotationAssertion( "NCIT:C34223") @@ -189301,8 +187847,11 @@ AnnotationAssertion( "UBERON:0005062") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural fold") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189313,6 +187862,7 @@ AnnotationAssertion( "UBERON:0005064") AnnotationAssertion(rdfs:label "left ventricular trabecular myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) # Class: (right ventricular trabecular myocardium) @@ -189322,12 +187872,12 @@ AnnotationAssertion( "UBERON:0005066") AnnotationAssertion(rdfs:label "right ventricular trabecular myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) # Class: (neural rod) AnnotationAssertion(Annotation( "GO:0014024") Annotation( "ZFA:0000133") "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000133") Annotation( "TAO") Annotation( "ZFIN:curator") "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]") AnnotationAssertion( "EFO:0003498") AnnotationAssertion( "TAO:0000133") AnnotationAssertion( "ZFA:0000133") @@ -189337,14 +187887,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural rod") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain-midbrain boundary) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001367") Annotation( "TAO") Annotation( "ZFIN:curator") "The boundary between the diencephalon and the mesencephalon.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001367") Annotation( "TAO") "relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO]") AnnotationAssertion( "EMAPA:36449") AnnotationAssertion( "TAO:0001367") AnnotationAssertion( "ZFA:0001367") @@ -189355,8 +187902,12 @@ AnnotationAssertion( "UBERON:0005075") AnnotationAssertion(rdfs:label "forebrain-midbrain boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain-spinal cord boundary) @@ -189366,7 +187917,11 @@ AnnotationAssertion( "UBERON:0005076") AnnotationAssertion(rdfs:label "hindbrain-spinal cord boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric ureteric bud) @@ -189375,6 +187930,8 @@ AnnotationAssertion( "UBERON:0005080") AnnotationAssertion(rdfs:label "metanephric ureteric bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureter ureteric bud) @@ -189383,6 +187940,8 @@ AnnotationAssertion( "UBERON:0005081") AnnotationAssertion(rdfs:label "ureter ureteric bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tube lumen) @@ -189394,25 +187953,25 @@ AnnotationAssertion( "UBERON:0005082") AnnotationAssertion(rdfs:label "tube lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectodermal placode) AnnotationAssertion(Annotation( "GO:0060788") "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].") AnnotationAssertion( "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness") -AnnotationAssertion( "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.") -AnnotationAssertion(Annotation( "GO") Annotation( "https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347") "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures") AnnotationAssertion( "AEO:0000218") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "AEO:0000112") "epithelial placode") AnnotationAssertion( "UBERON:0005085") AnnotationAssertion(rdfs:label "ectodermal placode") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair follicle placode) AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2008.12.005") "A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate.") -AnnotationAssertion(Annotation( "GO:0060789") "An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO].") AnnotationAssertion( "EMAPA:36479") AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2008.12.005") "hair placode") AnnotationAssertion( "vibrissa placode") @@ -189426,12 +187985,11 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tooth placode) AnnotationAssertion(Annotation( "GO:0060790") "An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001153") Annotation( "TAO") Annotation( "ZFIN:curator") "Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]") -AnnotationAssertion( "In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs.") AnnotationAssertion( "BTO:0001511") AnnotationAssertion( "TAO:0001153") AnnotationAssertion( "ZFA:0001153") @@ -189446,8 +188004,10 @@ AnnotationAssertion(Annotation( "UBERON:0005087") AnnotationAssertion(rdfs:label "tooth placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ) -SubClassOf(Annotation( "check for other species") Annotation( "Wikipedia:Tooth_development") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebaceous gland placode) @@ -189457,8 +188017,10 @@ AnnotationAssertion( "UBERON:0005088") AnnotationAssertion(rdfs:label "sebaceous gland placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ) SubClassOf(Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sweat gland placode) @@ -189468,14 +188030,14 @@ AnnotationAssertion( "UBERON:0005089") AnnotationAssertion(rdfs:label "sweat gland placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ) SubClassOf(Annotation( "Wikipathways:WP2062") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle structure) AnnotationAssertion(Annotation( "GO:0061061") "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].") -AnnotationAssertion( "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila") -AnnotationAssertion( "EMAPA:32715") AnnotationAssertion( "FMA:30316") AnnotationAssertion(Annotation( "FMA:30316") "musculus") AnnotationAssertion( "uberon") @@ -189489,7 +188051,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (right horn of sinus venosus) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000489") Annotation( "VHOG") Annotation( "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003") Annotation( "http://bgee.unil.ch/") "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]") AnnotationAssertion( "EHDAA2:0001841") AnnotationAssertion( "EHDAA:484") AnnotationAssertion( "EMAPA:16239") @@ -189510,8 +188071,7 @@ AnnotationAssertion( "GOC:mtg_kidney_jan10") "kidney anlage") AnnotationAssertion( "UBERON:0005095") AnnotationAssertion(rdfs:label "kidney rudiment") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) # Class: (descending thin limb) @@ -189541,7 +188101,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2276") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189564,6 +188123,7 @@ AnnotationAssertion( "renal connecting tubule") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (short descending thin limb) @@ -189573,9 +188133,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005099") AnnotationAssertion(rdfs:label "short descending thin limb") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (long descending thin limb) @@ -189583,28 +188142,27 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005100") AnnotationAssertion(rdfs:label "long descending thin limb") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (early distal convoluted tubule) AnnotationAssertion(Annotation( "GO:0072067") "The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO].") -AnnotationAssertion( "EMAPA:28393") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005101") AnnotationAssertion(rdfs:label "early distal convoluted tubule") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (late distal convoluted tubule) AnnotationAssertion(Annotation( "GO:0072068") "The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].") AnnotationAssertion( "TODO - CL") -AnnotationAssertion( "EMAPA:28393") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005102") AnnotationAssertion(rdfs:label "late distal convoluted tubule") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric epithelium) @@ -189614,16 +188172,21 @@ AnnotationAssertion( "UBERON:0005103") AnnotationAssertion(rdfs:label "mesonephric epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric tubule) AnnotationAssertion(Annotation( "GO:0072173") "A metanephric tubule is an epithelial tube that is part of the metanephros[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001526") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543") Annotation( "http://bgee.unil.ch/") "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]") AnnotationAssertion( "VHOG:0001526") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005106") AnnotationAssertion(rdfs:label "metanephric tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric epithelium) @@ -189632,6 +188195,9 @@ AnnotationAssertion( "UBERON:0005108") AnnotationAssertion(rdfs:label "metanephric epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric smooth muscle tissue) @@ -189640,17 +188206,21 @@ AnnotationAssertion( "UBERON:0005109") AnnotationAssertion(rdfs:label "metanephric smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric nephron) AnnotationAssertion(Annotation( "GO:0072273") "A metanephric nephron is the functional unit of the metanephros[GO].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000719") Annotation( "VHOG") Annotation( "DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994)") Annotation( "http://bgee.unil.ch/") "The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]") AnnotationAssertion( "UBERON:0005142") AnnotationAssertion( "VHOG:0000719") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005110") AnnotationAssertion(rdfs:label "metanephric nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") Annotation( "Wikipedia:Nephron") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) @@ -189661,6 +188231,9 @@ AnnotationAssertion( "UBERON:0005111") AnnotationAssertion(rdfs:label "metanephric pyramid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric cortex mesenchyme) @@ -189669,6 +188242,7 @@ AnnotationAssertion( "UBERON:0005113") AnnotationAssertion(rdfs:label "metanephric cortex mesenchyme") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (metanephric ascending thin limb) @@ -189678,6 +188252,8 @@ AnnotationAssertion( "UBERON:0005114") AnnotationAssertion(rdfs:label "metanephric ascending thin limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric cortical collecting duct) @@ -189687,6 +188263,8 @@ AnnotationAssertion( "UBERON:0005115") AnnotationAssertion(rdfs:label "metanephric cortical collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -189697,6 +188275,8 @@ AnnotationAssertion( "UBERON:0005116") AnnotationAssertion(rdfs:label "metanephric descending thin limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric distal convoluted tubule) @@ -189707,7 +188287,8 @@ AnnotationAssertion( "UBERON:0005117") AnnotationAssertion(rdfs:label "metanephric distal convoluted tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric early distal convoluted tubule) @@ -189717,6 +188298,8 @@ AnnotationAssertion( "UBERON:0005118") AnnotationAssertion(rdfs:label "metanephric early distal convoluted tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -189727,6 +188310,7 @@ AnnotationAssertion( "UBERON:0005119") AnnotationAssertion(rdfs:label "metanephric glomerular mesangium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric late distal convoluted tubule) @@ -189736,6 +188320,8 @@ AnnotationAssertion( "UBERON:0005120") AnnotationAssertion(rdfs:label "metanephric late distal convoluted tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -189746,6 +188332,8 @@ AnnotationAssertion( "UBERON:0005122") AnnotationAssertion(rdfs:label "metanephric macula densa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric proximal convoluted tubule) @@ -189756,7 +188344,8 @@ AnnotationAssertion( "UBERON:0005124") AnnotationAssertion(rdfs:label "metanephric proximal convoluted tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric proximal straight tubule) @@ -189767,9 +188356,9 @@ AnnotationAssertion( "UBERON:0005125") AnnotationAssertion(rdfs:label "metanephric proximal straight tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric thick ascending limb) @@ -189778,7 +188367,8 @@ AnnotationAssertion( "UBERON:0005127") AnnotationAssertion(rdfs:label "metanephric thick ascending limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric distal tubule) @@ -189788,7 +188378,8 @@ AnnotationAssertion( "UBERON:0005129") AnnotationAssertion(rdfs:label "metanephric distal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric loop of Henle) @@ -189797,8 +188388,9 @@ AnnotationAssertion( "UBERON:0005130") AnnotationAssertion(rdfs:label "metanephric loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric long nephron) @@ -189807,6 +188399,8 @@ AnnotationAssertion( "UBERON:0005132") AnnotationAssertion(rdfs:label "metanephric long nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric glomerulus vasculature) @@ -189816,6 +188410,7 @@ AnnotationAssertion( "UBERON:0005133") AnnotationAssertion(rdfs:label "metanephric glomerulus vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric nephron epithelium) @@ -189825,6 +188420,8 @@ AnnotationAssertion( "UBERON:0005134") AnnotationAssertion(rdfs:label "metanephric nephron epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric glomerular epithelium) @@ -189834,8 +188431,9 @@ AnnotationAssertion( "UBERON:0005135") AnnotationAssertion(rdfs:label "metanephric glomerular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric glomerular endothelium) @@ -189844,8 +188442,8 @@ AnnotationAssertion( "UBERON:0005136") AnnotationAssertion(rdfs:label "metanephric glomerular endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric capsule) @@ -189856,6 +188454,9 @@ AnnotationAssertion( "UBERON:0005137") AnnotationAssertion(rdfs:label "metanephric capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric long descending thin limb) @@ -189863,7 +188464,8 @@ AnnotationAssertion( "UBERON:0005139") AnnotationAssertion(rdfs:label "metanephric long descending thin limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric short nephron) @@ -189872,6 +188474,8 @@ AnnotationAssertion( "UBERON:0005140") AnnotationAssertion(rdfs:label "metanephric short nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric short descending thin limb) @@ -189880,7 +188484,8 @@ AnnotationAssertion( "UBERON:0005141") AnnotationAssertion(rdfs:label "metanephric short descending thin limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric glomerular capillary) @@ -189889,6 +188494,7 @@ AnnotationAssertion( "UBERON:0005144") AnnotationAssertion(rdfs:label "metanephric glomerular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -189899,6 +188505,8 @@ AnnotationAssertion( "UBERON:0005145") AnnotationAssertion(rdfs:label "metanephric comma-shaped body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric nephron tubule) @@ -189909,7 +188517,9 @@ AnnotationAssertion( "UBERON:0005146") AnnotationAssertion(rdfs:label "metanephric nephron tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) # Class: (metanephric renal vesicle) @@ -189923,6 +188533,8 @@ AnnotationAssertion( "UBERON:0005147") AnnotationAssertion(rdfs:label "metanephric renal vesicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189933,6 +188545,7 @@ AnnotationAssertion( "UBERON:0005148") AnnotationAssertion(rdfs:label "metanephric S-shaped body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (metanephric connecting tubule) @@ -189942,7 +188555,8 @@ AnnotationAssertion( "UBERON:0005149") AnnotationAssertion(rdfs:label "metanephric connecting tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metanephric proximal tubule) @@ -189952,7 +188566,8 @@ AnnotationAssertion( "UBERON:0005151") AnnotationAssertion(rdfs:label "metanephric proximal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (epithelial bud) @@ -189979,7 +188594,6 @@ SubClassOf(Annotation( "AEO AnnotationAssertion(Annotation( "GO:0007424") "An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.") AnnotationAssertion(Annotation( "FBbt:00005024") Annotation( ) "tracheal system") AnnotationAssertion( "BTO:0003870") -AnnotationAssertion(Annotation( ) "FBbt:00005024") AnnotationAssertion( "SPD:0000427") AnnotationAssertion( "TADS:0000043") AnnotationAssertion( "invertebrate tracheal system") @@ -189990,7 +188604,6 @@ AnnotationAssertion( "open tracheal system") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (reproductive structure) @@ -190002,6 +188615,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial fold) @@ -190022,6 +188637,9 @@ AnnotationAssertion( "UBERON:0005158") AnnotationAssertion(rdfs:label "parenchyma of central nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestigial structure) @@ -190031,14 +188649,14 @@ AnnotationAssertion( "UBERON:0005160") AnnotationAssertion(rdfs:label "vestigial structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multi cell part structure) AnnotationAssertion(Annotation( "CARO:0001000") "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.") -AnnotationAssertion(Annotation( "CARO") Annotation( "FMA") "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'") AnnotationAssertion( "AAO:0011000") AnnotationAssertion( "CARO:0001000") -AnnotationAssertion(Annotation( ) "FBbt:00007060") AnnotationAssertion( "FMA:83115") AnnotationAssertion(Annotation( "CARO:0001000") "multi-cell-component structure") AnnotationAssertion(Annotation( "CARO:0001000") "multi-cell-part structure") @@ -190112,7 +188730,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal interlobular vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -190122,7 +188741,6 @@ DisjointClasses( "http://medical-dictionary.thefreedictionary.com/tissue") "Connective tissue between the cellular elements of a structure.") AnnotationAssertion( "specify differentia from stroma") AnnotationAssertion( ) -AnnotationAssertion( "interstital") AnnotationAssertion( "FMA:86301") AnnotationAssertion( "SCTID:85293002") AnnotationAssertion( "interstitium") @@ -190137,7 +188755,6 @@ SubClassOf(Annotation( "FMA AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A layer of the ovarian follicle that consists of granulosa cells.") AnnotationAssertion( ) -AnnotationAssertion( "At one part of the mature follicle the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This is termed the discus proligerus. [Wikipedia:Membrana_granulosa, Wikipedia:Membrana_granulosa]") AnnotationAssertion( "membrana granulosa") AnnotationAssertion( "EFO:0003628") AnnotationAssertion( "EMAPA:35633") @@ -190160,14 +188777,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "granulosa cell layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic duct) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion).") AnnotationAssertion( "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001100") Annotation( "TAO") Annotation( "ZFIN:curator") "A duct that carries bile from the liver to the small intestine.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000219") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/hepatic+duct") "The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]") -AnnotationAssertion(Annotation( "GO:0061011") "The hepatic duct is the duct that leads from the liver to the bile duct[GO].") AnnotationAssertion( "EHDAA2:0000741") AnnotationAssertion( "EHDAA:3049") AnnotationAssertion( "EMAPA:16843") @@ -190184,7 +188803,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatic duct") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -190199,6 +188817,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "abdomen element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal segment element) @@ -190211,6 +188831,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "abdominal segment element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal region element) @@ -190225,6 +188846,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal region element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest organ) @@ -190237,14 +188860,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chest organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tooth enamel organ) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010747") Annotation( "Wikipedia:Enamel_organ") Annotation( "https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107") Annotation( "https://github.com/obophenotype/uberon/issues/1313") "A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005138") Annotation( "TAO") Annotation( "ZFIN:curator") "A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]") -AnnotationAssertion( "NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]") -AnnotationAssertion( "Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation") AnnotationAssertion( "BTO:0001722") AnnotationAssertion( "CALOHA:TS-0271") AnnotationAssertion( "EMAPA:32888") @@ -190265,9 +188887,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment ". Alternate definition: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla.") AnnotationAssertion(rdfs:label "tooth enamel organ") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk region element) @@ -190281,6 +188903,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk region element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic cavity element) @@ -190294,7 +188918,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic cavity element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic region element) @@ -190311,6 +188937,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic region element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic segment organ) @@ -190323,6 +188951,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic segment organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair medulla) @@ -190339,6 +188968,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal medulla collecting duct) @@ -190353,6 +188985,9 @@ AnnotationAssertion( "UBERON:0005185") AnnotationAssertion(rdfs:label "renal medulla collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deferent duct artery) @@ -190372,7 +189007,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "deferent duct artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (thoracic vein) @@ -190387,6 +189025,8 @@ AnnotationAssertion( "UBERON:0005194") AnnotationAssertion(rdfs:label "thoracic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (deferent duct vein) @@ -190397,6 +189037,9 @@ AnnotationAssertion( "UBERON:0005195") AnnotationAssertion(rdfs:label "deferent duct vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spleen germinal center) @@ -190416,24 +189059,25 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen germinal center") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical mammary gland) AnnotationAssertion(Annotation( "OBOL:automatic") "A mammary gland that is part of a cervical region.") -AnnotationAssertion( "mice have a single pair of cervical mammary glands") AnnotationAssertion( "MA:0000789") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005199") AnnotationAssertion(rdfs:label "cervical mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic mammary gland) AnnotationAssertion(Annotation( "Wikipedia:Mammary_gland#Other_mammals") Annotation( "https://orcid.org/0000-0002-6601-2165") "A lactiferous gland that is located in the thoracic region/breast.") -AnnotationAssertion( "Most primates have one pair of mammary glands, which are thoracic.") -AnnotationAssertion( ) AnnotationAssertion(Annotation( "FMA:62088") Annotation( ) "lactiferous gland") AnnotationAssertion(Annotation( "FMA:62088") Annotation( ) "mammary gland") AnnotationAssertion( "EHDAA2:0001056") @@ -190450,18 +189094,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (distal straight tubule macula densa) AnnotationAssertion(Annotation( "OBOL:automatic") "A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition].") AnnotationAssertion( "TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment") -AnnotationAssertion( "EMAPA:28399") AnnotationAssertion( "MA:0002604") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005202") AnnotationAssertion(rdfs:label "distal straight tubule macula densa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -190469,7 +189115,6 @@ SubClassOf(Annotation( "MA" AnnotationAssertion(Annotation( "ISBN:1451113412") Annotation( "MGI:Anna") Annotation( "PMID:15973734") Annotation( "http://medical-dictionary.thefreedictionary.com/tracheal+glands") Annotation( "https://github.com/obophenotype/uberon/issues/1197") "A tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen.") AnnotationAssertion( ) -AnnotationAssertion( "These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents.") AnnotationAssertion( "EMAPA:36574") AnnotationAssertion( "FMA:7473") AnnotationAssertion( "MA:0002937") @@ -190484,6 +189129,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trachea gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (larynx submucosa gland) @@ -190496,6 +189143,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "larynx submucosa gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of vagina) @@ -190507,6 +189157,10 @@ AnnotationAssertion(Annotation( "UBERON:0005205") AnnotationAssertion(rdfs:label "lamina propria of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroid plexus stroma) @@ -190518,6 +189172,10 @@ AnnotationAssertion( "UBERON:0005206") AnnotationAssertion(rdfs:label "choroid plexus stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -190532,6 +189190,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right atrium valve) @@ -190546,11 +189206,13 @@ AnnotationAssertion(Annotation( "UBERON:0005208") AnnotationAssertion(rdfs:label "right atrium valve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal medulla interstitium) AnnotationAssertion(Annotation( "Wikipedia:Bone_marrow_of_ovaryry_interstitium") "Tissue surrounding the loop of Henle in the renal medulla.") -AnnotationAssertion( "It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct.") AnnotationAssertion( "EMAPA:18326") AnnotationAssertion( "MA:0002619") AnnotationAssertion( "SCTID:245693005") @@ -190564,6 +189226,8 @@ AnnotationAssertion(Annotation( "UBERON:0005211") AnnotationAssertion(rdfs:label "renal medulla interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -190583,8 +189247,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Leydig cell region of testis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer renal medulla interstitium) @@ -190597,6 +189265,7 @@ AnnotationAssertion( "UBERON:0005213") AnnotationAssertion(rdfs:label "outer renal medulla interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -190612,6 +189281,7 @@ AnnotationAssertion(Annotation( "UBERON:0005214") AnnotationAssertion(rdfs:label "inner renal medulla interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -190620,8 +189290,6 @@ SubClassOf(Annotation( "MA" AnnotationAssertion(Annotation( "DOI:10.1038/ki.1991.49") Annotation( "PMID:18575881") Annotation( "http://orcid.org/0000-0002-6601-2165") "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.") AnnotationAssertion( "See https://sourceforge.net/p/geneontology/ontology-requests/10941/") AnnotationAssertion( ) -AnnotationAssertion( "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment.") -AnnotationAssertion( "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue.") AnnotationAssertion( "EMAPA:28518") AnnotationAssertion( "FMA:70983") AnnotationAssertion( "MA:0002616") @@ -190639,26 +189307,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (optic eminence surface ectoderm) - -AnnotationAssertion(Annotation( "OBOL:automatic") "An external ectoderm that is part of a optic eminence [Automatically generated definition].") -AnnotationAssertion( "EMAPA:16539") -AnnotationAssertion( "RETIRED_EHDAA2:0001311") -AnnotationAssertion( "VHOG:0000520") -AnnotationAssertion( "uberon") -AnnotationAssertion( "UBERON:0005216") -AnnotationAssertion(rdfs:label "optic eminence surface ectoderm") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) - # Class: (midbrain subarachnoid space) AnnotationAssertion(Annotation( "OBOL:automatic") "A subarachnoid space that is part of a midbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001304") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG]") AnnotationAssertion( "EMAPA:19055") AnnotationAssertion( "VHOG:0001304") AnnotationAssertion(Annotation( "VHOG:0001304") "subarachnoid space midbrain") @@ -190667,11 +189323,12 @@ AnnotationAssertion(Annotation( "UBERON:0005217") AnnotationAssertion(rdfs:label "midbrain subarachnoid space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diencephalon subarachnoid space) AnnotationAssertion(Annotation( "OBOL:automatic") "A subarachnoid space that is part of a diencephalon [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001302") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG]") AnnotationAssertion( "EMAPA:19053") AnnotationAssertion( "VHOG:0001302") AnnotationAssertion(Annotation( "VHOG:0001302") "subarachnoid space diencephalon") @@ -190679,11 +189336,12 @@ AnnotationAssertion( "UBERON:0005218") AnnotationAssertion(rdfs:label "diencephalon subarachnoid space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain subarachnoid space) AnnotationAssertion(Annotation( "OBOL:automatic") "A subarachnoid space that is part of a hindbrain [Automatically generated definition].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001303") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG]") AnnotationAssertion( "EMAPA:18211") AnnotationAssertion( "VHOG:0001303") AnnotationAssertion(Annotation( "VHOG:0001303") "subarachnoid space hindbrain") @@ -190692,6 +189350,8 @@ AnnotationAssertion(Annotation( "UBERON:0005219") AnnotationAssertion(rdfs:label "hindbrain subarachnoid space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver right lobe parenchyma) @@ -190705,6 +189365,8 @@ AnnotationAssertion( "UBERON:0005221") AnnotationAssertion(rdfs:label "liver right lobe parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver left lobe parenchyma) @@ -190718,6 +189380,8 @@ AnnotationAssertion( "UBERON:0005222") AnnotationAssertion(rdfs:label "liver left lobe parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper leg epithelium) @@ -190729,6 +189393,8 @@ AnnotationAssertion( "UBERON:0005225") AnnotationAssertion(rdfs:label "upper leg epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pedal digit epithelium) @@ -190744,6 +189410,8 @@ AnnotationAssertion( "pedal digit epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (manual digit epithelium) @@ -190760,6 +189428,8 @@ AnnotationAssertion( "manual digit epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (upper arm epithelium) @@ -190772,6 +189442,8 @@ AnnotationAssertion( "UBERON:0005228") AnnotationAssertion(rdfs:label "upper arm epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (lower leg epithelium) @@ -190784,6 +189456,8 @@ AnnotationAssertion( "UBERON:0005229") AnnotationAssertion(rdfs:label "lower leg epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (medial-nasal process ectoderm) @@ -190797,8 +189471,9 @@ AnnotationAssertion( "UBERON:0005233") AnnotationAssertion(rdfs:label "medial-nasal process ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic eminence ectoderm) @@ -190811,10 +189486,11 @@ AnnotationAssertion( "UBERON:0005234") AnnotationAssertion(rdfs:label "optic eminence ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basal plate metencephalon) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000320") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]") AnnotationAssertion( "EHDAA2:0001154") AnnotationAssertion( "EMAPA:17078") AnnotationAssertion( "VHOG:0000320") @@ -190838,6 +189514,8 @@ AnnotationAssertion(Annotation( "UBERON:0005243") AnnotationAssertion(rdfs:label "interventricular septum endocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bulbus cordis myocardium) @@ -190849,17 +189527,21 @@ AnnotationAssertion(Annotation( "UBERON:0005248") AnnotationAssertion(rdfs:label "bulbus cordis myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metanephric renal pelvis) AnnotationAssertion(Annotation( "OBOL:automatic") "A renal pelvis that is part of a metanephros.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000945") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639") Annotation( "http://bgee.unil.ch/") "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]") AnnotationAssertion( "VHOG:0000945") AnnotationAssertion(Annotation( "VHOG:0000945") "metanephros pelvis") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005249") AnnotationAssertion(rdfs:label "metanephric renal pelvis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomatodeum gland) @@ -190872,12 +189554,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomatodeum gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (yolk sac cavity) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical cavity that is part of a yolk sac [Automatically generated definition].") -AnnotationAssertion(Annotation( "ISBN:0073040584") "In mammals, the yolk sac cavity contains fluid rather than platelets") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2, there are separate primary and secondary yolk sac cavities") AnnotationAssertion( "EMAPA:16055") AnnotationAssertion( "FMA:63942") AnnotationAssertion( "VHOG:0000843") @@ -190888,11 +189570,14 @@ AnnotationAssertion(Annotation( "UBERON:0005251") AnnotationAssertion(rdfs:label "yolk sac cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head mesenchyme) AnnotationAssertion(Annotation( "ISBN:0683400088") Annotation( "MP:0011260") "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000113") Annotation( "TAO") Annotation( "ZFIN:curator") "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]") AnnotationAssertion( "EFO:0003492") AnnotationAssertion( "EHDAA2:0000732") AnnotationAssertion( "EHDAA:179") @@ -190912,6 +189597,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (upper leg mesenchyme) @@ -190924,6 +189612,8 @@ AnnotationAssertion( "UBERON:0005254") AnnotationAssertion(rdfs:label "upper leg mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit mesenchyme) @@ -190939,6 +189629,10 @@ AnnotationAssertion(Annotation( "UBERON:0005255") AnnotationAssertion(rdfs:label "pedal digit mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (trunk mesenchyme) @@ -190958,6 +189652,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (manual digit mesenchyme) @@ -190977,6 +189674,10 @@ AnnotationAssertion(Annotation( "UBERON:0005257") AnnotationAssertion(rdfs:label "manual digit mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper arm mesenchyme) @@ -190989,6 +189690,8 @@ AnnotationAssertion( "UBERON:0005258") AnnotationAssertion(rdfs:label "upper arm mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower leg mesenchyme) @@ -191000,6 +189703,8 @@ AnnotationAssertion( "UBERON:0005259") AnnotationAssertion(rdfs:label "lower leg mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal cortex artery) @@ -191014,7 +189719,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal cortex artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal cortex vein) @@ -191029,13 +189737,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal cortex vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal cortex interstitium) AnnotationAssertion(Annotation( "PMID:18575881") "A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells.") -AnnotationAssertion(Annotation( "PMID:18575881") "In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c.") AnnotationAssertion( "EMAPA:28136") AnnotationAssertion( "MA:0002608") AnnotationAssertion( "SCTID:243707006") @@ -191047,6 +189757,8 @@ AnnotationAssertion(Annotation( "UBERON:0005270") AnnotationAssertion(rdfs:label "renal cortex interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -191093,13 +189805,11 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005275") AnnotationAssertion(rdfs:label "dorsal skin of digit") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (dorsal skin of finger) AnnotationAssertion(Annotation( "OBOL:automatic") "A dorsal skin of digit that is part of a manual digit.") -AnnotationAssertion(Annotation( "FMA") "this class is explicitly the union of the two FMA classes") AnnotationAssertion( "FMA:38320") AnnotationAssertion( "FMA:60346") AnnotationAssertion( "dorsal finger skin") @@ -191109,11 +189819,12 @@ AnnotationAssertion( "UBERON:0005276") AnnotationAssertion(rdfs:label "dorsal skin of finger") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (dorsal skin of toe) AnnotationAssertion(Annotation( "OBOL:automatic") "A dorsal skin of digit that is part of a pedal digit.") -AnnotationAssertion(Annotation( "FMA") "this class is explicitly the union of the two FMA classes") AnnotationAssertion( "FMA:37868") AnnotationAssertion( "FMA:60523") AnnotationAssertion( "dorsal toe skin") @@ -191123,6 +189834,8 @@ AnnotationAssertion( "UBERON:0005277") AnnotationAssertion(rdfs:label "dorsal skin of toe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (ventricular system of central nervous system) @@ -191149,11 +189862,11 @@ AnnotationAssertion( "ventricular system of central nervous system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png"^^xsd:anyURI) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventricular system of brain) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000005") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") AnnotationAssertion( "CALOHA:TS-1295") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37447") AnnotationAssertion( "FMA:242787") @@ -191163,15 +189876,13 @@ AnnotationAssertion( "UBERON:0005282") AnnotationAssertion(rdfs:label "ventricular system of brain") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tela choroidea) AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Tela_chorioidea") Annotation( "http://isc.temple.edu/neuroanatomy/lab/embryo_new/choroid/") "A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm].") -AnnotationAssertion(Annotation( "ZFA:0000447") "Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447].") -AnnotationAssertion( "Vascularized tela choroidea is choroid plexus.") -AnnotationAssertion(Annotation( "ZFA") "Note that the structure in ZFA may be different") AnnotationAssertion( "FMA:242849") AnnotationAssertion( "TAO:0000447") AnnotationAssertion( "Wikipedia:Tela_chorioidea") @@ -191191,7 +189902,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (tela choroidea of fourth ventricle) AnnotationAssertion(Annotation( "Wikipedia:Tela_chorioidea_of_fourth_ventricle") Annotation( "ZFIN:curator") "Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005158") Annotation( "TAO") Annotation( "ZFIN:curator") "Tela chorioidea that lines the fourth ventricle.[TAO]") AnnotationAssertion(Annotation( "FMA:78493") Annotation( "FMA:TA") "tela choroidea") AnnotationAssertion( "BAMS:tc4v") AnnotationAssertion( "FMA:78493") @@ -191212,6 +189922,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tela choroidea of fourth ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -191235,15 +189946,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tela choroidea of telencephalic ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myelencephalon) AnnotationAssertion(Annotation( "BTO:0000758") Annotation( "Wikipedia:Myelencephalon") "The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000456") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/myelencephalon") "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000456") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") -AnnotationAssertion( "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes") AnnotationAssertion( "BTO:0000758") AnnotationAssertion( "CALOHA:TS-0607") AnnotationAssertion( "CALOHA:TS-2365") @@ -191253,7 +189962,6 @@ AnnotationAssertion( "EMAPA:17082") AnnotationAssertion( "HBA:9512") AnnotationAssertion( "MA:0000205") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D054024") AnnotationAssertion( "VHOG:0000456") AnnotationAssertion( "Wikipedia:Myelencephalon") AnnotationAssertion( "uberon") @@ -191262,9 +189970,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myelencephalon") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic tissue) @@ -191278,6 +189985,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic tissue) @@ -191294,12 +190002,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extraembryonic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gonadal ridge) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0011411") "The elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary.") AnnotationAssertion( "TODO - check developmental relationships. merge with urogenital ridge?") -AnnotationAssertion( "in eutherians, SRY transforms the indifferent gonad into testes") AnnotationAssertion( "AAO:0011047") AnnotationAssertion( "BTO:0001402") AnnotationAssertion( "EFO:0001414") @@ -191325,15 +190034,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gonadal ridge") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sex cord) AnnotationAssertion(Annotation( "Wikipedia:Sex_cords") Annotation( "http://www.answers.com/topic/sex-cord") "Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female.") -AnnotationAssertion( "EHDAA2:0004051") AnnotationAssertion( "NCIT:C34183") AnnotationAssertion( "RETIRED_EHDAA2:0001523") AnnotationAssertion( "SCTID:343823004") @@ -191347,7 +190054,8 @@ AnnotationAssertion( "UBERON:0005295") AnnotationAssertion(rdfs:label "sex cord") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovary sex cord) @@ -191371,6 +190079,8 @@ AnnotationAssertion( "UBERON:0005296") AnnotationAssertion(rdfs:label "ovary sex cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (testis sex cord) @@ -191391,6 +190101,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "testis sex cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (skin of clitoris) @@ -191403,11 +190115,13 @@ AnnotationAssertion( "UBERON:0005298") AnnotationAssertion(rdfs:label "skin of clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prepuce of clitoris) AnnotationAssertion(Annotation( "Wikipedia:Clitoral_hood") Annotation( "http://orcid.org/0000-0002-6601-2165") "A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans.") -AnnotationAssertion( "FMA has FMA:27886 skin of prepuce of clitoris") AnnotationAssertion( "EMAPA:30699") AnnotationAssertion( "FMA:20169") AnnotationAssertion( "NCIT:C32590") @@ -191425,25 +190139,27 @@ AnnotationAssertion( "prepuce of clitoris") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric nephron) AnnotationAssertion(Annotation( "GO:0039019") "A pronephric nephron is the functional unit of the pronephros[GO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011091") Annotation( "AAO") Annotation( "UBERON:0005309") "The structure that is the basic functional unit of the pronephros.[AAO]") AnnotationAssertion( "AAO:0011091") AnnotationAssertion( "XAO:0000285") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005309") AnnotationAssertion(rdfs:label "pronephric nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric nephron tubule) AnnotationAssertion(Annotation( "GO:0039020") "The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO].") -AnnotationAssertion(Annotation( "ISBN:0073040584") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001558") Annotation( "TAO") Annotation( "ZFIN:curator") "Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]") AnnotationAssertion( "TAO:0001558") AnnotationAssertion( "XAO:0004105") AnnotationAssertion( "ZFA:0001558") @@ -191453,13 +190169,14 @@ AnnotationAssertion(Annotation( "UBERON:0005310") AnnotationAssertion(rdfs:label "pronephric nephron tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "GO") ObjectSomeValuesFrom( )) # Class: (mammary placode) AnnotationAssertion(Annotation( "GO:0060596") "The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO].") AnnotationAssertion( "TODO develops_from") -AnnotationAssertion( "in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP]") AnnotationAssertion( "EMAPA:35541") AnnotationAssertion( "uberon") AnnotationAssertion( "mammary anlage") @@ -191479,6 +190196,8 @@ AnnotationAssertion( "UBERON:0005316") AnnotationAssertion(rdfs:label "endocardial endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary artery endothelium) @@ -191489,6 +190208,8 @@ AnnotationAssertion( "UBERON:0005317") AnnotationAssertion(rdfs:label "pulmonary artery endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric collecting duct) @@ -191499,6 +190220,8 @@ AnnotationAssertion( "UBERON:0005319") AnnotationAssertion(rdfs:label "mesonephric collecting duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric juxtaglomerular apparatus) @@ -191508,6 +190231,9 @@ AnnotationAssertion( "UBERON:0005320") AnnotationAssertion(rdfs:label "mesonephric juxtaglomerular apparatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric smooth muscle tissue) @@ -191516,11 +190242,12 @@ AnnotationAssertion( "UBERON:0005321") AnnotationAssertion(rdfs:label "mesonephric smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric nephron) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A nephron that is part of a mesonephros.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010387") Annotation( "AAO") Annotation( "PMID:9268568") "The structure that is the basic functional unit of the kidney.[AAO]") AnnotationAssertion( "AAO:0010387") AnnotationAssertion( "XAO:0000292") AnnotationAssertion( "ZFA:0005592") @@ -191530,6 +190257,9 @@ AnnotationAssertion(Annotation( "UBERON:0005322") AnnotationAssertion(rdfs:label "mesonephric nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) # Class: (mesonephric mesenchyme) @@ -191544,6 +190274,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesonephric mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric macula densa) @@ -191552,24 +190285,24 @@ AnnotationAssertion( "UBERON:0005324") AnnotationAssertion(rdfs:label "mesonephric macula densa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric glomerulus) AnnotationAssertion(Annotation( "GO:0061224") "The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010388") Annotation( "AAO") Annotation( "AAO:BJB") "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001238") Annotation( "VHOG") Annotation( "ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3") Annotation( "http://bgee.unil.ch/") "In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "XAO/AAO class belongs here, as it refers to mesonephric structure") AnnotationAssertion(Annotation( "AAO:0010388") Annotation( ) "glomerulus") AnnotationAssertion( "AAO:0010388") AnnotationAssertion( "EMAPA:30568") -AnnotationAssertion( "SCTID:362217000") AnnotationAssertion( "VHOG:0001238") AnnotationAssertion( "XAO:0000146") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005325") AnnotationAssertion(rdfs:label "mesonephric glomerulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric glomerulus vasculature) @@ -191578,6 +190311,7 @@ AnnotationAssertion( "UBERON:0005326") AnnotationAssertion(rdfs:label "mesonephric glomerulus vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric glomerular epithelium) @@ -191587,7 +190321,8 @@ AnnotationAssertion( "UBERON:0005327") AnnotationAssertion(rdfs:label "mesonephric glomerular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric comma-shaped body) @@ -191597,6 +190332,8 @@ AnnotationAssertion( "UBERON:0005328") AnnotationAssertion(rdfs:label "mesonephric comma-shaped body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric nephron tubule) @@ -191605,8 +190342,9 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005329") AnnotationAssertion(rdfs:label "mesonephric nephron tubule") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (mesonephric nephron epithelium) @@ -191615,6 +190353,8 @@ AnnotationAssertion( "UBERON:0005330") AnnotationAssertion(rdfs:label "mesonephric nephron epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric renal vesicle) @@ -191627,6 +190367,8 @@ AnnotationAssertion( "UBERON:0005331") AnnotationAssertion(rdfs:label "mesonephric renal vesicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -191637,11 +190379,12 @@ AnnotationAssertion( "UBERON:0005332") AnnotationAssertion(rdfs:label "mesonephric S-shaped body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary bud) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland.") -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/mammary+bud") "produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts") AnnotationAssertion( "UBERON:0004181") AnnotationAssertion( "EMAPA:35536") AnnotationAssertion( "lactiferous gland bud") @@ -191652,6 +190395,9 @@ AnnotationAssertion( "UBERON:0005333") AnnotationAssertion(rdfs:label "mammary bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (oral lamina propria) @@ -191662,6 +190408,8 @@ AnnotationAssertion( "UBERON:0005334") AnnotationAssertion(rdfs:label "oral lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract of ventricle) @@ -191676,6 +190424,8 @@ AnnotationAssertion( "UBERON:0005337") AnnotationAssertion(rdfs:label "outflow tract of ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract aortic component) @@ -191689,6 +190439,8 @@ AnnotationAssertion( "UBERON:0005338") AnnotationAssertion(rdfs:label "outflow tract aortic component") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow tract pulmonary component) @@ -191706,15 +190458,12 @@ SubClassOf( (cortical plate) AnnotationAssertion(Annotation( "MP:0008439") Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK10047") "The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP].") -AnnotationAssertion( "A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047]") -AnnotationAssertion( "in humans develops into cortical layers II-VI") AnnotationAssertion(Annotation( "BRAINSPAN:BRAINSPAN") Annotation( ) "CP") AnnotationAssertion(Annotation( "PMID:23375746") Annotation( ) "CxP") AnnotationAssertion( "BAMS:CTXpl") AnnotationAssertion( "DHBA:10515") AnnotationAssertion( "EMAPA:32711") AnnotationAssertion( "MBA:695") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D002540") AnnotationAssertion( "PBA:294021914") AnnotationAssertion( "neuronames:2702") AnnotationAssertion( "cerebral cortex cortical plate") @@ -191745,6 +190494,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spermatic cord") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -191753,11 +190504,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (Rathke's pouch) AnnotationAssertion(Annotation( "MP:0003817") Annotation( "Wikipedia:Rathke's_pouch") "A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP].") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000674") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/rathke's+pouch") "A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000674") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5") Annotation( "http://bgee.unil.ch/") "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]") -AnnotationAssertion(Annotation( "http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html") "median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus).") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium.") AnnotationAssertion( "AAO:0011094") AnnotationAssertion( "EHDAA2:0001588") AnnotationAssertion( "EMAPA:16725") @@ -191791,6 +190537,7 @@ AnnotationAssertion( "Rathke's pouch") SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK53175") ObjectSomeValuesFrom( )) @@ -191798,7 +190545,6 @@ SubClassOf(Annotation( "NCB # Class: (brain ependyma) AnnotationAssertion(Annotation( "ISBN:0387949542") Annotation( "http://orcid.org/0000-0002-6601-2165") "The ependymal cell layer that lines the brain ventricles.") -AnnotationAssertion(Annotation( "FMA") "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion") AnnotationAssertion( "EMAPA:35183") AnnotationAssertion( "FMA:242837") AnnotationAssertion( "MA:0000809") @@ -191809,6 +190555,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain ependyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventricle of nervous system) @@ -191827,7 +190575,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (spinal cord ependyma) AnnotationAssertion(Annotation( "ISBN:0387949542") Annotation( "http://orcid.org/0000-0002-6601-2165") "The ependymal cell layer that lines the spinal cord.") -AnnotationAssertion(Annotation( "FMA") "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion") AnnotationAssertion( "EMAPA:35791") AnnotationAssertion( "FMA:242839") AnnotationAssertion( "MA:0001125") @@ -191840,6 +190587,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spinal cord ependyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -191870,12 +190618,11 @@ AnnotationAssertion( "vagus X ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory lobe) AnnotationAssertion(Annotation( "UBERON:cjm") "The lobe at the anterior part of each cerebral hemisphere, responsible for olfactory functions.") -AnnotationAssertion(Annotation( "XAO:0004180") "Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000833") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)") Annotation( "http://bgee.unil.ch/") "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]") AnnotationAssertion( "BTO:0001362") AnnotationAssertion( "EFO:0000108") AnnotationAssertion( "EHDAA2_RETIRED:0001294") @@ -191893,7 +190640,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory lobe") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus granule cell layer) @@ -191906,6 +190652,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hippocampus granule cell layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus stratum oriens) @@ -191928,11 +190676,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hippocampus stratum oriens") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus stratum radiatum) AnnotationAssertion(Annotation( "BIRNLEX:1298") "The layer located immediately above the pyramidal cell layer in CA2 and CA1 and superficial to the stratum lucidum in CA3. Suprapyramidal region in which CA3 to CA3 associational connections and CA3 to CA1 Schaffer collateral connections are located.") -AnnotationAssertion( "contains septal and commissural fibers. It also contains Schaffer collateral fibers, which are the projection forward from CA3 to CA1. Some interneurons that can be found in more superficial layers can also be found here, including basket cells, bistratified cells, and radial trilaminar cells") AnnotationAssertion( "BAMS:Rad") AnnotationAssertion( "BIRNLEX:1298") AnnotationAssertion( "EMAPA:35413") @@ -191948,12 +190698,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hippocampus stratum radiatum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord ventral column) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0009679") "The area of white matter of the spinal cord located on either side of the ventral (anterior) medial fissure.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001622") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/anterior+column+of+spinal+cord") "The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "MA") "in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column.") AnnotationAssertion( "EV:0100326") AnnotationAssertion( "MA:0002751") AnnotationAssertion( "VHOG:0001622") @@ -192059,17 +190810,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dentate gyrus granule cell layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal striatum) AnnotationAssertion(Annotation( "NLXANAT:1010001") "Dorsal components of the striatum comprising the caudate nucleus and the putamen, in species that have distinct nuclei; the caudoputamen in species which don't.") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_striatum") "According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_striatum") "According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (putamen and the globus pallidus) and the caudate nucleus") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_striatum") "It may also refer to both the basal ganglia and the internal capsule collectively.") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_striatum") "It may also refer to the putamen and caudate collectively.") -AnnotationAssertion(Annotation( "neuronames:2340") "The term dorsal striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes most of the striatum ( Heimer-1995 ). The boundary between this structure and the ventral striatum is indistinct in sections stained for Nissl substance.") AnnotationAssertion( "BAMS:Dorsal_striatum") AnnotationAssertion( "BAMS:STRd") AnnotationAssertion( "BAMS:StrD") @@ -192092,7 +190840,7 @@ AnnotationAssertion(Annotation( "BTO:0004701") "striatum dorsale") AnnotationAssertion( "UBERON:0005382") AnnotationAssertion(rdfs:label "dorsal striatum") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -192102,7 +190850,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "NLXANAT:100312") "Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure.") AnnotationAssertion( "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)") AnnotationAssertion( "we do not currently place rodent-specific taxon constraints here as this would cause taxon violations. There is an argument for merging this into dorsal striatum and treating the distinction as phenotypic") -AnnotationAssertion( "In the human, histologically the caudate nucleus and putamen are identically and share a common embryological origin[ISBN:0123813611]") AnnotationAssertion( "BAMS:CP") AnnotationAssertion( "BAMS:CPu") AnnotationAssertion( "BM:Tel-C-Pu") @@ -192154,6 +190901,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasal cavity epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -192171,12 +190922,12 @@ AnnotationAssertion( "UBERON:0005385") AnnotationAssertion(rdfs:label "nasal cavity respiratory epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Wikipedia") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory segment of nasal mucosa) AnnotationAssertion(Annotation( "MESH:A04.531.520.573") Annotation( "Wikipedia:Olfactory_mucosa") "That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH].") -AnnotationAssertion(Annotation( "Wikipedia:Olfactory_mucosa") "The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa].") AnnotationAssertion( "CALOHA:TS-2197") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37918") AnnotationAssertion( "FMA:77199") @@ -192196,23 +190947,27 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory segment of nasal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (photoreceptor array) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An array of photoreceptors and any supporting cells found in an eye.") -AnnotationAssertion(Annotation( ) "FBbt:00004200") AnnotationAssertion( "light-sensitive tissue") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005388") AnnotationAssertion(rdfs:label "photoreceptor array") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transparent eye structure) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.") -AnnotationAssertion( "directing or focusing light onto light receptors") AnnotationAssertion( "lens") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005389") @@ -192327,8 +191082,6 @@ SubClassOf(Annotation( "BRA # Class: (cortical layer IV) AnnotationAssertion(Annotation( "NLXANAT:090810") "Layer of neocortex lying deep to the external pyramidal cell layer defined cytoarchitecturally by the presence of numerous small cells.") -AnnotationAssertion(Annotation( "PMID:23027930") "...") -AnnotationAssertion(Annotation( "ISBN:0471888893") "Relatively undeveloped in some mammals such as the tenrec.") AnnotationAssertion( "ABA:CTX4") AnnotationAssertion( "EMAPA:35258") AnnotationAssertion( "FMA:77811") @@ -192435,7 +191188,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Carotid_artery") Annotation( "https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764") "One of: the common carotid artery, or its branches, the external and internal carotid arteries.") AnnotationAssertion( "This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000097") Annotation( "TAO") Annotation( "ZFIN:curator") "Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]") AnnotationAssertion( "AAO:0010217") AnnotationAssertion( "BTO:0000168") AnnotationAssertion( "CALOHA:TS-0116") @@ -192473,8 +191225,6 @@ SubClassOf(Annotation( "FMA # Class: (brain arachnoid mater) AnnotationAssertion(Annotation( "OBOL:automatic") "An arachnoid mater that surrounds a brain.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000230") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/arachnoid+mater") "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000230") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639") Annotation( "http://bgee.unil.ch/") "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:32661") AnnotationAssertion( "FMA:83981") AnnotationAssertion( "MA:0000814") @@ -192489,7 +191239,10 @@ AnnotationAssertion( "UBERON:0005397") AnnotationAssertion(rdfs:label "brain arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female reproductive gland) @@ -192502,6 +191255,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "female reproductive gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (male reproductive gland) @@ -192517,6 +191271,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male reproductive gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (telencephalon arachnoid mater) @@ -192528,11 +191284,12 @@ AnnotationAssertion( "UBERON:0005400") AnnotationAssertion(rdfs:label "telencephalon arachnoid mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cerebral hemisphere gray matter) AnnotationAssertion(Annotation( "OBOL:automatic") "A gray matter that is part of a cerebral hemisphere.") -AnnotationAssertion(Annotation( "BTO") "BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon") AnnotationAssertion( "BTO:0000823") AnnotationAssertion( "CALOHA:TS-2361") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37477") @@ -192545,11 +191302,12 @@ AnnotationAssertion( "UBERON:0005401") AnnotationAssertion(rdfs:label "cerebral hemisphere gray matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventral striatum) AnnotationAssertion(Annotation( "NLX:57107") "A composite structure of the telencephalon that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the anterior perforated substance, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance (Heimer-1995; adapted from Brain Info).") -AnnotationAssertion(Annotation( "neuronames:2341") "The term ventral striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the olfactory tubercle, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance ( Heimer-1995 ).") AnnotationAssertion( "BAMS:STRv") AnnotationAssertion( "BAMS:StrV") AnnotationAssertion( "BAMS:Ventral_striatum") @@ -192560,7 +191318,6 @@ AnnotationAssertion( "FMA:77614") AnnotationAssertion( "MA:0002972") AnnotationAssertion( "MBA:493") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066328") AnnotationAssertion( "NLX:57107") AnnotationAssertion( "PBA:10091") AnnotationAssertion( "Wikipedia:Ventral_striatum") @@ -192572,7 +191329,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ventral striatum") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -192605,13 +191362,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (circumventricular organ) AnnotationAssertion(Annotation( "MP:0013562") "Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow.") -AnnotationAssertion( "All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330)") -AnnotationAssertion( "CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006267") AnnotationAssertion( "EMAPA:35243") AnnotationAssertion( "FMA:84081") AnnotationAssertion( "MA:0002942") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066280") AnnotationAssertion( "NLXANAT:20090312") AnnotationAssertion( "Wikipedia:Circumventricular_organs") AnnotationAssertion( "neuronames:1242") @@ -192623,22 +191376,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "circumventricular organ") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (alimentary part of gastrointestinal system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the digestive system that excludes the hepatobiliary system.") AnnotationAssertion( "the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system") -AnnotationAssertion(Annotation( "ncithesaurus:Gastrointestinal_System") "The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000412") Annotation( "VHOG") Annotation( "ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3") Annotation( "http://bgee.unil.ch/") "All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]") -AnnotationAssertion(Annotation( "MA") "that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.") AnnotationAssertion( "BTO:0000058") AnnotationAssertion( "CALOHA:TS-0407") AnnotationAssertion( "EHDAA2:0000110") AnnotationAssertion( "EHDAA:514") AnnotationAssertion( "EMAPA:16246") -AnnotationAssertion( "EV:0100056") AnnotationAssertion( "FMA:71132") AnnotationAssertion( "GAID:294") AnnotationAssertion( "MA:0000323") @@ -192667,14 +191415,9 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cartilaginous otic capsule) AnnotationAssertion(Annotation( "OBOL:automatic") "An otic capsule endochondral element that is composed primarily of cartilage tissue.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001500") Annotation( "TAO") Annotation( "ZFIN:curator") "Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001500") Annotation( "TAO") "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001500") Annotation( "TAO") "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]") -AnnotationAssertion( "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA") AnnotationAssertion( "UBERON:0010351") AnnotationAssertion( "EHDAA2:0001333") AnnotationAssertion( "EHDAA:4704") -AnnotationAssertion( "EMAPA:17596") AnnotationAssertion( "EMAPA:18803") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37467") AnnotationAssertion( "TAO:0001500") @@ -192686,13 +191429,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cartilaginous otic capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (bony otic capsule) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0000039") "The cartilage or bony capsule surrounding the inner ear mechanism.") -AnnotationAssertion( "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)") -AnnotationAssertion( "EMAPA:17596") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37466") AnnotationAssertion( "MA:0000252") AnnotationAssertion( "otic capsule bone") @@ -192701,6 +191444,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bony otic capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -192727,13 +191473,14 @@ AnnotationAssertion( "Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995)") AnnotationAssertion(rdfs:label "forelimb bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (hindlimb bud) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A limb bud that develops into a hindlimb.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010382") Annotation( "AAO") Annotation( "XAO:curator") "The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]") AnnotationAssertion( "AAO:0010382") AnnotationAssertion( "EHDAA:2358") AnnotationAssertion( "EMAPA:16779") @@ -192751,12 +191498,13 @@ AnnotationAssertion( "Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick.") AnnotationAssertion(rdfs:label "hindlimb bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage bud) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb bud that develops into a forelimb or pectoral fin.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000141") Annotation( "TAO") Annotation( "ZFIN:curator") "Fin bud that develops into the pectoral fin.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001754") Annotation( "VHOG") Annotation( "DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)") Annotation( "http://bgee.unil.ch/") "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]") AnnotationAssertion( "EFO:0003430") AnnotationAssertion( "TAO:0000141") AnnotationAssertion( "VHOG:0001754") @@ -192771,15 +191519,15 @@ AnnotationAssertion( "at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future") AnnotationAssertion(rdfs:label "pectoral appendage bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage bud) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb bud that develops into a hindlimb or pelvic fin.") AnnotationAssertion(Annotation( "PMID:15893975") ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001384") Annotation( "TAO") Annotation( "ZFIN:curator") "Fin bud that develops into the pelvic fin.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001260") Annotation( "VHOG") Annotation( "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268") Annotation( "http://bgee.unil.ch/") "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]") AnnotationAssertion( "EFO:0003469") AnnotationAssertion( "TAO:0001384") AnnotationAssertion( "VHOG:0001260") @@ -192793,14 +191541,14 @@ AnnotationAssertion( "at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future") AnnotationAssertion(rdfs:label "pelvic appendage bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage apical ectodermal ridge) AnnotationAssertion(Annotation( "OBOL:automatic") "An apical ectodermal ridge that is part of a pectoral appendage bud.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001064") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge") "An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000085") Annotation( "TAO") Annotation( "ZFIN:curator") "Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001064") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1440-169X.2007.00942.x") Annotation( "http://bgee.unil.ch/") "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]") AnnotationAssertion( "EFO:0003487") AnnotationAssertion( "EHDAA2:0000138") AnnotationAssertion( "EMAPA:16778") @@ -192823,14 +191571,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral appendage apical ectodermal ridge") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pelvic appendage apical ectodermal ridge) AnnotationAssertion(Annotation( "OBOL:automatic") "An apical ectodermal ridge that is part of a pelvic appendage bud.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001066") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge") "An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001385") Annotation( "TAO") Annotation( "ZIFIN:curator") "Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001066") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1440-169X.2007.00942.x") Annotation( "http://bgee.unil.ch/") "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]") AnnotationAssertion( "EFO:0003681") AnnotationAssertion( "EHDAA2:0003194") AnnotationAssertion( "EMAPA:16892") @@ -192849,6 +191596,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic appendage apical ectodermal ridge") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (developing anatomical structure) @@ -192859,7 +191608,6 @@ AnnotationAssertion( "AEO:0000125") AnnotationAssertion( "CALOHA:TS-2122") AnnotationAssertion( "EHDAA2:0003125") -AnnotationAssertion(Annotation( ) "FBbt:00007006") AnnotationAssertion( "FMA:292313") AnnotationAssertion( "MIAA:0000019") AnnotationAssertion( "uberon") @@ -192875,7 +191623,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (presumptive retinal pigmented epithelium) AnnotationAssertion(Annotation( "ZFIN:curator") "Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000492") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001306") AnnotationAssertion( "EMAPA:16677") AnnotationAssertion( "TAO:0000064") @@ -192895,12 +191642,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive retinal pigmented epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive neural retina) AnnotationAssertion(Annotation( "ZFIN:curator") "Portion of tissue that is the inner layer of the optic cup and will become the neural retina.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000490") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001304") AnnotationAssertion( "EMAPA:16675") AnnotationAssertion( "TAO:0001071") @@ -192920,14 +191669,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive neural retina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens vesicle) AnnotationAssertion(Annotation( "ZFIN:curator") Annotation( "https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834") "Portion of tissue that gives rise to the lens.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001163") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/lens+vesicle") "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001163") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]") -AnnotationAssertion(Annotation( "ZFA") "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals") AnnotationAssertion( "EHDAA2:0000983") AnnotationAssertion( "EHDAA:4737") AnnotationAssertion( "EMAPA:17163") @@ -192946,6 +191695,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lens vesicle") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (corneal primordium) @@ -192958,15 +191708,13 @@ AnnotationAssertion( "corneal primordium") SubClassOf(Annotation( "ZFA") ) SubClassOf(Annotation( "Obol") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (vagal neural crest) AnnotationAssertion(Annotation( "ZFIN:curator") "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000818") Annotation( "TAO") Annotation( "ZFIN:curator") "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001208") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") -AnnotationAssertion(Annotation( "filemaps.com") "In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)") AnnotationAssertion( "EHDAA2:0002156") AnnotationAssertion( "EHDAA:669") AnnotationAssertion( "TAO:0000818") @@ -192980,13 +191728,13 @@ AnnotationAssertion(Annotation( "UBERON:0005428") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vagal neural crest") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (aortic sac) AnnotationAssertion(Annotation( "MP:0012510") "The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.") -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/aortic+sac") "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].") AnnotationAssertion( "EHDAA2:0004145") AnnotationAssertion( "EHDAA:9826") AnnotationAssertion( "EMAPA:36461") @@ -193000,7 +191748,7 @@ AnnotationAssertion( "aortic sac") SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -193058,13 +191806,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "segment of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (foramen rotundum) AnnotationAssertion(Annotation( "Wikipedia:Foramen_rotundum") "The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001543") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001543") Annotation( "VHOG") Annotation( "PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)") Annotation( "http://bgee.unil.ch/") "It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]") -AnnotationAssertion(Annotation( "AAO") "todo - check placement of AAO class") AnnotationAssertion( "AAO:0000194") AnnotationAssertion( "EHDAA2:0000552") AnnotationAssertion( "EHDAA:10629") @@ -193081,6 +191829,10 @@ AnnotationAssertion( "foramen rotundum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (segment of manus) @@ -193097,19 +191849,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "segment of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jugular foramen) AnnotationAssertion(Annotation( "Wikipedia:Jugular_foramen") "The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000249") Annotation( "AAO") Annotation( "AAO:LAP") "Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001113") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/jugular+foramen") "One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000249") Annotation( "AAO") "relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]") AnnotationAssertion( "AAO:0000249") AnnotationAssertion( "EHDAA2:0000893") AnnotationAssertion( "EHDAA:10631") AnnotationAssertion( "EMAPA:18713") AnnotationAssertion( "FMA:56432") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000080869") AnnotationAssertion( "NCIT:C12496") AnnotationAssertion( "SCTID:361735006") AnnotationAssertion(Annotation( "ncithesaurus:Jugular_Foramen") "UMLS:C0222712") @@ -193122,15 +191873,15 @@ AnnotationAssertion( "jugular foramen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left thymus lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A thymus lobe that is in the left side of a thymus.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:71195") AnnotationAssertion( "RETIRED_EHDAA2:0000964") AnnotationAssertion( "SCTID:188079002") @@ -193142,6 +191893,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left umbilical artery) @@ -193154,13 +191907,12 @@ AnnotationAssertion( "UBERON:0005458") AnnotationAssertion(rdfs:label "left umbilical artery") SubClassOf( ) -SubClassOf(Annotation( "check this") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "check this") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left umbilical vein) AnnotationAssertion(Annotation( "OBOL:automatic") "An umbilical vein that is in the left side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0000967") AnnotationAssertion( "EMAPA:16358") AnnotationAssertion( "EMAPA:16377") @@ -193170,11 +191922,13 @@ AnnotationAssertion( "UBERON:0005459") AnnotationAssertion(rdfs:label "left umbilical vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left vitelline vein) AnnotationAssertion(Annotation( "OBOL:automatic") "A vitelline vein that is in the left side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0000971") AnnotationAssertion( "EMAPA:16380") AnnotationAssertion( "EMAPA:16698") @@ -193184,6 +191938,9 @@ AnnotationAssertion( "UBERON:0005460") AnnotationAssertion(rdfs:label "left vitelline vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (levator scapulae muscle) @@ -193209,12 +191966,16 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Kardong") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "cervical nerve and dorsal scapular nerve") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Posterior tubercles of transverse processes of C1 - C4 vertebrae") Annotation( "dbpedia") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Superior part of medial border of scapula") Annotation( "dbpedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcapsular sinus of lymph node) @@ -193240,11 +192001,14 @@ AnnotationAssertion( "subcapsular sinus of lymph node") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right thymus lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A thymus lobe that is in the right side of a thymus.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:71194") AnnotationAssertion( "RETIRED_EHDAA2:0001758") AnnotationAssertion( "SCTID:187981000") @@ -193256,6 +192020,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right umbilical artery) @@ -193268,13 +192034,12 @@ AnnotationAssertion( "UBERON:0005470") AnnotationAssertion(rdfs:label "right umbilical artery") SubClassOf( ) -SubClassOf(Annotation( "check this") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "check this") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right umbilical vein) AnnotationAssertion(Annotation( "OBOL:automatic") "An umbilical vein that is in the right side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0001761") AnnotationAssertion( "EMAPA:16359") AnnotationAssertion( "EMAPA:16378") @@ -193284,11 +192049,13 @@ AnnotationAssertion( "UBERON:0005471") AnnotationAssertion(rdfs:label "right umbilical vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right vitelline vein) AnnotationAssertion(Annotation( "OBOL:automatic") "A vitelline vein that is in the right side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EHDAA2:0001766") AnnotationAssertion( "EMAPA:16381") AnnotationAssertion( "EMAPA:16699") @@ -193298,6 +192065,9 @@ AnnotationAssertion( "UBERON:0005472") AnnotationAssertion(rdfs:label "right vitelline vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal nerve trunk) @@ -193311,6 +192081,8 @@ AnnotationAssertion( "UBERON:0005476") AnnotationAssertion(rdfs:label "spinal nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach fundus epithelium) @@ -193326,6 +192098,7 @@ AnnotationAssertion( "UBERON:0005477") AnnotationAssertion(rdfs:label "stomach fundus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sulcus limitans of neural tube) @@ -193346,16 +192119,20 @@ SubClassOf(Annotation( "EHD AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Either of the two lateral lobes that constitute the thymus.") AnnotationAssertion( ) -AnnotationAssertion( "each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP]") AnnotationAssertion( "FMA:71193") AnnotationAssertion( "RETIRED_EHDAA2:0002021") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "lateral lobe of thymus") AnnotationAssertion(Annotation( "FMA:71193") "lobe of thymus") +AnnotationAssertion( "thymus subunit") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005483") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (venous dural sinus) @@ -193383,15 +192160,15 @@ AnnotationAssertion( "venous dural sinus") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitelline vein) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0010666") "The paired veins that carry blood from the yolk sac back to the embryo.") -AnnotationAssertion(Annotation( "XAO") Annotation( "XAO:0004147") "One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000401") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460") Annotation( "http://bgee.unil.ch/") "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]") -AnnotationAssertion(Annotation( "XAO") "check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO") AnnotationAssertion( "EMAPA:36021") AnnotationAssertion( "FMA:70305") AnnotationAssertion( "NCIT:C34329") @@ -193416,7 +192193,9 @@ AnnotationAssertion( "vitelline vein") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glossopharyngeal neural crest) @@ -193446,15 +192225,12 @@ AnnotationAssertion( "UBERON:0005496") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural tube lateral wall") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-neural ectoderm) AnnotationAssertion( "todo - epidermis? todo - track down EHDAA2 class in new release") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001372") Annotation( "VHOG") Annotation( "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)") Annotation( "http://bgee.unil.ch/") "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]") -AnnotationAssertion( "After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.") AnnotationAssertion( "EFO:0003643") AnnotationAssertion( "EHDAA:257") AnnotationAssertion( "EMAPA:16074") @@ -193475,12 +192251,11 @@ AnnotationAssertion( "Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).") AnnotationAssertion(rdfs:label "non-neural ectoderm") SubClassOf(Annotation( "ZFA") ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (primitive heart tube) AnnotationAssertion(Annotation( "ZFA:0000149") "Multi-tissue structure that arises from the heart rudiment and will become the heart tube.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006179") AnnotationAssertion( "EHDAA2:0001512") AnnotationAssertion( "EHDAA:424") AnnotationAssertion( "EHDAA:436") @@ -193497,14 +192272,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primitive heart tube") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (rhombomere 1) AnnotationAssertion(Annotation( "ZFA:0001031") "Hindbrain segment or neuromere 1.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001031") Annotation( "TAO") Annotation( "ZFIN:curator") "Hindbrain segment or neuromere. Kimmel et al, 1995.[TAO]") -AnnotationAssertion( "1"^^xsd:nonNegativeInteger) AnnotationAssertion( "DHBA:12667") AnnotationAssertion( "DMBA:16915") AnnotationAssertion( "EFO:0003608") @@ -193521,7 +192295,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rhombomere 1") SubClassOf( ) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rhombomere lateral wall) @@ -193533,13 +192307,13 @@ AnnotationAssertion(Annotation( "UBERON:0005501") AnnotationAssertion(rdfs:label "rhombomere lateral wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thymus primordium) AnnotationAssertion(Annotation( "ZFA:0001077") "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID].") AnnotationAssertion(Annotation( "ISBN:0781714125") "we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001077") Annotation( "TAO") Annotation( "ZFIN:curator") "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]") -AnnotationAssertion(Annotation( "ISBN:0781714125") "variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals") AnnotationAssertion( "EFO:0003622") AnnotationAssertion( "EHDAA2:0002023") AnnotationAssertion( "EHDAA:2969") @@ -193553,18 +192327,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus primordium") -SubClassOf(Annotation( "ZFA") ) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "mesenchymal") Annotation( "ZFA") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal neural crest) AnnotationAssertion(Annotation( "ZFA:0000080") "Cranial neural crest which gives rise to the trigeminal ganglion.") AnnotationAssertion( "todo - compare ZFA and EHDAA2 representation") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000269") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EFO:0003484") AnnotationAssertion( "EHDAA2:0002083") AnnotationAssertion( "EHDAA:667") @@ -193578,14 +192350,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trigeminal neural crest") SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (gonad primordium) AnnotationAssertion(Annotation( "ZFA:0001262") "Portion of tissue that gives rise to the immature gonad.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001262") Annotation( "TAO") Annotation( "ZFIN:curator") "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]") -AnnotationAssertion( "this is a very broad grouping class") AnnotationAssertion( "EFO:0003651") AnnotationAssertion( "EHDAA:5927") AnnotationAssertion( "EMAPA:17204") @@ -193611,7 +192382,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (facio-acoustic neural crest) AnnotationAssertion(Annotation( "ZFA:0000762") "Cranial neural crest that gives rise to the facio-acoustic ganglion.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000268") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43") Annotation( "http://bgee.unil.ch/") "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000492") AnnotationAssertion( "EHDAA:658") AnnotationAssertion( "EMAPA:16312") @@ -193624,6 +192394,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facio-acoustic neural crest") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -193640,13 +192411,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rhombomere 1 lateral wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head somite) AnnotationAssertion(Annotation( "PMID:11830559") "Somite located in the head region, caudal to the otic vesicle.") -AnnotationAssertion( "in humans this includes somites 1-4") -AnnotationAssertion(Annotation( "PMID:11830559") "They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter") AnnotationAssertion( "EHDAA2:0003437") AnnotationAssertion( "EMAPA:16172") AnnotationAssertion( "XAO:0000313") @@ -193656,6 +192426,9 @@ AnnotationAssertion(Annotation( "UBERON:0005594") AnnotationAssertion(rdfs:label "head somite") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -193689,11 +192462,12 @@ AnnotationAssertion( "UBERON:0005598") AnnotationAssertion(rdfs:label "trunk somite") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal mesogastrium) AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") "The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000352") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/mesogastrium") "The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]") AnnotationAssertion( "EHDAA2:0000416") AnnotationAssertion( "EHDAA:3001") AnnotationAssertion( "EMAPA:17025") @@ -193720,13 +192494,12 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005604") AnnotationAssertion(rdfs:label "extrahepatic part of hepatic duct") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (hyaloid cavity) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001477") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/hyaloid+fossa") "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]") AnnotationAssertion( "EHDAA2:0000789") AnnotationAssertion( "EHDAA:4733") AnnotationAssertion( "EMAPA:17302") @@ -193737,15 +192510,12 @@ AnnotationAssertion( "UBERON:0005606") AnnotationAssertion(rdfs:label "hyaloid cavity") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac artery) AnnotationAssertion(Annotation( "Wikipedia:Iliac_artery") Annotation( "https://orcid.org/0000-0002-6601-2165") "Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery.") -AnnotationAssertion( "this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods") -AnnotationAssertion(Annotation( "XAO") "we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific") AnnotationAssertion( "BTO:0004665") AnnotationAssertion( "EHDAA:2551") AnnotationAssertion( "EMAPA:17309") @@ -193785,8 +192555,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (left dorsal aorta) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000484") Annotation( "VHOG") Annotation( "ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572") Annotation( "http://bgee.unil.ch/") "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]") -AnnotationAssertion(Annotation( "http://emedicine.medscape.com/article/899609-overview") "Contributes to the arch of aorta in humans") AnnotationAssertion( "EHDAA2:0000936") AnnotationAssertion( "EHDAA:404") AnnotationAssertion( "EMAPA:16205") @@ -193797,12 +192565,12 @@ AnnotationAssertion( "UBERON:0005613") AnnotationAssertion(rdfs:label "left dorsal aorta") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens anterior epithelium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.") -AnnotationAssertion( "Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm") AnnotationAssertion( "lens epithelium") AnnotationAssertion( "EHDAA2:0000984") AnnotationAssertion( "EHDAA:9059") @@ -193823,8 +192591,9 @@ AnnotationAssertion(Annotation( "UBERON:0005614") AnnotationAssertion(rdfs:label "lens anterior epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenteric artery) @@ -193846,12 +192615,12 @@ AnnotationAssertion( "UBERON:0005616") AnnotationAssertion(rdfs:label "mesenteric artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenteric vein) AnnotationAssertion(Annotation( "MESH:A07.231.908.670.385") Annotation( "Wikipedia:Mesenteric_vein") "A vein that returns blood from the intestines.") -AnnotationAssertion( "In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein") AnnotationAssertion( "BTO:0002781") AnnotationAssertion( "EHDAA:4442") AnnotationAssertion( "EMAPA:17348") @@ -193867,11 +192636,11 @@ AnnotationAssertion(Annotation( "UBERON:0005617") AnnotationAssertion(rdfs:label "mesenteric vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right dorsal aorta) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000485") Annotation( "VHOG") Annotation( "ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572") Annotation( "http://bgee.unil.ch/") "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]") -AnnotationAssertion(Annotation( "http://emedicine.medscape.com/article/899609-overview") "Normally regresses in humans") AnnotationAssertion( "EHDAA2:0001720") AnnotationAssertion( "EHDAA:406") AnnotationAssertion( "EMAPA:16206") @@ -193882,6 +192651,7 @@ AnnotationAssertion( "UBERON:0005622") AnnotationAssertion(rdfs:label "right dorsal aorta") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (suprarenal artery) @@ -193901,6 +192671,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "suprarenal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tubotympanic recess lumen) @@ -193914,14 +192686,15 @@ AnnotationAssertion(Annotation( "UBERON:0005625") AnnotationAssertion(rdfs:label "tubotympanic recess lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventral mesogastrium) AnnotationAssertion(Annotation( "Wikipedia:Ventral_mesentery") "Portion of ventral mesentery closest to the stomach.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005133") Annotation( "TAO") Annotation( "ZFIN:curator") "The mesentery that originates from the ventral side of the peritoneal cavity.[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000351") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/mesogastrium") "The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG]") AnnotationAssertion( "EHDAA2:0002176") AnnotationAssertion( "EHDAA:3005") AnnotationAssertion( "EMAPA:17026") @@ -193944,7 +192717,6 @@ SubClassOf(Annotation( "EHD # Class: (vascular plexus) AnnotationAssertion(Annotation( "http://www.medilexicon.com/medicaldictionary.php?t=70052") "A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part.") -AnnotationAssertion(Annotation( "Wikipedia:Plexus#Circulatory_system") "In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system].") AnnotationAssertion( "AEO:0000219") AnnotationAssertion( "EHDAA2:0004112") AnnotationAssertion( "EMAPA:35904") @@ -193954,25 +192726,21 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005629") AnnotationAssertion(rdfs:label "vascular plexus") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic membrane) AnnotationAssertion(Annotation( "ISBN:0073040584") "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.") -AnnotationAssertion( "stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 is a mereological sum.") AnnotationAssertion( "EHDAA2:0004714") AnnotationAssertion( "FMA:305915") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D005321") AnnotationAssertion( "SCTID:362840007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005631") AnnotationAssertion(rdfs:label "extraembryonic membrane") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (caecum epithelium) @@ -193985,6 +192753,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "caecum epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pyloric region epithelium) @@ -193996,6 +192766,8 @@ AnnotationAssertion( "UBERON:0005637") AnnotationAssertion(rdfs:label "pyloric region epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior chamber epithelium) @@ -194005,6 +192777,8 @@ AnnotationAssertion( "UBERON:0005638") AnnotationAssertion(rdfs:label "anterior chamber epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens vesicle epithelium) @@ -194016,11 +192790,12 @@ AnnotationAssertion( "UBERON:0005656") AnnotationAssertion(rdfs:label "lens vesicle epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (2nd arch ectoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An ectoderm that is part of a pharyngeal arch 2.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001062") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000055") AnnotationAssertion( "EMAPA:16277") AnnotationAssertion( "EMAPA:16397") @@ -194032,11 +192807,12 @@ AnnotationAssertion( "UBERON:0005660") AnnotationAssertion(rdfs:label "2nd arch ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (3rd arch ectoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An ectoderm that is part of a pharyngeal arch 3.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000946") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000072") AnnotationAssertion( "EMAPA:16400") AnnotationAssertion( "EMAPA:16582") @@ -194048,11 +192824,12 @@ AnnotationAssertion( "UBERON:0005661") AnnotationAssertion(rdfs:label "3rd arch ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (4th arch ectoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An ectoderm that is part of a pharyngeal arch 4.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001095") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0004032") AnnotationAssertion( "EMAPA:16762") AnnotationAssertion( "EMAPA:16764") @@ -194064,11 +192841,12 @@ AnnotationAssertion( "UBERON:0005662") AnnotationAssertion(rdfs:label "4th arch ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (2nd arch endoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An endoderm that is part of a pharyngeal arch 2.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001108") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000061") AnnotationAssertion( "EMAPA:16274") AnnotationAssertion( "EMAPA:16276") @@ -194080,11 +192858,12 @@ AnnotationAssertion( "UBERON:0005664") AnnotationAssertion(rdfs:label "2nd arch endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (3rd arch endoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An endoderm that is part of a pharyngeal arch 3.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001081") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000075") AnnotationAssertion( "EMAPA:16401") AnnotationAssertion( "EMAPA:16585") @@ -194096,11 +192875,12 @@ AnnotationAssertion( "UBERON:0005665") AnnotationAssertion(rdfs:label "3rd arch endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (4th arch endoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "An endoderm that is part of a pharyngeal arch 4.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001092") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0004033") AnnotationAssertion( "EMAPA:16765") AnnotationAssertion( "EMAPA:16767") @@ -194112,6 +192892,8 @@ AnnotationAssertion( "UBERON:0005666") AnnotationAssertion(rdfs:label "4th arch endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (connecting stalk mesoderm) @@ -194119,14 +192901,13 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005667") AnnotationAssertion(rdfs:label "connecting stalk mesoderm") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (peritoneal cavity mesothelium) AnnotationAssertion(Annotation( "OBOL:automatic") "A mesothelium that is part of a peritoneal cavity.") -AnnotationAssertion(Annotation( "EMAPA") "we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood") AnnotationAssertion(Annotation( "EMAPA:16139") Annotation( ) "peritoneum") AnnotationAssertion( "BTO:0003156") AnnotationAssertion( "EHDAA2:0001447") @@ -194141,6 +192922,8 @@ AnnotationAssertion( "UBERON:0005669") AnnotationAssertion(rdfs:label "peritoneal cavity mesothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung endothelium) @@ -194150,6 +192933,9 @@ AnnotationAssertion( "UBERON:0005672") AnnotationAssertion(rdfs:label "right lung endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (left lung endothelium) @@ -194159,6 +192945,9 @@ AnnotationAssertion( "UBERON:0005673") AnnotationAssertion(rdfs:label "left lung endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (caecum mesentery) @@ -194168,6 +192957,8 @@ AnnotationAssertion( "UBERON:0005677") AnnotationAssertion(rdfs:label "caecum mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midgut dorsal mesentery) @@ -194181,6 +192972,8 @@ AnnotationAssertion( "UBERON:0005685") AnnotationAssertion(rdfs:label "midgut dorsal mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (caecum dorsal mesentery) @@ -194190,6 +192983,8 @@ AnnotationAssertion( "UBERON:0005686") AnnotationAssertion(rdfs:label "caecum dorsal mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (orbitosphenoid cartilage element) @@ -194201,14 +192996,18 @@ AnnotationAssertion(Annotation( "UBERON:0005687") AnnotationAssertion(rdfs:label "orbitosphenoid cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (lens vesicle cavity) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical cavity that is part of a lens vesicle.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000531") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429") Annotation( "http://bgee.unil.ch/") "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]") AnnotationAssertion( "cavity of lens") AnnotationAssertion(Annotation( "EHDAA2:0000986") "lens cavity") AnnotationAssertion( "EHDAA2:0000986") @@ -194219,12 +193018,13 @@ AnnotationAssertion( "UBERON:0005688") AnnotationAssertion(rdfs:label "lens vesicle cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (2nd arch mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a pharyngeal arch 2.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001102") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000066") AnnotationAssertion( "EHDAA:625") AnnotationAssertion( "EMAPA:16279") @@ -194237,11 +193037,12 @@ AnnotationAssertion( "UBERON:0005689") AnnotationAssertion(rdfs:label "2nd arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (3rd arch mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a pharyngeal arch 3.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001083") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000081") AnnotationAssertion( "EHDAA:1094") AnnotationAssertion( "EMAPA:16402") @@ -194254,11 +193055,12 @@ AnnotationAssertion( "UBERON:0005690") AnnotationAssertion(rdfs:label "3rd arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (4th arch mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a pharyngeal arch 4.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001052") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000096") AnnotationAssertion( "EHDAA:1677") AnnotationAssertion( "EMAPA:16770") @@ -194271,6 +193073,8 @@ AnnotationAssertion( "UBERON:0005691") AnnotationAssertion(rdfs:label "4th arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic eminence mesenchyme) @@ -194283,6 +193087,9 @@ AnnotationAssertion( "UBERON:0005702") AnnotationAssertion(rdfs:label "optic eminence mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (foregut duodenum mesentery) @@ -194292,6 +193099,9 @@ AnnotationAssertion( "UBERON:0005711") AnnotationAssertion(rdfs:label "foregut duodenum mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (midgut duodenum mesentery) @@ -194302,6 +193112,9 @@ AnnotationAssertion( "UBERON:0005712") AnnotationAssertion(rdfs:label "midgut duodenum mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (footplate apical ectodermal ridge) @@ -194313,6 +193126,7 @@ AnnotationAssertion( "UBERON:0005719") AnnotationAssertion(rdfs:label "footplate apical ectodermal ridge") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (hindbrain venous system) @@ -194326,11 +193140,13 @@ AnnotationAssertion(Annotation( "UBERON:0005720") AnnotationAssertion(rdfs:label "hindbrain venous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric mesoderm) AnnotationAssertion(Annotation( "OBOL:automatic") "A mesoderm that has the potential to develop into a pronephros.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011090") Annotation( "AAO") Annotation( "XAO:curator") "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]") AnnotationAssertion( "AAO:0011090") AnnotationAssertion( "EFO:0003479") AnnotationAssertion( "TAO:0000067") @@ -194347,7 +193163,11 @@ AnnotationAssertion( "the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 \"Developmental Biology\", PMID:10720431 \"Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm\"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney") AnnotationAssertion(rdfs:label "pronephric mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) # Class: (olfactory system) @@ -194355,9 +193175,6 @@ SubClassOf(Annotation( "Bge AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A sensory system that is capable of olfaction (the sensory perception of smell).") AnnotationAssertion( "consider splitting into main and accessory. See also: vomeronasal organ") AnnotationAssertion( "we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system") -AnnotationAssertion(Annotation( "Wikipedia:Olfactory_system") "The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000978") Annotation( "AAO") Annotation( "AAO:EJS") "The sensory system used for olfaction (the sense of smell).[AAO]") -AnnotationAssertion( "In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].") AnnotationAssertion( "AAO:0000334") AnnotationAssertion( "AAO:0000978") AnnotationAssertion( "BILA:0000144") @@ -194380,7 +193197,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "olfactory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (chemosensory system) @@ -194391,6 +193209,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chemosensory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic mesoderm) @@ -194404,15 +193224,15 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005728") AnnotationAssertion(rdfs:label "extraembryonic mesoderm") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pectoral appendage field) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001453") Annotation( "TAO") Annotation( "ZFIN:curator") "Embryonic region that develops into the pectoral fin bud.[TAO]") AnnotationAssertion( "TAO:0001453") AnnotationAssertion( "ZFA:0001453") AnnotationAssertion( "pectoral appendage field of lateral plate mesoderm") @@ -194421,11 +193241,13 @@ AnnotationAssertion( "UBERON:0005729") AnnotationAssertion(rdfs:label "pectoral appendage field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage field) AnnotationAssertion(Annotation( "OBOL:automatic") "A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001454") Annotation( "TAO") Annotation( "ZFIN:curator") "Embryonic region that develops into the pelvic fin bud.[TAO]") AnnotationAssertion( "TAO:0001454") AnnotationAssertion( "ZFA:0001454") AnnotationAssertion( "pelvic appendage field of lateral plate mesoderm") @@ -194434,6 +193256,9 @@ AnnotationAssertion( "UBERON:0005730") AnnotationAssertion(rdfs:label "pelvic appendage field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired limb/fin field) @@ -194446,7 +193271,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ISBN:9780878932504") Annotation( "ZFA-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb field) @@ -194457,12 +193287,13 @@ AnnotationAssertion( "the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)") AnnotationAssertion(rdfs:label "limb field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica adventitia of blood vessel) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Tunica_externa_(vessels)") "The outermost layer of a blood vessel, composed mainly of fibrous tissue.") AnnotationAssertion( "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings") -AnnotationAssertion(Annotation( "Wikipedia:Tunica_externa_(vessels)") "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].") AnnotationAssertion( "BTO:0002010") AnnotationAssertion( "EMAPA:36299") AnnotationAssertion( "NCIT:C33818") @@ -194479,6 +193310,7 @@ AnnotationAssertion(Annotation( "UBERON:0005734") AnnotationAssertion(rdfs:label "tunica adventitia of blood vessel") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -194498,6 +193330,8 @@ AnnotationAssertion( "UBERON:0005740") AnnotationAssertion(rdfs:label "tunica intima of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adventitia) @@ -194506,7 +193340,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0002010") AnnotationAssertion( "FMA:45635") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D063194") AnnotationAssertion( "SCTID:30180000") AnnotationAssertion( "Wikipedia:Adventitia") AnnotationAssertion(Annotation( "Wikipedia:Adventitia") "tunica advetitia") @@ -194518,13 +193351,11 @@ AnnotationAssertion( "adventitia") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone foramen) AnnotationAssertion(Annotation( "TAO:curator") "Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.") -AnnotationAssertion(Annotation( "FMA") "in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).") AnnotationAssertion(Annotation( "ZFA:0005386") "foramen") AnnotationAssertion( "AAO:0010438") AnnotationAssertion( "TAO:0001736") @@ -194536,13 +193367,12 @@ AnnotationAssertion( "bone foramen") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic foramen) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010704") Annotation( "Wikipedia:Optic_canal") Annotation( "https://github.com/obophenotype/uberon/issues/1213") "An opening in the skull through which cranial nerve II passes.[MP].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001408") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/optic+foramen") "An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002025") Annotation( "TAO") Annotation( "TAO:wd") "Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO]") -AnnotationAssertion(Annotation( "MP:0010704") Annotation( "MP") "The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery") AnnotationAssertion( "UBERON:0006269") AnnotationAssertion( "AAO:0000342") AnnotationAssertion( "EHDAA2:0001312") @@ -194568,17 +193398,19 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "optic foramen") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8e/Orbita_mensch.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomerular tuft) AnnotationAssertion(Annotation( "MP:0005325") Annotation( "Wikipedia:Glomerulus") Annotation( "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron") "The capillary loops of the kidney that normally function as a filtration unit[MP].") -AnnotationAssertion(Annotation( "GudMap") "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus") AnnotationAssertion( "EMAPA:28239") -AnnotationAssertion( "SCTID:362217000") AnnotationAssertion( "Wikipedia:Glomerulus") AnnotationAssertion( "uberon") AnnotationAssertion( "glomerular capillary tuft") @@ -194587,6 +193419,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular tuft") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194596,7 +193429,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0011498") Annotation( "https://orcid.org/0000-0002-6601-2165") "A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP].") AnnotationAssertion( "TODO - check this. BTO has podocytes under here") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005253") Annotation( "TAO") Annotation( "ZFIN:curator") "Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]") AnnotationAssertion( "BTO:0002296") AnnotationAssertion( "EMAPA:27979") AnnotationAssertion( "EMAPA:28260") @@ -194656,7 +193488,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Formerly had rdfs:label 'visceral layer of glomerular capsule'. The current label 'glomerular visceral epithelium' was copied from UBERON:0006852, which is now obsolete since it represented the same entity as this IRI.") AnnotationAssertion(rdfs:label "glomerular visceral epithelium") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194673,8 +193504,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005753") AnnotationAssertion(rdfs:label "caudal part of nephrogenic cord") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (rostral part of nephrogenic cord) @@ -194683,16 +193513,13 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005754") AnnotationAssertion(rdfs:label "rostral part of nephrogenic cord") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urorectal septum) AnnotationAssertion(Annotation( "MP:anna") Annotation( "Wikipedia:Urorectal_septum") "The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP].") AnnotationAssertion( "todo - use to define cloacal septation in GO") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000018") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/urorectal+septum") "A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000018") Annotation( "VHOG") Annotation( "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.388-89 and Figure 300") Annotation( "http://bgee.unil.ch/") "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0002152") AnnotationAssertion( "EHDAA:5921") AnnotationAssertion( "EMAPA:17212") @@ -194727,11 +193554,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acellular membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basement membrane of epithelium) AnnotationAssertion(Annotation( "Wikipedia:Basement_membrane") Annotation( "http://orcid.org/0000-0002-6601-2165") "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.") -AnnotationAssertion( "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.") AnnotationAssertion(Annotation( "http://palaeos.com/metazoa/porifera/homoscleromorpha.html") ) AnnotationAssertion( "AAO:0010596") AnnotationAssertion( "FMA:63872") @@ -194746,6 +193574,7 @@ AnnotationAssertion( "FMA:63872") "basement membrane") AnnotationAssertion( "UBERON:0005769") AnnotationAssertion(rdfs:label "basement membrane of epithelium") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194756,13 +193585,11 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (glomerular basement membrane) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0011348") "The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005285") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-000824-1") "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]") AnnotationAssertion(Annotation( ) "GBM") AnnotationAssertion( "EMAPA:28251") AnnotationAssertion( "EMAPA:30965") AnnotationAssertion( "FMA:74274") AnnotationAssertion( "MA:0001659") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D050533") AnnotationAssertion( "NCIT:C32683") AnnotationAssertion( "SCTID:243897006") AnnotationAssertion( "TAO:0005285") @@ -194778,7 +193605,8 @@ AnnotationAssertion( "glomerular basement membrane") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194798,6 +193626,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lamina densa of glomerular basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina rara interna) @@ -194815,6 +193648,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lamina rara interna") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina rara externa) @@ -194831,6 +193668,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lamina rara externa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nephric ridge) @@ -194844,8 +193685,7 @@ AnnotationAssertion( "VHOG:0001240") "nephric cord") AnnotationAssertion( "UBERON:0005792") AnnotationAssertion(rdfs:label "nephric ridge") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194857,7 +193697,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005795") AnnotationAssertion(rdfs:label "embryonic uterus") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (section of aorta) @@ -194874,17 +193714,13 @@ AnnotationAssertion( "FMA:13087") "segment of aorta") AnnotationAssertion( "UBERON:0005800") AnnotationAssertion(rdfs:label "section of aorta") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal aorta) AnnotationAssertion(Annotation( "GO:0035907") Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8525/") "The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_aorta") "Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000014") Annotation( "TAO") Annotation( "ZFIN:curator") "Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "BTO:0004673") "The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000014") Annotation( "TAO") "relationship loss: part_of axial vasculature (TAO:0001073)[TAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000264") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620") Annotation( "http://bgee.unil.ch/") "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]") AnnotationAssertion( "AAO:0011029") AnnotationAssertion( "BTO:0004673") AnnotationAssertion( "EHDAA:402") @@ -194908,6 +193744,7 @@ AnnotationAssertion( "dorsal aorta") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -194926,7 +193763,6 @@ AnnotationAssertion( "UBERON:0005806") AnnotationAssertion(rdfs:label "portal system") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone tissue of long bone) @@ -194938,6 +193774,8 @@ AnnotationAssertion(Annotation( "UBERON:0005808") AnnotationAssertion(rdfs:label "bone tissue of long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortex of manus bone) @@ -194946,7 +193784,9 @@ AnnotationAssertion( "UBERON:0005809") AnnotationAssertion(rdfs:label "cortex of manus bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tubercle) @@ -194974,6 +193814,8 @@ AnnotationAssertion( "UBERON:0005814") AnnotationAssertion(rdfs:label "arch of atlas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fasciculus of spinal cord) @@ -194984,6 +193826,9 @@ AnnotationAssertion( "UBERON:0005837") AnnotationAssertion(rdfs:label "fasciculus of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fasciculus of brain) @@ -194994,6 +193839,9 @@ AnnotationAssertion( "UBERON:0005838") AnnotationAssertion(rdfs:label "fasciculus of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord segment) @@ -195010,8 +193858,7 @@ AnnotationAssertion( "TAO:0001332") Annotation( ) "spinal neuromeres") AnnotationAssertion( "UBERON:0005844") AnnotationAssertion(rdfs:label "spinal cord segment") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (caudal segment of spinal cord) @@ -195030,6 +193877,8 @@ AnnotationAssertion( "for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned") AnnotationAssertion(rdfs:label "caudal segment of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (developing mesenchymal condensation) @@ -195048,7 +193897,6 @@ SubClassOf(Annotation( "AEO # Class: (cartilaginous condensation) AnnotationAssertion(Annotation( "GO:curator") "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.") -AnnotationAssertion(Annotation( "VSAO") "isa cell condensation in VSAO; has_part chondroblast in AEO") AnnotationAssertion( "AEO:0000147") AnnotationAssertion( "EHDAA2_RETIRED:0003147") AnnotationAssertion( "EMAPA:32731") @@ -195075,13 +193923,14 @@ AnnotationAssertion( "UBERON:0005865") AnnotationAssertion(rdfs:label "pre-muscle condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pre-cartilage condensation) AnnotationAssertion(Annotation( "AEO:0000150") Annotation( "AEO:JB") "A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.") -AnnotationAssertion(Annotation( "http://dictionary.reference.com/browse/precartilage") "A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.") AnnotationAssertion( "AEO:0000150") AnnotationAssertion( "EHDAA2:0003150") AnnotationAssertion( "EMAPA:32736") @@ -195092,8 +193941,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005866") AnnotationAssertion(rdfs:label "pre-cartilage condensation") +SubClassOf( ) SubClassOf(Annotation( "AEO") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195139,15 +193988,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "maxillary prominence") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory pit) AnnotationAssertion(Annotation( "GO:0060166") Annotation( "Wikipedia:Nasal_pit") "An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO].") AnnotationAssertion( "we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode") -AnnotationAssertion(Annotation( "Wikipedia:Nasal_pit") "By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit].") AnnotationAssertion( "AAO:0011068") AnnotationAssertion( "EFO:0003496") AnnotationAssertion( "EHDAA2:0001295") @@ -195173,7 +194020,6 @@ SubClassOf(Annotation( "XAO # Class: (1st arch pharyngeal cleft) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "VHOG:OG") "A groove that is situated between the 1st and 2nd pharyngeal arch.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000969") Annotation( "VHOG") Annotation( "DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)") Annotation( "http://bgee.unil.ch/") "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000009") AnnotationAssertion( "EHDAA:575") AnnotationAssertion( "EMAPA:16119") @@ -195191,6 +194037,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "1st arch pharyngeal cleft") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (2nd arch pharyngeal cleft) @@ -195212,6 +194061,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "2nd arch pharyngeal cleft") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (3rd arch pharyngeal cleft) @@ -195233,6 +194085,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "3rd arch pharyngeal cleft") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (4th arch pharyngeal cleft) @@ -195255,17 +194110,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "4th arch pharyngeal cleft") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (undifferentiated genital tubercle) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0011771") Annotation( "https://github.com/obophenotype/uberon/issues/1230") "The embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000583") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/genital+tubercle") "The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]") -AnnotationAssertion(Annotation( "MP") "embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000583") Annotation( "VHOG") Annotation( "DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009)") Annotation( "http://bgee.unil.ch/") "In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]") -AnnotationAssertion( "All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313]") -AnnotationAssertion( "GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771]") -AnnotationAssertion( "todo - add taxon constraints") -AnnotationAssertion(Annotation( "EMAPA") "we assume the EMAPA class is the undifferentiated form based on TS timings") AnnotationAssertion( "EHDAA2:0000705") AnnotationAssertion( "EHDAA:5925") AnnotationAssertion( "EMAPA:17382") @@ -195283,7 +194134,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "undifferentiated genital tubercle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1230") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195293,7 +194144,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "PMID:23020903") Annotation( "http://orcid.org/0000-0002-6601-2165") "An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches.") AnnotationAssertion( "Note we use overlaps as the relationship to the arches") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former") AnnotationAssertion(Annotation( "Wikipedia:Pharyngeal_groove") "pharyngeal groove") AnnotationAssertion( "AAO:0010623") AnnotationAssertion( "EMAPA:32750") @@ -195315,7 +194165,6 @@ AnnotationAssertion( "pharyngeal cleft") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg"^^xsd:anyURI) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2-adbuced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195349,7 +194198,7 @@ AnnotationAssertion( "neural tube alar plate") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/336"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195357,7 +194206,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hyoid arch skeleton) AnnotationAssertion(Annotation( "OBOL:automatic") "A subdivision of skeleton that supports pharyngeal arch 2.") -AnnotationAssertion(Annotation( "AAO") "it's not clear where AAO:'hyobranchial skeleton' belongs") AnnotationAssertion( "AAO:0000665") AnnotationAssertion( "AAO:0010370") AnnotationAssertion( "TAO:0001276") @@ -195378,7 +194226,6 @@ SubClassOf(Annotation( "cjm # Class: (coelomic epithelium) AnnotationAssertion(Annotation( "Wikipedia:Coelomic_epithelium") Annotation( "XAO:0000329") "The epithelial lining of the surface of the coelom.") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'") AnnotationAssertion( "Wikipedia:Coelomic_epithelium") AnnotationAssertion( "XAO:0000329") AnnotationAssertion( "celomic epithelium") @@ -195405,12 +194252,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "leg bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of the manus skeleton. Note that this includes the carpal bones.") AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:35391") AnnotationAssertion( "MA:0000619") AnnotationAssertion( "SCTID:426741001") @@ -195427,13 +194275,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "manus bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of the pes skeleton.") AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:35354") AnnotationAssertion( "GAID:192") AnnotationAssertion( "MA:0000643") @@ -195451,18 +194300,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pes bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (occipital region) AnnotationAssertion(Annotation( "TAO:0001414") Annotation( "UBERONREF:0000007") "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.") AnnotationAssertion( "TODO - check") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010199") Annotation( "AAO") Annotation( "AAO:EJS") "An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001414") Annotation( "TAO") Annotation( "TAO:MAH") "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]") AnnotationAssertion( "AAO:0010199") AnnotationAssertion( "BTO:0004675") AnnotationAssertion( "FMA:49187") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D009778") AnnotationAssertion( "SCTID:362618001") AnnotationAssertion( "TAO:0001414") AnnotationAssertion( "XAO:0003173") @@ -195495,18 +194343,24 @@ AnnotationAssertion( "duct of seminal vesicle") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (duct of male reproductive system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any of the ducts that are part of a male reproductive system.") -AnnotationAssertion( "this class groups the individual ducts in a variety of species") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0005904") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct of male reproductive system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serous sac) @@ -195517,6 +194371,7 @@ AnnotationAssertion( "UBERON:0005906") AnnotationAssertion(rdfs:comment "See notes for serous membrane") AnnotationAssertion(rdfs:label "serous sac") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195532,10 +194387,11 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0005908") AnnotationAssertion(rdfs:label "conjunctival sac") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "HPO:pr") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endo-epithelium) @@ -195547,6 +194403,8 @@ AnnotationAssertion( "UBERON:0005911") AnnotationAssertion(rdfs:label "endo-epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (zone of bone organ) @@ -195562,10 +194420,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (external naris) AnnotationAssertion(Annotation( "Wikipedia:Nostril") Annotation( "http://orcid.org/0000-0002-6601-2165") "A naris that provides one of the small external openings of the head that give passage to air for breathing.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000024") Annotation( "AAO") Annotation( "AAO:LAP") "Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000024") Annotation( "AAO") "relationship loss: subclass nasal opening (AAO:0000316)[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000544") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27") Annotation( "http://bgee.unil.ch/") "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG]") -AnnotationAssertion( "Fish have two pairs of external nostrils.") AnnotationAssertion(Annotation( "ZFA:0000550") "naris") AnnotationAssertion( "AAO:0000024") AnnotationAssertion( "AAO:0000983") @@ -195594,8 +194448,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "external naris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195617,6 +194474,7 @@ AnnotationAssertion( "bulb of hair follicle") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair root sheath) @@ -195629,6 +194487,7 @@ AnnotationAssertion( "hair root sheath") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair inner root sheath) @@ -195677,10 +194536,8 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "FMA:71221") Annotation( "VSAO:0000056") Annotation( "Wikipedia:Axial_skeleton") Annotation( "https://github.com/obophenotype/uberon/issues/44") Annotation( "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton") "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000056") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]") AnnotationAssertion( "AAO:0000963") AnnotationAssertion( "EMAPA:17214") -AnnotationAssertion( "EMAPA:18043") AnnotationAssertion( "MA:0000308") AnnotationAssertion( "NCIT:C32172") AnnotationAssertion( "SCTID:361725000") @@ -195698,7 +194555,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195717,7 +194573,6 @@ AnnotationAssertion( "neurocranial trabecula") SubClassOf( ) SubClassOf(Annotation( "ZFA") ) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (outflow tract of atrium) @@ -195729,6 +194584,8 @@ AnnotationAssertion( "UBERON:0005946") AnnotationAssertion(rdfs:label "outflow tract of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow part of right ventricle) @@ -195755,6 +194612,8 @@ AnnotationAssertion(Annotation( "UBERON:0005953") AnnotationAssertion(rdfs:label "outflow part of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:17276708") ObjectSomeValuesFrom( )) @@ -195778,6 +194637,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outflow part of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow part of right atrium) @@ -195789,6 +194650,8 @@ AnnotationAssertion( "UBERON:0005965") AnnotationAssertion(rdfs:label "outflow part of right atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outflow part of left atrium) @@ -195800,6 +194663,8 @@ AnnotationAssertion( "UBERON:0005966") AnnotationAssertion(rdfs:label "outflow part of left atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye trabecular meshwork) @@ -195848,7 +194713,7 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195882,6 +194747,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "crista terminalis") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195894,6 +194760,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heart layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (coronary vessel) @@ -195907,6 +194776,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "coronary vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left bundle branch) @@ -195931,7 +194803,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left bundle branch") SubClassOf( ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195956,7 +194829,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right bundle branch") SubClassOf( ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195975,6 +194849,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "atrium myocardial trabecula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -195991,7 +194868,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "atrioventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PMID:15797462") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vitelline artery) @@ -196006,13 +194887,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "vitelline artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ventral branch") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (integumentary adnexa) AnnotationAssertion(Annotation( "http://code.google.com/p/caro2/issues/detail?id=5") Annotation( "http://orcid.org/0000-0002-6601-2165") "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.") AnnotationAssertion( "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.") -AnnotationAssertion(Annotation( "MP:0010678") "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37883") AnnotationAssertion( "Wikipedia:Skin_appendage") AnnotationAssertion(Annotation( "GO:GO") "body hair or bristle") @@ -196039,7 +194922,8 @@ AnnotationAssertion( "UBERON:0006004") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair follicle matrix region") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -196066,6 +194950,10 @@ AnnotationAssertion(Annotation( "UBERON:0006008") AnnotationAssertion(rdfs:label "fibrous ring of heart") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior surface of head) @@ -196073,7 +194961,9 @@ AnnotationAssertion( "UBERON:0006056") AnnotationAssertion(rdfs:label "posterior surface of head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multi-limb segment region) @@ -196091,7 +194981,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Vertebral_column#Structure_of_individual_vertebrae") "A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses).") AnnotationAssertion( "AAO:0000739") AnnotationAssertion( "FMA:24530") -AnnotationAssertion( "NCIT:C116112") AnnotationAssertion( "Wikipedia:Vertebral_column#Structure_of_individual_vertebrae") AnnotationAssertion( "vertebra process") AnnotationAssertion(Annotation( "FMA:24530") "vertebral process") @@ -196099,7 +194988,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0006061") AnnotationAssertion(rdfs:label "process of vertebra") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilaginous neural arch) @@ -196126,11 +195015,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculature of hindlimb zeugopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of tail) AnnotationAssertion(Annotation( "OBOL:automatic") "A bone that is part of a post-anal tail.") -AnnotationAssertion(Annotation( "MA") "MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future.") AnnotationAssertion( "EMAPA:18042") AnnotationAssertion( "MA:0000696") AnnotationAssertion( "uberon") @@ -196140,12 +195030,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of tail") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (caudal region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this.") -AnnotationAssertion( "This region is reduced in humans and corresponds to the coccyx") -AnnotationAssertion(Annotation( "XAO") "We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud") AnnotationAssertion( "XAO:0000087") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "post-anal caudal region") @@ -196162,7 +195052,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cervical region of vertebral column) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/") "That portion of the spine comprising the cervical vertebrae. The neck area of the spine.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000092") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_1994") "Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]") AnnotationAssertion( "AAO:0000092") AnnotationAssertion( "BTO:0004148") AnnotationAssertion( "EHDAA2:0000238") @@ -196185,14 +195074,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical region of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic region of vertebral column) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/") "That part of the spine comprising the thoracic vertebrae.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000612") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_1994") "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]") -AnnotationAssertion( "AAO:0000612") AnnotationAssertion( "BTO:0004150") AnnotationAssertion( "EHDAA:5063") AnnotationAssertion( "EMAPA:17396") @@ -196211,14 +195100,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic region of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (caudal region of vertebral column) AnnotationAssertion(Annotation( "UBERONREF:0000006") "Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000082") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_1994") "Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]") -AnnotationAssertion(Annotation( "AAO") "in AAO, this is posterior to the caudal-sacral region") AnnotationAssertion( "AAO:0000082") AnnotationAssertion( "EMAPA:18043") AnnotationAssertion( "MA:0003158") @@ -196232,8 +195121,10 @@ AnnotationAssertion(Annotation( "UBERON:0006076") AnnotationAssertion(rdfs:label "caudal region of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of vertebral column) @@ -196250,8 +195141,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subdivision of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fundus of urinary bladder) @@ -196283,6 +195176,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-modified") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -196295,7 +195189,6 @@ AnnotationAssertion( "BAMS:BNC") AnnotationAssertion( "BIRNLEX:1629") AnnotationAssertion( "EV:0100182") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001479") AnnotationAssertion(Annotation( "BIRNLEX:1629") "UMLS:C0004781") AnnotationAssertion(Annotation( "BIRNLEX:1629") "neuronames:224") AnnotationAssertion(Annotation( "BIRNLEX:1629") "basal nuclei") @@ -196308,6 +195201,7 @@ AnnotationAssertion(Annotation( "UBERON:0006098") AnnotationAssertion(rdfs:label "basal nuclear complex") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear canal) @@ -196326,6 +195220,7 @@ AnnotationAssertion( "MA:0003176") "spiral vessel") AnnotationAssertion( "UBERON:0006106") AnnotationAssertion(rdfs:label "cochlear canal") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -196340,6 +195235,7 @@ AnnotationAssertion( "UBERON:0006127") AnnotationAssertion(rdfs:label "funiculus of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (funiculus of neuraxis) @@ -196351,13 +195247,13 @@ AnnotationAssertion( "UBERON:0006133") AnnotationAssertion(rdfs:label "funiculus of neuraxis") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve fiber) AnnotationAssertion(Annotation( "Wikipedia:Nervous_system_fiber") "A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.") AnnotationAssertion( ) -AnnotationAssertion( "neurofibrous") AnnotationAssertion( "BAMS:nfi") AnnotationAssertion( "FMA:5914") AnnotationAssertion( "MESH:D009412") @@ -196385,7 +195281,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin") AnnotationAssertion( "FMA:5915") AnnotationAssertion( "GAID:745") AnnotationAssertion( "MESH:D009413") @@ -196397,6 +195292,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myelinated nerve fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -196423,6 +195320,9 @@ AnnotationAssertion( "UBERON:0006170") AnnotationAssertion(rdfs:label "mesonephric capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric proximal tubule) @@ -196431,7 +195331,8 @@ AnnotationAssertion( "UBERON:0006173") AnnotationAssertion(rdfs:label "pronephric proximal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (pronephric distal tubule) @@ -196439,8 +195340,8 @@ AnnotationAssertion( "UBERON:0006175") AnnotationAssertion(rdfs:label "pronephric distal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric glomerular mesangium) @@ -196449,6 +195350,7 @@ AnnotationAssertion( "UBERON:0006182") AnnotationAssertion(rdfs:label "mesonephric glomerular mesangium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mesonephric glomerular capillary) @@ -196458,6 +195360,7 @@ AnnotationAssertion( "UBERON:0006183") AnnotationAssertion(rdfs:label "mesonephric glomerular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -196468,27 +195371,31 @@ AnnotationAssertion( "UBERON:0006189") AnnotationAssertion(rdfs:label "mesonephric connecting tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (mesonephric distal tubule) AnnotationAssertion(Annotation( "GO:0061273") "The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule.") -AnnotationAssertion(Annotation( "ZFA") "ZFA has terms for developing tubule") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006190") AnnotationAssertion(rdfs:label "mesonephric distal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (mesonephric proximal tubule) AnnotationAssertion(Annotation( "GO:0061275") "The mesonephric proximal tubule extends from the capsule to the distal tubule.") -AnnotationAssertion(Annotation( "ZFA") "ZFA has terms for developing tubule") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006192") AnnotationAssertion(rdfs:label "mesonephric proximal tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (iridocorneal angle) @@ -196525,8 +195432,11 @@ AnnotationAssertion( "aortico-pulmonary spiral septum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PMID:6844926") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (auditory hillocks) @@ -196600,8 +195510,13 @@ AnnotationAssertion(Annotation( "UBERON:0006213") AnnotationAssertion(rdfs:label "carpus cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carpus pre-cartilage condensation) @@ -196615,14 +195530,18 @@ AnnotationAssertion(Annotation( "UBERON:0006214") AnnotationAssertion(rdfs:label "carpus pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rhombic lip) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0012525") "The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001440") Annotation( "TAO") Annotation( "ZFIN:curator") "The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]") AnnotationAssertion( "UBERON:0013163") AnnotationAssertion( "DHBA:10664") AnnotationAssertion( "EHDAA2:0000231") @@ -196644,14 +195563,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "rhombic lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal membrane) AnnotationAssertion(Annotation( "MP:0011837") Annotation( "MP:anna") Annotation( "Wikipedia:Cloacal_membrane") "The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001198") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001198") Annotation( "VHOG") Annotation( "PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)") Annotation( "http://bgee.unil.ch/") "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000257") AnnotationAssertion( "EHDAA:214") AnnotationAssertion( "EHDAA:2933") @@ -196698,6 +195617,7 @@ AnnotationAssertion( "UBERON:0006219") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "deltoid pre-muscle mass") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -196720,7 +195640,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (elbow joint primordium) @@ -196747,16 +195669,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ethmoid bone primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AAO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facio-acoustic VII-VIII preganglion complex) AnnotationAssertion( "EHDAA:1477") AnnotationAssertion( "EMAPA:16660") AnnotationAssertion( "RETIRED_EHDAA2:0000496") -AnnotationAssertion( "VHOG:0000715") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "EMAPA:16660") "facio-acoustic preganglion complex") AnnotationAssertion( "UBERON:0006232") @@ -196779,6 +195702,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "female genital tubercle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (femur pre-cartilage condensation) @@ -196793,13 +195717,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "femur pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (foregut-midgut junction) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical junctions that overlaps the foregut and midgut.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000291") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000569") AnnotationAssertion( "EHDAA:526") AnnotationAssertion( "EMAPA:16363") @@ -196809,7 +195735,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "foregut-midgut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tetrapod frontal bone primordium) @@ -196823,11 +195752,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tetrapod frontal bone primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future brain) AnnotationAssertion(Annotation( "NLX:94995") "The embryonic precursor of the brain.") -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Cumbo_terms") "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)") AnnotationAssertion( "BAMS:Enc") AnnotationAssertion( "BTO:0004726") AnnotationAssertion( "EFO:0003431") @@ -196849,14 +195779,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future brain") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (future central tendon) AnnotationAssertion(Annotation( "OBOL:automatic") "A tendon that has the potential to develop into a central tendon.") -AnnotationAssertion( "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.") AnnotationAssertion( "EHDAA2:0000593") AnnotationAssertion( "EHDAA:4118") AnnotationAssertion( "EMAPA:25035") @@ -196867,9 +195796,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future central tendon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "mesenchyme") Annotation( "cranial part") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future forebrain) @@ -196894,7 +195826,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future forebrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future spinal cord) @@ -196914,8 +195848,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future spinal cord") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -196933,10 +195866,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gallbladder primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (humerus cartilage element) @@ -196951,8 +195885,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "humerus cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -196970,8 +195906,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "humerus pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -196987,9 +195925,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "iliac pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ischial cartilage element) @@ -197004,7 +195945,8 @@ AnnotationAssertion( "ischial cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (ischial pre-cartilage condensation) @@ -197019,8 +195961,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ischial pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (knee joint primordium) @@ -197032,14 +195977,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "knee joint primordium") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lingual swellings) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000449") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/lingual+swellings") "Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000449") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)") Annotation( "http://bgee.unil.ch/") "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000996") AnnotationAssertion( "EMAPA:17186") AnnotationAssertion( "VHOG:0000449") @@ -197049,9 +195992,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "the collection consisting of the two lateral swellings and the medial swelling") AnnotationAssertion(rdfs:label "lingual swellings") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197069,6 +196011,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male genital tubercle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (mouth-foregut junction) @@ -197083,7 +196026,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mouth-foregut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasolacrimal groove) @@ -197105,9 +196051,9 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "nasolacrimal groove") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png"^^xsd:anyURI) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197116,7 +196062,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "VHOG:0001212") "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.") AnnotationAssertion( "TODO - check ordering; awaiting confirmation from JB") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001212") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]") AnnotationAssertion( "EHDAA2:0001278") AnnotationAssertion( "EHDAA:264") AnnotationAssertion( "EMAPA:16101") @@ -197128,8 +196073,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "notochordal plate") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (notochordal process) @@ -197165,12 +196111,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "orbital fissure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (otic pit) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0011172") "The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001147") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://medical-dictionary.thefreedictionary.com/Otic+pit") "A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]") AnnotationAssertion( "UBERON:0009123") AnnotationAssertion( "EHDAA2:0001336") AnnotationAssertion( "EHDAA:929") @@ -197192,10 +196139,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pleuroperitoneal canal) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "VHOG:0001505") "Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001505") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]") AnnotationAssertion( "EHDAA2:0001481") AnnotationAssertion( "EHDAA:4128") -AnnotationAssertion( "EMAPA:17704") AnnotationAssertion( "EMAPA:17707") AnnotationAssertion( "SCTID:361413002") AnnotationAssertion( "VHOG:0001505") @@ -197206,9 +196151,11 @@ AnnotationAssertion( "pleuroperitoneal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future cardiac ventricle) @@ -197235,8 +196182,7 @@ AnnotationAssertion( "UBERON:0006283") AnnotationAssertion(rdfs:comment "The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]") AnnotationAssertion(rdfs:label "future cardiac ventricle") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197244,7 +196190,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (early prosencephalic vesicle) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000644") Annotation( "VHOG") Annotation( "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500") Annotation( "http://bgee.unil.ch/") "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]") AnnotationAssertion( "DHBA:10595") AnnotationAssertion( "EHDAA2:0001571") AnnotationAssertion( "EHDAA:1356") @@ -197277,6 +196222,8 @@ AnnotationAssertion( "rib cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197293,8 +196240,10 @@ AnnotationAssertion( "rib pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2-abduced") Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (scapula cartilage element) @@ -197308,15 +196257,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "scapula cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (scapula pre-cartilage condensation) AnnotationAssertion(Annotation( "OBOL:automatic") "A scapula endochondral element that is composed primarily of a pre-cartilage condensation.") -AnnotationAssertion(Annotation( "PMID:21455939") "the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005).") AnnotationAssertion( "EHDAA2:0001778") AnnotationAssertion( "EHDAA:6041") AnnotationAssertion( "EMAPA:18027") @@ -197326,13 +196275,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "scapula pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder joint primordium) -AnnotationAssertion(Annotation( "EHDAA2") "this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness") AnnotationAssertion( "EHDAA2:0001836") AnnotationAssertion( "EHDAA:8493") AnnotationAssertion( "EMAPA:17712") @@ -197340,6 +196289,7 @@ AnnotationAssertion( "UBERON:0006292") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "shoulder joint primordium") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -197348,7 +196298,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (spleen primordium) AnnotationAssertion(Annotation( "ISBN:0123747295") Annotation( "MP:0011263") "A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP].") -AnnotationAssertion(Annotation( "EMAPA") "check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme") AnnotationAssertion( "UBERON:0009750") AnnotationAssertion( "EHDAA2:0001904") AnnotationAssertion( "EHDAA:3003") @@ -197363,7 +196312,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen primordium") SubClassOf(Annotation( "XAO") ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2-modified") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) @@ -197379,8 +196331,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model") AnnotationAssertion(rdfs:label "future trigeminal ganglion") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -197402,11 +196353,14 @@ AnnotationAssertion(Annotation( "UBERON:0006311") AnnotationAssertion(rdfs:label "chamber of eyeball") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ocular refractive media) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.") -AnnotationAssertion( "ocular refraction") AnnotationAssertion( "MA:0001911") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006312") @@ -197431,6 +196385,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bodily fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brainstem nucleus) @@ -197442,14 +196398,13 @@ AnnotationAssertion(Annotation( "UBERON:0006331") AnnotationAssertion(rdfs:label "brainstem nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior lateral line) AnnotationAssertion(Annotation( "ZFA:0000944") "One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.") AnnotationAssertion( "check XAO/AAO") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000944") Annotation( "TAO") Annotation( "ZFIN:curator") "One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000944") Annotation( "TAO") "relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000944") Annotation( "TAO") "relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO]") AnnotationAssertion( "AAO:0011024") AnnotationAssertion( "EFO:0003595") AnnotationAssertion( "TAO:0000944") @@ -197473,6 +196428,7 @@ AnnotationAssertion( "UBERON:0006338") AnnotationAssertion(rdfs:label "lateral ventricle choroid plexus stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fourth ventricle choroid plexus stroma) @@ -197483,6 +196439,7 @@ AnnotationAssertion( "UBERON:0006340") AnnotationAssertion(rdfs:label "fourth ventricle choroid plexus stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer renal medulla peritubular capillary) @@ -197495,6 +196452,8 @@ AnnotationAssertion( "UBERON:0006341") AnnotationAssertion(rdfs:label "outer renal medulla peritubular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (communicating artery) @@ -197509,6 +196468,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "communicating artery") EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (superior vesical vein) @@ -197522,6 +196482,7 @@ AnnotationAssertion( "superior vesical vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") Annotation( "MA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (premacula segment of distal straight tubule) @@ -197546,7 +196507,6 @@ SubClassOf(Annotation( "MA" AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0009103") "The unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species.") AnnotationAssertion( ) -AnnotationAssertion( "found in most mammals, with the exception of humans") AnnotationAssertion( "EMAPA:29769") AnnotationAssertion( "MA:0000406") AnnotationAssertion( "SCTID:27962002") @@ -197560,7 +196520,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "os penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (os clitoris) @@ -197578,7 +196540,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "os clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197589,9 +196553,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "BTO:0003627") "A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart).") AnnotationAssertion(Annotation( "BTO:0003627") "anulus") AnnotationAssertion( "BTO:0003627") -AnnotationAssertion( "EMAPA:32670") AnnotationAssertion( "FMA:76704") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000070616") AnnotationAssertion(Annotation( "FMA:76704") "anulus fibrosus") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "fibrocartilaginous ring") AnnotationAssertion( "uberon") @@ -197604,7 +196566,6 @@ SubClassOf( (right lung lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A lobe of lung that is part of a right lung.") -AnnotationAssertion(Annotation( "ISBN:0123813611") "4 in mice, divided into 3 in human by two interlobal fissures") AnnotationAssertion( "EMAPA:35155") AnnotationAssertion( "MA:0001791") AnnotationAssertion( "NCIT:C48944") @@ -197616,6 +196577,8 @@ AnnotationAssertion( "UBERON:0006518") AnnotationAssertion(rdfs:label "right lung lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alveolar system) @@ -197630,6 +196593,7 @@ AnnotationAssertion(Annotation( "UBERON:0006524") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alveolar system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197641,6 +196605,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006525") AnnotationAssertion(rdfs:label "left lung alveolar system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197652,6 +196617,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006526") AnnotationAssertion(rdfs:label "right lung alveolar system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197659,10 +196625,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (seminal fluid) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended.") -AnnotationAssertion( "this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)") -AnnotationAssertion( "we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid") -AnnotationAssertion(Annotation( "DOI:10.1046/j.1365-2540.2001.00961.x") "This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation") -AnnotationAssertion( "seminal fluid may have a role in sperm capacitation, sperm motility") AnnotationAssertion( "BTO:0001232") AnnotationAssertion( "CALOHA:TS-0918") AnnotationAssertion( "EMAPA:36543") @@ -197679,6 +196641,9 @@ AnnotationAssertion(Annotation( "UBERON:0006530") AnnotationAssertion(rdfs:label "seminal fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -197710,6 +196675,8 @@ AnnotationAssertion( "UBERON:0006535") AnnotationAssertion(rdfs:label "skin secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male reproductive gland secretion) @@ -197723,6 +196690,8 @@ AnnotationAssertion( "UBERON:0006536") AnnotationAssertion(rdfs:label "male reproductive gland secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female reproductive gland secretion) @@ -197735,6 +196704,8 @@ AnnotationAssertion( "UBERON:0006537") AnnotationAssertion(rdfs:label "female reproductive gland secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system fluid/secretion) @@ -197749,6 +196720,8 @@ AnnotationAssertion( "UBERON:0006538") AnnotationAssertion(rdfs:label "respiratory system fluid/secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland fluid/secretion) @@ -197765,6 +196738,8 @@ AnnotationAssertion( "UBERON:0006539") AnnotationAssertion(rdfs:label "mammary gland fluid/secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer medulla inner stripe loop of Henle) @@ -197775,6 +196750,8 @@ AnnotationAssertion( "UBERON:0006541") AnnotationAssertion(rdfs:label "outer medulla inner stripe loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer medulla outer stripe loop of Henle) @@ -197785,6 +196762,8 @@ AnnotationAssertion( "UBERON:0006542") AnnotationAssertion(rdfs:label "outer medulla outer stripe loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney vasculature) @@ -197799,17 +196778,21 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal duct) AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-071029-9") "A tube in the kidney that collect and transport urine.") -AnnotationAssertion(Annotation( "ZFA") "in ZFA this is defined as part of mesonephros") AnnotationAssertion( "TAO:0005289") AnnotationAssertion( "ZFA:0005289") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006553") AnnotationAssertion(rdfs:label "renal duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (excretory tube) @@ -197818,14 +196801,13 @@ AnnotationAssertion( "UBERON:0006555") AnnotationAssertion(rdfs:label "excretory tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic part of lymphoid system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.") AnnotationAssertion( "consider merging with lymph vasculature") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010522") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]") -AnnotationAssertion( "lymporeticular") -AnnotationAssertion(Annotation( "FMA") "in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system") AnnotationAssertion( "AAO:0010522") AnnotationAssertion( "CALOHA:TS-2024") AnnotationAssertion( "EFO:0000870") @@ -197862,10 +196844,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pharynx) AnnotationAssertion(Annotation( "GO:0060465") "The pharynx is the part of the digestive system immediately posterior to the mouth[GO].") -AnnotationAssertion( "currently this is an extremely generic class, encompassing both protostomes and deuterostomes.") -AnnotationAssertion( "2023-04-20") -AnnotationAssertion( "branchial") -AnnotationAssertion( "pharyngeal") AnnotationAssertion( "MAT:0000049") AnnotationAssertion( "MESH:D010614") AnnotationAssertion( "MIAA:0000049") @@ -197887,11 +196865,12 @@ AnnotationAssertion( "UBERON:0006563") AnnotationAssertion(rdfs:label "tunica media of pulmonary trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female urethral meatus) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "Wikipedia:External_urethral_orifice_(female)") "A urethral meatus that is part of a female urethra[Automatically generated definition].") -AnnotationAssertion(Annotation( "Wikipedia:External_urethral_orifice_(female)") "The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts.") AnnotationAssertion( "EMAPA:36453") AnnotationAssertion( "FMA:85266") AnnotationAssertion( "MA:0002639") @@ -197908,14 +196887,13 @@ AnnotationAssertion(Annotation( "UBERON:0006565") AnnotationAssertion(rdfs:label "female urethral meatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left ventricle myocardium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A myocardium that is part of a left ventricle of a heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:9558") "Myocardium of ventricle which is continuous with the tunica media of aorta.") -AnnotationAssertion( "EMAPA:17339") AnnotationAssertion( "FMA:9558") AnnotationAssertion( "MA:0002983") AnnotationAssertion( "SCTID:362021000") @@ -197926,14 +196904,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left ventricle myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (right ventricle myocardium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A myocardium that is part of a right ventricle of a heart.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA:9535") "Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.") -AnnotationAssertion( "EMAPA:17342") AnnotationAssertion( "FMA:9535") AnnotationAssertion( "MA:0002984") AnnotationAssertion( "SCTID:362020004") @@ -197945,6 +196923,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right ventricle myocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypothalamic nucleus) @@ -197960,6 +196940,8 @@ AnnotationAssertion( "UBERON:0006568") AnnotationAssertion(rdfs:label "hypothalamic nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diencephalic nucleus) @@ -197970,6 +196952,8 @@ AnnotationAssertion( "UBERON:0006569") AnnotationAssertion(rdfs:label "diencephalic nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula carnea of right ventricle) @@ -197981,6 +196965,8 @@ AnnotationAssertion( "UBERON:0006570") AnnotationAssertion(rdfs:label "trabecula carnea of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecula carnea of left ventricle) @@ -197992,11 +196978,12 @@ AnnotationAssertion( "UBERON:0006571") AnnotationAssertion(rdfs:label "trabecula carnea of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectinate line) AnnotationAssertion(Annotation( "Wikipedia:Pectinate_line") "The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:.") -AnnotationAssertion(Annotation( "FMA") "FMA also has FMA:29321 but it's not clear how this differs") AnnotationAssertion( "EMAPA:19159") AnnotationAssertion( "FMA:75383") AnnotationAssertion( "NCIT:C34245") @@ -198015,7 +197002,11 @@ AnnotationAssertion( "pectinate line") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibular organ) @@ -198027,12 +197018,13 @@ AnnotationAssertion( "UBERON:0006585") AnnotationAssertion(rdfs:label "vestibular organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (otolymph) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Transudate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph).") -AnnotationAssertion(Annotation( "MESH:A12.207.571") "Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571])") AnnotationAssertion( "UBERON:0007793") AnnotationAssertion( "EMAPA:36547") AnnotationAssertion( "GAID:1183") @@ -198060,7 +197052,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive blood) @@ -198074,6 +197069,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive structure) @@ -198088,6 +197085,8 @@ AnnotationAssertion( "UBERON:0006598") AnnotationAssertion(rdfs:label "presumptive structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive enteric nervous system) @@ -198101,7 +197100,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive enteric nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK10065") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive ectoderm) @@ -198117,7 +197118,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive mesoderm) @@ -198132,14 +197136,14 @@ AnnotationAssertion( "presumptive mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mandibular symphysis) AnnotationAssertion(Annotation( "TAO:wd") Annotation( "Wikipedia:Symphysis_menti") Annotation( "ZFA:0005488") "A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified].") AnnotationAssertion( "this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001851") Annotation( "TAO") Annotation( "TAO:wd") "Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]") -AnnotationAssertion(Annotation( "ISBN:0073040584") "in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible") AnnotationAssertion( "AAO:0000277") AnnotationAssertion( "FMA:75779") AnnotationAssertion( "MA:0001490") @@ -198161,17 +197165,14 @@ AnnotationAssertion( ObjectIntersectionOf( ObjectExactCardinality(2 ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "connects adjacent mandibles") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (aponeurosis) AnnotationAssertion(Annotation( "AEO:0000092") Annotation( "Wikipedia:Aponeurosis") "A sheet of extracellular matrix.") -AnnotationAssertion(Annotation( "Wikipedia:Aponeurosis") "Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis].") -AnnotationAssertion(Annotation( "ZFA") "in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections") AnnotationAssertion( "AEO:0000092") AnnotationAssertion( "EHDAA2:0003092") AnnotationAssertion( "FMA:9722") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D000070606") AnnotationAssertion( "NCIT:C32133") AnnotationAssertion( "SCTID:331712004") AnnotationAssertion(Annotation( "ncithesaurus:Aponeurosis") "UMLS:C0225205") @@ -198186,7 +197187,6 @@ AnnotationAssertion( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) # Class: (venous sinus) @@ -198207,7 +197207,6 @@ SubClassOf( (right external ear) AnnotationAssertion(Annotation( "OBOL:automatic") "An external ear that is in the right side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "FMA:53643") "right auricular region") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37361") AnnotationAssertion( "FMA:53643") @@ -198217,11 +197216,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left external ear) AnnotationAssertion(Annotation( "OBOL:automatic") "An external ear that is in the left side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "FMA:53644") "left auricular region") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37360") AnnotationAssertion( "FMA:53644") @@ -198231,6 +197231,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculo-phrenic artery) @@ -198246,7 +197248,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "musculo-phrenic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of oviduct) @@ -198267,6 +197270,10 @@ AnnotationAssertion( "UBERON:0006642") AnnotationAssertion(rdfs:label "muscle layer of oviduct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adventitia of epididymis) @@ -198278,6 +197285,10 @@ AnnotationAssertion( "UBERON:0006645") AnnotationAssertion(rdfs:label "adventitia of epididymis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of epididymis) @@ -198288,6 +197299,10 @@ AnnotationAssertion( "UBERON:0006646") AnnotationAssertion(rdfs:label "muscle layer of epididymis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adventitia of ductus deferens) @@ -198305,6 +197320,9 @@ AnnotationAssertion( "UBERON:0006647") AnnotationAssertion(rdfs:label "adventitia of ductus deferens") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adventitia of seminal vesicle) @@ -198320,6 +197338,10 @@ AnnotationAssertion( "UBERON:0006648") AnnotationAssertion(rdfs:label "adventitia of seminal vesicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscular layer of vagina) @@ -198333,12 +197355,15 @@ AnnotationAssertion( "UBERON:0006652") AnnotationAssertion(rdfs:label "muscular layer of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glans clitoris) AnnotationAssertion(Annotation( "BTO:0003117") Annotation( "Wikipedia:Clitoral_glans") "Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP].") AnnotationAssertion( "BTO:0003117") -AnnotationAssertion( "EMAPA:19170") AnnotationAssertion( "EMAPA:30829") AnnotationAssertion( "FMA:19999") AnnotationAssertion( "NCIT:C32681") @@ -198355,19 +197380,16 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (glenoid fossa) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") "Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000749") Annotation( "AAO") Annotation( "AAO:LAP") "Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000749") Annotation( "AAO") "relationship loss: part_of scapular area (AAO:0000935)[AAO]") -AnnotationAssertion(Annotation( "ad") "The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans") -AnnotationAssertion(Annotation( "FMA") "FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself") AnnotationAssertion( "AAO:0000749") AnnotationAssertion( "EMAPA:25122") AnnotationAssertion( "FMA:23275") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D061165") AnnotationAssertion( "NCIT:C32682") AnnotationAssertion( "SCTID:181914008") AnnotationAssertion(Annotation( "ncithesaurus:Glenoid_Fossa") "UMLS:C1261046") @@ -198386,12 +197408,11 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png"^^xsd:anyURI) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "to be revised after scapulocoracoid fixes") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interphalangeal joint) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A joint that connects one phalanx to another along a proximodistal axis.") -AnnotationAssertion(Annotation( "ncithesaurus:Interphalangeal_Joint") "Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37884") AnnotationAssertion( "FMA:42765") AnnotationAssertion( "NCIT:C101527") @@ -198403,18 +197424,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interphalangeal joint") EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "two phalanges in series") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscular coat) AnnotationAssertion(Annotation( "Wikipedia:Muscular_layer") "A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis.") AnnotationAssertion( "currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "BTO:0004838") "An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO].") -AnnotationAssertion( "typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.") AnnotationAssertion( "BTO:0004838") AnnotationAssertion( "SCTID:86915006") AnnotationAssertion(Annotation( "ncithesaurus:Muscle_Layer") "UMLS:C0225358") @@ -198432,10 +197450,9 @@ AnnotationAssertion(Annotation( "Wikipedia:Muscularis_externa") "tunica muscularis") AnnotationAssertion( "UBERON:0006660") AnnotationAssertion(rdfs:label "muscular coat") -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicranial aponeurosis) @@ -198473,12 +197490,13 @@ AnnotationAssertion( "carotid canal") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central tendon of diaphragm) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0012061") "The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001399") Annotation( "VHOG") Annotation( "DOI:10.1016/j.resp.2006.06.003") Annotation( "http://bgee.unil.ch/") "In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]") AnnotationAssertion( "EMAPA:17702") AnnotationAssertion( "FMA:58279") AnnotationAssertion( "NCIT:C34119") @@ -198494,20 +197512,24 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "central tendon of diaphragm") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous valve) AnnotationAssertion(Annotation( "OBOL:automatic") "A valve that is part of a vein.") AnnotationAssertion( "FMA:68095") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D055422") AnnotationAssertion(Annotation( "FMA:68095") "valve of vein") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006675") AnnotationAssertion(rdfs:label "venous valve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface of epithelium) @@ -198518,6 +197540,8 @@ AnnotationAssertion( "UBERON:0006677") AnnotationAssertion(rdfs:label "surface of epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypoglossal canal) @@ -198533,8 +197557,10 @@ AnnotationAssertion(Annotation( "UBERON:0006682") AnnotationAssertion(rdfs:label "hypoglossal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal vein) @@ -198550,16 +197576,16 @@ AnnotationAssertion(Annotation( "UBERON:0006686") AnnotationAssertion(rdfs:label "spinal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebral canal) AnnotationAssertion(Annotation( "Wikipedia:Spinal_canal") Annotation( "http://orcid.org/0000-0002-6601-2165") "A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes.") AnnotationAssertion( "TODO - check neural vs vertebral canal; embryonic vs adult?") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000693") Annotation( "AAO") Annotation( "AAO:LAP") "Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO]") AnnotationAssertion( "AAO:0000693") AnnotationAssertion( "FMA:9680") AnnotationAssertion( "GAID:242") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D013115") AnnotationAssertion( "NCIT:C33869") AnnotationAssertion( "NCIT:C34221") AnnotationAssertion( "SCTID:361746009") @@ -198578,8 +197604,11 @@ AnnotationAssertion( "vertebral canal") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebellum vasculature) @@ -198589,11 +197618,13 @@ AnnotationAssertion( "UBERON:0006694") AnnotationAssertion(rdfs:label "cerebellum vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesopodium region) AnnotationAssertion(Annotation( "MA:th") Annotation( "Wikipedia:Carpus_and_tarsus_of_land_vertebrates") Annotation( "https://orcid.org/0000-0002-6601-2165") "The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus).") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group") AnnotationAssertion( "Wikipedia:Carpus_and_tarsus_of_land_vertebrates") AnnotationAssertion( "carpus/tarsus") AnnotationAssertion(Annotation( "MA:th") "mesopodial limb segment") @@ -198603,14 +197634,15 @@ AnnotationAssertion( "UBERON:0006716") AnnotationAssertion(rdfs:label "mesopodium region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA:th") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autopodial skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in an autopodium region.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005019") Annotation( "VSAO") Annotation( "VSAO:NI") "Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group") AnnotationAssertion( "VSAO:0005019") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "autopod skeleton") AnnotationAssertion(Annotation( "VSAO:0005019") "autopodial skeleton") @@ -198621,8 +197653,11 @@ AnnotationAssertion(Annotation( "UBERON:0006717") AnnotationAssertion(rdfs:label "autopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear modiolus) @@ -198647,6 +197682,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cochlear modiolus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -198654,7 +197690,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (spiral ligament) AnnotationAssertion(Annotation( "Wikipedia:Spiral_ligament") Annotation( "https://github.com/obophenotype/mouse-anatomy-ontology/issues/71") "A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis.") -AnnotationAssertion(Annotation( "FMA") "this is not classified as a ligament in FMA") AnnotationAssertion( "UBERON:0028186") AnnotationAssertion( "BIRNLEX:2524") AnnotationAssertion( "EMAPA:35798") @@ -198672,6 +197707,7 @@ AnnotationAssertion( "UBERON:0006725") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spiral ligament") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -198680,7 +197716,6 @@ SubClassOf(Annotation( "MES # Class: (median lingual swelling) AnnotationAssertion(Annotation( "Wikipedia:Tuberculum_impar") "During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000730") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2002.00073.x") Annotation( "http://bgee.unil.ch/") "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0001081") AnnotationAssertion( "EMAPA:17187") AnnotationAssertion( "FMA:312476") @@ -198696,16 +197731,13 @@ AnnotationAssertion( "The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview]") AnnotationAssertion(rdfs:label "median lingual swelling") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral lingual swelling) AnnotationAssertion(Annotation( "Wikipedia:Lateral_lingual_swelling") "During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000731") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)") Annotation( "http://bgee.unil.ch/") "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]") -AnnotationAssertion( "paired") AnnotationAssertion( "EHDAA2:0000911") AnnotationAssertion( "EMAPA:17189") AnnotationAssertion( "FMA:313628") @@ -198719,8 +197751,7 @@ AnnotationAssertion(Annotation( "UBERON:0006757") AnnotationAssertion(rdfs:label "lateral lingual swelling") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -198754,7 +197785,11 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "corneo-scleral junction") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of conjunctiva) @@ -198773,6 +197808,7 @@ AnnotationAssertion( "epithelium of conjunctiva") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (glandular epithelium) @@ -198788,6 +197824,8 @@ AnnotationAssertion( "UBERON:0006799") AnnotationAssertion(rdfs:label "glandular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal skeleton) @@ -198802,15 +197840,15 @@ AnnotationAssertion( "nasal skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "facial series") Annotation( "Kardong-abduced") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (areolar connective tissue) AnnotationAssertion(Annotation( "FMA:63897") "Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000027") Annotation( "AAO") Annotation( "AAO:LAP") "Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000027") Annotation( "AAO") "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]") -AnnotationAssertion(Annotation( "AAO") "cushions body organs") AnnotationAssertion( "AAO:0000027") AnnotationAssertion( "FMA:63897") AnnotationAssertion( "SCTID:68477002") @@ -198833,17 +197871,20 @@ AnnotationAssertion( "UBERON:0006828") AnnotationAssertion(rdfs:label "trabecula carnea of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of open tracheal system trachea) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical space that surrounded_by a open tracheal system trachea.") AnnotationAssertion(Annotation( "FBbt:00007410") Annotation( ) "tracheal lumen") -AnnotationAssertion(Annotation( ) "FBbt:00007410") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006832") AnnotationAssertion(rdfs:label "lumen of open tracheal system trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of trachea) @@ -198856,13 +197897,14 @@ AnnotationAssertion( "UBERON:0006833") AnnotationAssertion(rdfs:label "lumen of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (uterus or analog) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of a the reproductive tract in a female organism that is the site of embryo development.") AnnotationAssertion(Annotation( "FBbt:00004924") Annotation( ) "uterus") -AnnotationAssertion(Annotation( ) "FBbt:00004924") AnnotationAssertion( "TADS:0000421") AnnotationAssertion( "WBbt:0006760") AnnotationAssertion( "uberon") @@ -198870,8 +197912,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "uterus or analog") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central vein of liver) @@ -198892,7 +197937,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "central vein of liver") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (root of cranial nerve) @@ -198910,6 +197956,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "root of cranial nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface groove) @@ -198930,13 +197979,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "VSAO:0000157") Annotation( "https://github.com/obophenotype/uberon/issues/204") Annotation( "https://github.com/obophenotype/uberon/issues/339") "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "TAO:0000583") "Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000751") Annotation( "AAO") Annotation( "AAO:LAP") "Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000751") Annotation( "AAO") "relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000751") Annotation( "AAO") "relationship loss: part_of scapular area (AAO:0000935)[AAO]") -AnnotationAssertion( "scapular") -AnnotationAssertion(Annotation( "ISBN:978-0-12-319060-4") "present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals.") -AnnotationAssertion( "chick scapula is of dual origin and segmentally organized") AnnotationAssertion( "UBERON:0001124") AnnotationAssertion( "UBERON:0010904") AnnotationAssertion( "AAO:0000751") @@ -198970,9 +198012,11 @@ AnnotationAssertion( "scapula") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ZFA-abduced") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal cortex peritubular capillary) @@ -198985,6 +198029,8 @@ AnnotationAssertion( "UBERON:0006851") AnnotationAssertion(rdfs:label "renal cortex peritubular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal cortex tubule) @@ -198997,6 +198043,7 @@ AnnotationAssertion(Annotation( "UBERON:0006853") AnnotationAssertion(rdfs:label "renal cortex tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (distal straight tubule postmacula segment) @@ -199011,14 +198058,13 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0006854") AnnotationAssertion(rdfs:label "distal straight tubule postmacula segment") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (muscular coat of ureter) AnnotationAssertion(Annotation( "OBOL:automatic") "A muscular coat that is part of a ureter.") -AnnotationAssertion( "EMAPA:28811") AnnotationAssertion( "FMA:15893") AnnotationAssertion( "MA:0002654") AnnotationAssertion( "SCTID:3563003") @@ -199032,14 +198078,14 @@ AnnotationAssertion(Annotation( "UBERON:0006855") AnnotationAssertion(rdfs:label "muscular coat of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (adrenal/interrenal gland) AnnotationAssertion(Annotation( "GO:0030325") "This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO].") AnnotationAssertion( "keep this grouping class so long as it is required for GO") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001141") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9") Annotation( "http://bgee.unil.ch/") "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]") -AnnotationAssertion( "VHOG:0001141") AnnotationAssertion(Annotation( "VHOG:0001141") "adrenal gland - interrenal gland") AnnotationAssertion( "adrenal gland/interrenal tissue") AnnotationAssertion( "uberon") @@ -199050,6 +198096,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adrenal/interrenal gland") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199058,8 +198106,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (diaphysis proper) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these.") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate") AnnotationAssertion( "FMA:32688") AnnotationAssertion( "MA:0002803") AnnotationAssertion(Annotation( "FMA:32688") "body proper of long bone") @@ -199076,7 +198122,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (diaphysis of femur) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "Wikipedia:Body_of_femur") "A diaphysis that is part of a femur[Automatically generated definition].") -AnnotationAssertion(Annotation( "Wikipedia:Body_of_femur") "The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37538") AnnotationAssertion( "FMA:32847") AnnotationAssertion( "MA:0003055") @@ -199094,6 +198139,9 @@ AnnotationAssertion( "diaphysis of femur") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal metaphysis of femur) @@ -199104,7 +198152,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal metaphysis of femur") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (metaphysis of femur) @@ -199118,13 +198167,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metaphysis of femur") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (terminal part of digestive tract) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.") -AnnotationAssertion( "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.") -AnnotationAssertion(Annotation( ) "FBbt:00005756") AnnotationAssertion( "WBbt:0005773") AnnotationAssertion(Annotation( "FBbt:00005756") "rectum") AnnotationAssertion( "uberon") @@ -199139,7 +198188,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (seminal fluid secreting gland) AnnotationAssertion(Annotation( "OBOL:automatic") "A gland that secretes a seminal fluid.") -AnnotationAssertion(Annotation( ) "FBbt:00004958") AnnotationAssertion( "WBbt:0006870") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0006868") @@ -199147,12 +198195,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "seminal fluid secreting gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic footplate) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "MP:0004576") Annotation( "UBERON:cjm") Annotation( "https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2218") "The distal elements of the developing limb of vertebrates that will give rise to the pes (foot).") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER") AnnotationAssertion( "UBERON:0004343") AnnotationAssertion( "foot plate") AnnotationAssertion( "footplate") @@ -199169,7 +198218,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic footplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (handplate apical ectodermal ridge) @@ -199180,6 +198231,8 @@ AnnotationAssertion( "UBERON:0006872") AnnotationAssertion(rdfs:label "handplate apical ectodermal ridge") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic handplate) @@ -199197,7 +198250,9 @@ AnnotationAssertion(Annotation( "UBERON:0006875") AnnotationAssertion(rdfs:label "embryonic handplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of organ) @@ -199210,11 +198265,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of liver) AnnotationAssertion(Annotation( "OBOL:automatic") "A vasculature that is part of a liver.") -AnnotationAssertion(Annotation( "EHDAA2") "the EHDAA2 term and the FMA term may not be exact equivalents - check") AnnotationAssertion( "EHDAA2:0003454") AnnotationAssertion( "EMAPA:35501") AnnotationAssertion( "FMA:73748") @@ -199227,6 +198283,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of liver") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head mesenchyme from mesoderm) @@ -199257,8 +198316,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "head mesenchyme from mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") Annotation( "XAO") ObjectSomeValuesFrom( )) # Class: (mandibular process mesenchyme) @@ -199274,13 +198333,13 @@ AnnotationAssertion( "UBERON:0006905") AnnotationAssertion(rdfs:label "mandibular process mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (slow muscle tissue) AnnotationAssertion(Annotation( "BTO:0002317") "The darker-colored muscle tissue of some mammals, composed of slow twitch muscle fibers.") AnnotationAssertion( "check if relationship to cell types should be more specific type I cells") -AnnotationAssertion( "The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)") -AnnotationAssertion(Annotation( "CALOHA") "check if CALOHA term is for fiber or tissue.") AnnotationAssertion( "BTO:0002317") AnnotationAssertion( "CALOHA:TS-0940") AnnotationAssertion( "NCIT:C12614") @@ -199293,6 +198352,8 @@ AnnotationAssertion(Annotation( "UBERON:0006907") AnnotationAssertion(rdfs:label "slow muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fast muscle tissue) @@ -199309,6 +198370,8 @@ AnnotationAssertion( "The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)") AnnotationAssertion(rdfs:label "fast muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of digestive tract) @@ -199327,12 +198390,13 @@ AnnotationAssertion( "UBERON:0006909") AnnotationAssertion(rdfs:label "lumen of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lip epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a lip.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005334") Annotation( "TAO") Annotation( "ZFIN:ZDB-PUB-060921-12") "The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]") AnnotationAssertion( "BTO:0004468") AnnotationAssertion( "TAO:0005334") AnnotationAssertion( "ZFA:0005334") @@ -199340,11 +198404,12 @@ AnnotationAssertion( "UBERON:0006913") AnnotationAssertion(rdfs:label "lip epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (squamous epithelium) AnnotationAssertion(Annotation( "Wikipedia:Squamous_epithelium") "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.") -AnnotationAssertion(Annotation( "FBbt") "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium") AnnotationAssertion( "BTO:0002072") AnnotationAssertion( "NCIT:C12848") AnnotationAssertion( "SCTID:40118003") @@ -199354,6 +198419,8 @@ AnnotationAssertion( "UBERON:0006914") AnnotationAssertion(rdfs:label "squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratified squamous epithelium) @@ -199368,6 +198435,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratified squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (non-keratinized epithelium of tongue) @@ -199377,11 +198446,12 @@ AnnotationAssertion( "UBERON:0006916") AnnotationAssertion(rdfs:label "non-keratinized epithelium of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (tongue squamous epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "A squamous epithelium that is part of a tongue.") -AnnotationAssertion(Annotation( "MA") "this is a singleton subclass of tongue epithelium in MA") AnnotationAssertion( "MA:0002786") AnnotationAssertion(Annotation( "OBOL:automatic") "squamous epithelium of tongue") AnnotationAssertion( "uberon") @@ -199389,12 +198459,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tongue squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus squamous epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "A squamous epithelium that is part of a esophagus.") -AnnotationAssertion(Annotation( "MA") "MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass") AnnotationAssertion( "BTO:0003635") AnnotationAssertion( "CALOHA:TS-1250") AnnotationAssertion( "EMAPA:35324") @@ -199409,6 +198481,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "esophagus squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (stomach squamous epithelium) @@ -199420,6 +198494,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (cervix squamous epithelium) @@ -199436,6 +198511,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervix squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (vagina squamous epithelium) @@ -199450,13 +198526,13 @@ AnnotationAssertion( "UBERON:0006923") AnnotationAssertion(rdfs:label "vagina squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (stomach glandular epithelium) AnnotationAssertion(Annotation( "ISBN:0073040584") "A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.") AnnotationAssertion( "we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.") -AnnotationAssertion( "EMAPA:17623") AnnotationAssertion( "EMAPA:35814") AnnotationAssertion( "FMA:63458") AnnotationAssertion( "MA:0002784") @@ -199467,6 +198543,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach glandular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199482,6 +198559,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "digestive system gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (glandular columnar epithelium) @@ -199493,6 +198572,8 @@ AnnotationAssertion( "UBERON:0006929") AnnotationAssertion(rdfs:label "glandular columnar epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (glandular cuboidal epithelium) @@ -199501,6 +198582,8 @@ AnnotationAssertion( "UBERON:0006930") AnnotationAssertion(rdfs:label "glandular cuboidal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (stomach glandular region mucosa) @@ -199512,6 +198595,8 @@ AnnotationAssertion( "UBERON:0006931") AnnotationAssertion(rdfs:label "stomach glandular region mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibular epithelium) @@ -199530,11 +198615,12 @@ AnnotationAssertion( "vestibular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sensory epithelium) AnnotationAssertion(Annotation( "BTO:0000314") "Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.") -AnnotationAssertion(Annotation( "FMA") "note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical") AnnotationAssertion( "CALOHA:TS-0682") AnnotationAssertion( "FMA:62410") AnnotationAssertion( "SCTID:309045006") @@ -199545,6 +198631,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (crista ampullaris neuroepithelium) @@ -199575,6 +198662,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thymus subcapsular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner ear epithelium) @@ -199587,6 +198676,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inner ear epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pinna surface epithelium) @@ -199599,13 +198691,12 @@ AnnotationAssertion( "UBERON:0006938") AnnotationAssertion(rdfs:label "pinna surface epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (efferent duct) AnnotationAssertion(Annotation( "Wikipedia:Efferent_ducts") "The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010532") Annotation( "AAO") Annotation( "AAO:BJB") "Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]") -AnnotationAssertion( "There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis") -AnnotationAssertion(Annotation( "EMAPA") "Check EMAPA") AnnotationAssertion( "AAO:0010532") AnnotationAssertion( "EMAPA:18993") AnnotationAssertion( "FMA:19081") @@ -199622,8 +198713,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "efferent duct") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg"^^xsd:anyURI) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199633,8 +198724,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (male genital duct) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra.") -AnnotationAssertion( "we use this as a generic grouping class for a number of taxa") -AnnotationAssertion(Annotation( "FMA") "in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct") AnnotationAssertion( "UBERON:0010140") AnnotationAssertion( "FMA:55678") AnnotationAssertion( "TAO:0001268") @@ -199646,7 +198735,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male genital duct") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199663,6 +198754,9 @@ AnnotationAssertion( "UBERON:0006948") AnnotationAssertion(rdfs:label "efferent duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ejaculatory duct epithelium) @@ -199674,11 +198768,13 @@ AnnotationAssertion( "UBERON:0006953") AnnotationAssertion(rdfs:label "ejaculatory duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland myoepithelium) AnnotationAssertion(Annotation( "MGI:anna") "The outer cell layer of the mammary gland epithelium bilayer which is located basal to the luminal (secretory) cells and adjacent to the basement membrane.") -AnnotationAssertion( "The cells of this structure are specialized epithelial cells that express smooth muscle-specific contractile and cytoskeletal properties; during lactation, MECs contract in response to oxytocin to generate the contractile force required for milk ejection; MECs are involved in all developmental stages of mammary gland morphogenesis, modulating proliferation and differentiation of luminal cells; they take part in the formation of extracellular matrix, synthesizing its components and secreting proteinases and their inhibitors; in addition, MECs are regarded as natural cancer suppressors: they secrete suppressor proteins limiting cancer growth, invasiveness, and neoangiogenesis; MECs are markedly resistant to malignant transformation and they are able to suppress the transformation of neighboring luminal cells[MP]") AnnotationAssertion( "BTO:0002310") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37903") AnnotationAssertion( "FMA:67798") @@ -199690,6 +198786,8 @@ AnnotationAssertion( "UBERON:0006954") AnnotationAssertion(rdfs:label "mammary gland myoepithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (uterine epithelium) @@ -199701,6 +198799,8 @@ AnnotationAssertion(Annotation( "UBERON:0006955") AnnotationAssertion(rdfs:label "uterine epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovary stroma) @@ -199725,14 +198825,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ovary stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (pars distalis of adenohypophysis) AnnotationAssertion(Annotation( "Dorlands_Medical_Dictionary:MerckSource") Annotation( "Wikipedia:Pars_distalis") "The distal part of adenohypophysis: the part that makes up the main body of the gland.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010542") Annotation( "AAO") Annotation( "AAO:BJB") "Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000244") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") Annotation( "http://www.thefreedictionary.com/pars+anterior") "The anterior part of the adenohypophysis. [TFD][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000244") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5") Annotation( "http://bgee.unil.ch/") "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]") AnnotationAssertion(Annotation( "BIRNLEX:1022") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "DHP") AnnotationAssertion(Annotation( "EHDAA2:0001416") Annotation( "MA:0000854") Annotation( "ZFA:0001195") "pars anterior") AnnotationAssertion( "AAO:0010542") @@ -199767,7 +198867,7 @@ AnnotationAssertion(Annotation( "UBERON:0006964") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pars distalis of adenohypophysis") -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (vascular cord) @@ -199780,6 +198880,7 @@ AnnotationAssertion( "UBERON:0006965") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vascular cord") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199795,7 +198896,8 @@ AnnotationAssertion( "UBERON:0006966") AnnotationAssertion(rdfs:label "coronary capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (anatomical surface) @@ -199811,7 +198913,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.") AnnotationAssertion(rdfs:label "anatomical surface") -SubClassOf(Annotation( "via morphological boundary in CARO") ) +SubClassOf( ) # Class: (cardiogenic splanchnic mesoderm) @@ -199837,7 +198939,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiogenic splanchnic mesoderm") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -199852,11 +198955,12 @@ AnnotationAssertion( "cleaving embryo") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sexually immature organism) AnnotationAssertion(Annotation( "OBOL:automatic") "A multicellular organism that is at the juvenile stage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002047") Annotation( "TAO") Annotation( "TAO:wd") "Whole organism that is not fully grown or sexually mature.[TAO]") AnnotationAssertion( "juvenile") AnnotationAssertion( "BILA:0000076") AnnotationAssertion( "TAO:0002047") @@ -199867,15 +198971,16 @@ AnnotationAssertion( "UBERON:0007021") AnnotationAssertion(rdfs:label "sexually immature organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adult organism) AnnotationAssertion(Annotation( "OBOL:automatic") "A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002046") Annotation( "TAO") Annotation( "TAO:wd") "Whole organism that is fully grown or sexually mature.[TAO]") AnnotationAssertion( "adult") AnnotationAssertion( "BILA:0000078") -AnnotationAssertion(Annotation( ) "FBbt:00003004") AnnotationAssertion( "HAO:0000087") AnnotationAssertion( "NCIT:C17600") AnnotationAssertion( "TAO:0002046") @@ -199887,10 +198992,12 @@ AnnotationAssertion( "UBERON:0007023") AnnotationAssertion(rdfs:label "adult organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive gut) -AnnotationAssertion(Annotation( "NCBIBook:NBK10107") "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis") AnnotationAssertion( "BILA:0000084") AnnotationAssertion( "NCIT:C34268") AnnotationAssertion( "SCTID:360394002") @@ -199906,8 +199013,10 @@ AnnotationAssertion( "UBERON:0007026") AnnotationAssertion(rdfs:label "presumptive gut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mechanosensory system) @@ -199917,6 +199026,8 @@ AnnotationAssertion( "UBERON:0007037") AnnotationAssertion(rdfs:label "mechanosensory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mandibular neural crest) @@ -199946,8 +199057,6 @@ SubClassOf(Annotation( "ZFA # Class: (primary circulatory organ) AnnotationAssertion(Annotation( "GO:0007507") "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].") -AnnotationAssertion( "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis") -AnnotationAssertion( "SPD:0000130") AnnotationAssertion( "TADS:0000147") AnnotationAssertion( "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg") AnnotationAssertion(Annotation( "Wikipedia:Heart") "dorsal tube") @@ -199959,14 +199068,13 @@ AnnotationAssertion( "Gene notes: Bmp, Nkx, Gata") AnnotationAssertion(rdfs:label "primary circulatory organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chorionic villus) AnnotationAssertion(Annotation( "BTO:0001161") Annotation( "Wikipedia:Chorionic_villi") "One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.") -AnnotationAssertion( "The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively") -AnnotationAssertion( "The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.") AnnotationAssertion( "BTO:0001161") AnnotationAssertion( "EHDAA2:0004717") AnnotationAssertion( "MESH:D002824") @@ -199990,6 +199098,7 @@ AnnotationAssertion( "UBERON:0007106") AnnotationAssertion(rdfs:label "chorionic villus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP-def") ObjectSomeValuesFrom( )) @@ -200017,15 +199126,14 @@ AnnotationAssertion( "neck of femur") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal pouch 1) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "PMID:16313389") Annotation( "VHOG:0000970") "A pharyngeal pouch that is between pharyngeal arches 1 and 2.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000970") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") ". [][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000970") Annotation( "VHOG") Annotation( "DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)") Annotation( "http://bgee.unil.ch/") "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery") -AnnotationAssertion(Annotation( "EHDAA2") "we use adjacency relations rather than part_of, as in EHDAA2.") AnnotationAssertion( "UBERON:0005718") AnnotationAssertion( "AAO:0011114") AnnotationAssertion( "EFO:0003631") @@ -200060,21 +199168,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal pouch 1") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal pouch 2) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "PMID:16313389") "A pharyngeal puch that is between the pharyngeal arches 2 and 3.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000967") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011115") Annotation( "AAO") Annotation( "ISBN:0-226-55763-4") "Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000967") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion( "the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract.") -AnnotationAssertion(Annotation( "WP") "Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve") AnnotationAssertion( "UBERON:0005715") AnnotationAssertion( "AAO:0011115") AnnotationAssertion( "EFO:0003633") AnnotationAssertion( "EHDAA2:0000058") AnnotationAssertion( "EMAPA:16275") -AnnotationAssertion( "EMAPA:16276") AnnotationAssertion( "FMA:295676") AnnotationAssertion( "NCIT:C34289") AnnotationAssertion( "RETIRED_EHDAA2:0000060") @@ -200103,14 +199208,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal pouch 2") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal pouch 3) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "PMID:16313389") Annotation( "Wikipedia:Pharyngeal_pouch_(embryology)#Third_pouch") "A pharyngeal pouch that between pharyngeal arches 3 and 4.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000966") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011116") Annotation( "AAO") Annotation( "ISBN:0-226-55763-4") "Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000966") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "WP") "The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve") AnnotationAssertion( "UBERON:0005716") AnnotationAssertion( "AAO:0011116") AnnotationAssertion( "EFO:0003634") @@ -200143,14 +199247,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal pouch 3") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal pouch 4) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "PMID:16313389") Annotation( "Wikipedia:Pharyngeal_pouch_(embryology)#Fourth_pouch") "A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes).") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000971") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0011117") Annotation( "AAO") Annotation( "ISBN:0-226-55763-4") "Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000971") Annotation( "VHOG") Annotation( "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)") Annotation( "http://bgee.unil.ch/") "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]") -AnnotationAssertion(Annotation( "MP") "Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands.") AnnotationAssertion( "AAO:0011117") AnnotationAssertion( "EFO:0003637") AnnotationAssertion( "EHDAA2:0000091") @@ -200183,6 +199286,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal pouch 4") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glomeral mesenchyme) @@ -200193,8 +199299,7 @@ AnnotationAssertion(Annotation( "XAO:0000110") "glomerulus") AnnotationAssertion( "UBERON:0007128") AnnotationAssertion(rdfs:label "glomeral mesenchyme") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk ganglion) @@ -200212,11 +199317,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural keel) AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-961014-576") "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000131") Annotation( "TAO") Annotation( "ZFIN:curator") "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]") AnnotationAssertion( "EFO:0003497") AnnotationAssertion( "TAO:0000131") AnnotationAssertion( "ZFA:0000131") @@ -200239,7 +199345,9 @@ AnnotationAssertion( "UBERON:0007142") AnnotationAssertion(rdfs:label "left internal carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right internal carotid artery) @@ -200252,12 +199360,13 @@ AnnotationAssertion( "UBERON:0007143") AnnotationAssertion(rdfs:label "right internal carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic post-anal tail) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail.") -AnnotationAssertion( "By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx).") AnnotationAssertion( "EMAPA:16748") AnnotationAssertion( "FMA:85540") AnnotationAssertion(Annotation( "FMA:85540") "embryo tail") @@ -200267,7 +199376,6 @@ AnnotationAssertion(Annotation( "UBERON:0007144") AnnotationAssertion(rdfs:label "embryonic post-anal tail") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of midgut) @@ -200280,7 +199388,9 @@ AnnotationAssertion( "UBERON:0007147") AnnotationAssertion(rdfs:label "lumen of midgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of hindgut) @@ -200292,7 +199402,9 @@ AnnotationAssertion( "UBERON:0007148") AnnotationAssertion(rdfs:label "lumen of hindgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of anal canal) @@ -200304,7 +199416,9 @@ AnnotationAssertion( "UBERON:0007158") AnnotationAssertion(rdfs:label "lumen of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of colon) @@ -200318,7 +199432,9 @@ AnnotationAssertion(Annotation( "UBERON:0007159") AnnotationAssertion(rdfs:label "lumen of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inferior petrosal sinus) @@ -200345,6 +199461,8 @@ AnnotationAssertion( "UBERON:0007171") AnnotationAssertion(rdfs:label "border of scapula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (angle of scapula) @@ -200433,6 +199551,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lamina propria of mucosa of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of infundibulum of uterine tube) @@ -200445,7 +199565,10 @@ AnnotationAssertion( "UBERON:0007181") AnnotationAssertion(rdfs:label "serosa of infundibulum of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of infundibulum of uterine tube) @@ -200459,7 +199582,11 @@ AnnotationAssertion( "UBERON:0007182") AnnotationAssertion(rdfs:label "muscle layer of infundibulum of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelium of serous pericardium) @@ -200475,6 +199602,8 @@ AnnotationAssertion( "UBERON:0007188") AnnotationAssertion(rdfs:label "mesothelium of serous pericardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stroma of bone marrow) @@ -200487,6 +199616,10 @@ AnnotationAssertion( "UBERON:0007195") AnnotationAssertion(rdfs:label "stroma of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -200508,7 +199641,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tracheobronchial tree") +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -200541,6 +199676,8 @@ AnnotationAssertion(Annotation( "UBERON:0007198") AnnotationAssertion(rdfs:label "hermaphrodite anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brachiocephalic vasculature) @@ -200570,6 +199707,8 @@ AnnotationAssertion( "mesenchyme derived from head neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme derived from trunk neural crest) @@ -200586,6 +199725,8 @@ AnnotationAssertion( "mesenchyme derived from trunk neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (late embryonic stage) @@ -200609,6 +199750,7 @@ AnnotationAssertion( "late embryonic stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/355"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/565"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -200641,6 +199783,7 @@ AnnotationAssertion(Annotation( "UBERON:0007221") AnnotationAssertion(rdfs:label "neonate stage") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/350"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -200654,14 +199797,12 @@ AnnotationAssertion( "UBERON:0007223") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "osseus cochlea") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch mandibular component) AnnotationAssertion( "relationship to Meckel's cartilage to be added") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000510") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000031") AnnotationAssertion( "EHDAA:583") AnnotationAssertion( "EMAPA:16382") @@ -200672,23 +199813,19 @@ AnnotationAssertion(Annotation( "VHOG:0000510") "ventral visceral arch 1") AnnotationAssertion( "UBERON:0007237") AnnotationAssertion(rdfs:label "1st arch mandibular component") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (1st arch maxillary component) AnnotationAssertion( "relationship to palatoquadrate to be added") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000511") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000038") AnnotationAssertion( "EHDAA:595") AnnotationAssertion( "EMAPA:16388") -AnnotationAssertion( "VHOG:0000511") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007238") AnnotationAssertion(rdfs:label "1st arch maxillary component") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (tunica media of artery) @@ -200706,6 +199843,7 @@ AnnotationAssertion( "UBERON:0007239") AnnotationAssertion(rdfs:label "tunica media of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica adventitia of artery) @@ -200721,6 +199859,7 @@ AnnotationAssertion( "UBERON:0007240") AnnotationAssertion(rdfs:label "tunica adventitia of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -200737,6 +199876,8 @@ AnnotationAssertion( "UBERON:0007241") AnnotationAssertion(rdfs:label "tunica adventitia of vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica intima of vein) @@ -200751,6 +199892,9 @@ AnnotationAssertion( "UBERON:0007242") AnnotationAssertion(rdfs:label "tunica intima of vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica media of vein) @@ -200765,6 +199909,8 @@ AnnotationAssertion( "UBERON:0007243") AnnotationAssertion(rdfs:label "tunica media of vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nuclear complex of neuraxis) @@ -200778,11 +199924,12 @@ AnnotationAssertion( "UBERON:0007245") AnnotationAssertion(rdfs:label "nuclear complex of neuraxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of superior olivary complex) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.") -AnnotationAssertion( "this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.") AnnotationAssertion( "FMA:72246") AnnotationAssertion( "SCTID:369024009") AnnotationAssertion(Annotation( "FMA:72246") "superior olivary complex nucleus") @@ -200792,6 +199939,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus of superior olivary complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (preoptic nucleus) @@ -200799,11 +199949,12 @@ AnnotationAssertion(Annotation( "Hardisty, p. 320-1") ) AnnotationAssertion( "CALOHA:TS-0822") AnnotationAssertion( "EV:0100226") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D011301") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007251") AnnotationAssertion(rdfs:label "preoptic nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intervertebral disk of cervical vertebra) @@ -200817,6 +199968,11 @@ AnnotationAssertion( "UBERON:0007252") AnnotationAssertion(rdfs:label "intervertebral disk of cervical vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intervertebral disk of thoracic vertebra) @@ -200828,6 +199984,11 @@ AnnotationAssertion( "UBERON:0007254") AnnotationAssertion(rdfs:label "intervertebral disk of thoracic vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intervertebral disk of atlas) @@ -200846,6 +200007,8 @@ AnnotationAssertion( "intervertebral disk of atlas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trachea pre-cartilage rings) @@ -200856,6 +200019,8 @@ AnnotationAssertion( "UBERON:0007267") AnnotationAssertion(rdfs:label "trachea pre-cartilage rings") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pectoral appendage musculature) @@ -200872,12 +200037,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral appendage musculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage musculature) AnnotationAssertion(Annotation( "OBOL:automatic") "Any collection of muscles that is part of a pelvic appendage.") AnnotationAssertion( "currently defined by location rather than attachment") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000258") Annotation( "TAO") Annotation( "TAO:curator") "Musculature that is part of the pelvic fin.[TAO]") AnnotationAssertion( "TAO:0000258") AnnotationAssertion( "ZFA:0000258") AnnotationAssertion(Annotation( "ZFA:0000258") Annotation( ) "pelvic fin musculature") @@ -200885,6 +200052,9 @@ AnnotationAssertion( "UBERON:0007270") AnnotationAssertion(rdfs:label "pelvic appendage musculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendage musculature) @@ -200897,19 +200067,22 @@ AnnotationAssertion( "UBERON:0007271") AnnotationAssertion(rdfs:label "appendage musculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage skeleton) AnnotationAssertion(Annotation( "VSAO:0005000") Annotation( "VSAO:NI") "Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.") -AnnotationAssertion( ) AnnotationAssertion( "VSAO:0005000") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "VSAO:0005000") Annotation( "VSAO:NI") "cheiropterygium") AnnotationAssertion( "UBERON:0007272") AnnotationAssertion(rdfs:label "pectoral appendage skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage skeleton) @@ -200918,14 +200091,15 @@ AnnotationAssertion( "UBERON:0007273") AnnotationAssertion(rdfs:label "pelvic appendage skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive hindbrain) AnnotationAssertion(Annotation( "Wikipedia:Rhombencephalon") "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.") AnnotationAssertion( "TODO - unify naming conventions") -AnnotationAssertion(Annotation( "NPX:PDR") "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].") AnnotationAssertion( "BAMS:HB") AnnotationAssertion( "CALOHA:TS-2118") AnnotationAssertion( "EFO:0003440") @@ -200943,9 +200117,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive hindbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO-abduced") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive sinus venosus) @@ -200956,20 +200132,23 @@ AnnotationAssertion( "UBERON:0007278") AnnotationAssertion(rdfs:label "presumptive sinus venosus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive endocardium) AnnotationAssertion(Annotation( "OBOL:automatic") "A presumptive structure that has the potential to develop into a endocardium.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002233") Annotation( "TAO") Annotation( "ZFIN:curator") "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]") AnnotationAssertion( "TAO:0002233") AnnotationAssertion( "ZFA:0001724") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007280") AnnotationAssertion(rdfs:label "presumptive endocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive midbrain hindbrain boundary) @@ -200985,7 +200164,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive midbrain hindbrain boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive segmental plate) @@ -200999,13 +200180,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive segmental plate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") Annotation( "EDHAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive neural plate) AnnotationAssertion(Annotation( "OBOL:automatic") "A presumptive structure that has the potential to develop into a neural plate.") AnnotationAssertion( "consider merging") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000063") Annotation( "TAO") Annotation( "ZFIN:curator") "Region of the gastrula which gives rise to the neural plate.[TAO]") AnnotationAssertion( "EFO:0003424") AnnotationAssertion( "TAO:0000063") AnnotationAssertion( "ZFA:0000063") @@ -201019,6 +200201,7 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive paraxial mesoderm) @@ -201034,6 +200217,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive paraxial mesoderm") EquivalentClasses(Annotation( "https://github.com/obophenotype/uberon/issues/1277") ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive forebrain midbrain boundary) @@ -201046,7 +200232,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive forebrain midbrain boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive rhombomere 1) @@ -201057,6 +200245,8 @@ AnnotationAssertion( "UBERON:0007289") AnnotationAssertion(rdfs:label "presumptive rhombomere 1") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive pronephric mesoderm) @@ -201070,6 +200260,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive pronephric mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric proximal convoluted tubule) @@ -201080,7 +200272,8 @@ AnnotationAssertion( "UBERON:0007298") AnnotationAssertion(rdfs:label "pronephric proximal convoluted tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (pectoral appendage blood vessel) @@ -201092,6 +200285,8 @@ AnnotationAssertion( "UBERON:0007300") AnnotationAssertion(rdfs:label "pectoral appendage blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendage blood vessel) @@ -201104,6 +200299,7 @@ AnnotationAssertion( "UBERON:0007301") AnnotationAssertion(rdfs:label "appendage blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage vasculature) @@ -201116,6 +200312,8 @@ AnnotationAssertion( "UBERON:0007302") AnnotationAssertion(rdfs:label "pectoral appendage vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal vasculature) @@ -201127,6 +200325,8 @@ AnnotationAssertion( "UBERON:0007303") AnnotationAssertion(rdfs:label "pharyngeal vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendage vasculature) @@ -201138,6 +200338,8 @@ AnnotationAssertion( "UBERON:0007304") AnnotationAssertion(rdfs:label "appendage vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric glomerular capillary) @@ -201148,6 +200350,7 @@ AnnotationAssertion( "UBERON:0007306") AnnotationAssertion(rdfs:label "pronephric glomerular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -201161,6 +200364,7 @@ AnnotationAssertion( "UBERON:0007307") AnnotationAssertion(rdfs:label "pronephric glomerular basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (saphenous vein) @@ -201176,15 +200380,14 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0007318") AnnotationAssertion(rdfs:label "saphenous vein") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreatic lobule) AnnotationAssertion(Annotation( "ISBN:0123813611") "A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans.") AnnotationAssertion( "TODO - check") AnnotationAssertion( ) -AnnotationAssertion( "In mice many lobules lack islets, in contrast to other mammals including humans") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37710") AnnotationAssertion( "FMA:16012") AnnotationAssertion( "MA:0000721") @@ -201195,7 +200398,9 @@ AnnotationAssertion( "UBERON:0007324") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pancreatic lobule") +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -201203,16 +200408,11 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pancreatic duct) AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "GOC:ymb") Annotation( "Wikipedia:Pancreatic_duct") Annotation( "https://github.com/obophenotype/uberon/issues/1250") Annotation( "https://orcid.org/0000-0002-2244-7917") Annotation( "https://orcid.org/0000-0002-6601-2165") Annotation( "https://orcid.org/0000-0002-9900-7880") "A duct that collects and carries secretions of the exocrine pancreas to the intestine.") -AnnotationAssertion( "this class groups together accessory (dorsal) and main (ventral) pancreatic ducts") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000254") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000254") Annotation( "VHOG") Annotation( "DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)") Annotation( "http://bgee.unil.ch/") "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]") -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms") AnnotationAssertion( "EHDAA:9194") AnnotationAssertion( "EMAPA:32952") AnnotationAssertion( "FMA:10419") AnnotationAssertion( "MA:0000124") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D010183") AnnotationAssertion( "SCTID:181278006") AnnotationAssertion( "TAO:0001372") AnnotationAssertion( "VHOG:0000254") @@ -201230,7 +200430,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -201243,6 +200445,9 @@ AnnotationAssertion(Annotation( "UBERON:0007352") AnnotationAssertion(rdfs:label "stria vascularis vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface of tongue) @@ -201254,6 +200459,8 @@ AnnotationAssertion( "UBERON:0007367") AnnotationAssertion(rdfs:label "surface of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (superior surface of tongue) @@ -201265,6 +200472,8 @@ AnnotationAssertion( "UBERON:0007371") AnnotationAssertion(rdfs:label "superior surface of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (roof of mouth) @@ -201290,7 +200499,6 @@ AnnotationAssertion(Annotation( "this grouping class exists primarily to align with GO - see GO:0008544.") AnnotationAssertion( "BSA:0000073") AnnotationAssertion( "BTO:0000313") -AnnotationAssertion(Annotation( ) "FBbt:00004993") AnnotationAssertion( "HAO:0000298") AnnotationAssertion( "TADS:0000109") AnnotationAssertion( "WBbt:0005733") @@ -201307,14 +200515,14 @@ AnnotationAssertion( "outer epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Epidermis_(zoology)") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enveloping layer of ectoderm) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Outermost layer of cells surrounding the embryo.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000086") Annotation( "TAO") Annotation( "ZFIN:curator") "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000086") Annotation( "TAO") "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]") -AnnotationAssertion( "Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.") AnnotationAssertion( "EFO:0003425") AnnotationAssertion( "TAO:0000086") AnnotationAssertion( "ZFA:0000086") @@ -201325,6 +200533,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enveloping layer of ectoderm") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -201337,6 +200547,8 @@ AnnotationAssertion( "UBERON:0007384") AnnotationAssertion(rdfs:label "appendage lymph vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage lymph vessel) @@ -201348,6 +200560,7 @@ AnnotationAssertion( "UBERON:0007385") AnnotationAssertion(rdfs:label "pectoral appendage lymph vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage lymph vessel) @@ -201357,11 +200570,12 @@ AnnotationAssertion( "UBERON:0007386") AnnotationAssertion(rdfs:label "pelvic appendage lymph vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired limb/fin cartilage) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A cartilage tissue that is part of a paired limb or fin.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001543") Annotation( "TAO") Annotation( "ZFIN:curator") "Cartilage which is part of one of the paired fins.[TAO]") AnnotationAssertion( "TAO:0001543") AnnotationAssertion( "ZFA:0001543") AnnotationAssertion( "uberon") @@ -201369,12 +200583,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage cartilage tissue) AnnotationAssertion(Annotation( "OBOL:automatic") "A cartilage tissue that is part of a pectoral appendage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000257") Annotation( "TAO") Annotation( "ZFIN:curator") "Cartilage which is part of the pectoral fin.[TAO]") AnnotationAssertion( "TAO:0000257") AnnotationAssertion( "ZFA:0000257") AnnotationAssertion( "uberon") @@ -201382,13 +200597,14 @@ AnnotationAssertion(Annotation( "UBERON:0007390") AnnotationAssertion(rdfs:label "pectoral appendage cartilage tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic appendage cartilage tissue) AnnotationAssertion(Annotation( "OBOL:automatic") "A cartilage tissue that is part of a pelvic appendage.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001459") Annotation( "TAO") Annotation( "ZFIN:curator") "Cartilage which is part of the pelvic fin.[TAO]") AnnotationAssertion( "TAO:0001459") AnnotationAssertion( "ZFA:0001459") AnnotationAssertion( "uberon") @@ -201396,13 +200612,14 @@ AnnotationAssertion(Annotation( "UBERON:0007391") AnnotationAssertion(rdfs:label "pelvic appendage cartilage tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of midbrain tegmentum) AnnotationAssertion(Annotation( "OBOL:automatic") "A nucleus of brain that spans a midbrain tegmentum.") -AnnotationAssertion( "this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species") AnnotationAssertion( "UBERON:0012277") AnnotationAssertion( "FMA:258768") AnnotationAssertion( "ZFA:0005577") @@ -201412,6 +200629,8 @@ AnnotationAssertion( "UBERON:0007414") AnnotationAssertion(rdfs:label "nucleus of midbrain tegmentum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural decussation) @@ -201431,6 +200650,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural decussation") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (decussation of diencephalon) @@ -201454,7 +200674,8 @@ AnnotationAssertion( "UBERON:0007473") AnnotationAssertion(rdfs:label "lumen of epithelial sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (matrix-based tissue) @@ -201465,6 +200686,8 @@ AnnotationAssertion( "UBERON:0007475") AnnotationAssertion(rdfs:label "matrix-based tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (keratin-based acellular structure) @@ -201477,7 +200700,9 @@ AnnotationAssertion(Annotation( "UBERON:0007490") AnnotationAssertion(rdfs:label "keratin-based acellular structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial sac) @@ -201489,6 +200714,7 @@ AnnotationAssertion( "epithelial sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "AEO") ) +SubClassOf( ) # Class: (epithelial tube open at both ends) @@ -201532,6 +200758,8 @@ AnnotationAssertion( "UBERON:0007521") AnnotationAssertion(rdfs:label "smooth muscle sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated muscle sphincter) @@ -201543,6 +200771,8 @@ AnnotationAssertion( "UBERON:0007522") AnnotationAssertion(rdfs:label "striated muscle sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dense mesenchyme tissue) @@ -201578,12 +200808,13 @@ AnnotationAssertion( "UBERON:0007530") AnnotationAssertion(rdfs:label "migrating mesenchyme population") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regenerating anatomical structure) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An anatomical structure that is undergoing regeneration.") AnnotationAssertion( "we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005147") Annotation( "TAO") Annotation( "ZFIN:curator") "A portion of tissue that is regrowing after damage or amputation.[TAO]") AnnotationAssertion( "AEO:0000200") AnnotationAssertion( "EHDAA2:0003233") AnnotationAssertion( "TAO:0005147") @@ -201596,13 +200827,14 @@ AnnotationAssertion( "UBERON:0007567") AnnotationAssertion(rdfs:label "regenerating anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliated columnar oviduct epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "A ciliated columnar epithelium that is part of a oviduct.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label") AnnotationAssertion( "FMA:62016") AnnotationAssertion( "MA:0001719") AnnotationAssertion( "uberon") @@ -201626,18 +200858,18 @@ AnnotationAssertion( "cuboidal oviduct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) # Class: (ciliated columnar epithelium) AnnotationAssertion(Annotation( "FMA:64798") "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].") -AnnotationAssertion( "In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system") -AnnotationAssertion( "Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]") AnnotationAssertion( "FMA:64798") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007592") AnnotationAssertion(rdfs:label "ciliated columnar epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) # Class: (ciliated epithelium) @@ -201646,6 +200878,8 @@ AnnotationAssertion( "UBERON:0007601") AnnotationAssertion(rdfs:label "ciliated epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratified columnar epithelium) @@ -201668,6 +200902,7 @@ AnnotationAssertion( "UBERON:0007606") AnnotationAssertion(rdfs:label "ciliated stratified columnar epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) # Class: (layer of synovial tissue) @@ -201685,7 +200920,9 @@ AnnotationAssertion(Annotation( "UBERON:0007616") AnnotationAssertion(rdfs:label "layer of synovial tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (synovial cavity of joint) @@ -201700,10 +200937,11 @@ AnnotationAssertion(Annotation( "UBERON:0007617") AnnotationAssertion(rdfs:label "synovial cavity of joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limiting membrane of retina) -AnnotationAssertion(Annotation( "MA") "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together") AnnotationAssertion( "MA:0001318") AnnotationAssertion( "SCTID:280667001") AnnotationAssertion(Annotation( "MA:0001318") Annotation( "https://github.com/obophenotype/uberon/issues/52") "retina lamina") @@ -201725,6 +200963,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pigment epithelium of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of medulla oblongata) @@ -201735,6 +200975,9 @@ AnnotationAssertion( "UBERON:0007635") AnnotationAssertion(rdfs:label "nucleus of medulla oblongata") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus stratum lucidum) @@ -201743,9 +200986,7 @@ AnnotationAssertion(Annotation( "BAMS:SLu") AnnotationAssertion( "BIRNLEX:4108") AnnotationAssertion( "EMAPA:35411") -AnnotationAssertion( "NCIT:C33629") AnnotationAssertion(Annotation( "BIRNLEX:4108") "OldNeuroNames:-975815906") -AnnotationAssertion( "SCTID:419156002") AnnotationAssertion(Annotation( "ncithesaurus:Stratum_Lucidum") "UMLS:C0221922") AnnotationAssertion( "Wikipedia:Stratum_lucidum_of_hippocampus") AnnotationAssertion( "neuronames:1777") @@ -201755,7 +200996,10 @@ AnnotationAssertion(Annotation( "UBERON:0007637") AnnotationAssertion(rdfs:label "hippocampus stratum lucidum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hippocampus alveus) @@ -201782,6 +201026,7 @@ AnnotationAssertion(Annotation( "BAMS:alv") "alveus of the hippocampus") AnnotationAssertion( "UBERON:0007639") AnnotationAssertion(rdfs:label "hippocampus alveus") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -201789,14 +201034,12 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (trigeminal nuclear complex) AnnotationAssertion(Annotation( "Wikipedia:Trigeminal_nerve_nuclei") "The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].") -AnnotationAssertion(Annotation( "MA") "in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.") AnnotationAssertion( "BIRNLEX:4096") AnnotationAssertion( "BM:V") AnnotationAssertion( "CALOHA:TS-2077") AnnotationAssertion( "DHBA:266441713") AnnotationAssertion( "FMA:71248") AnnotationAssertion( "HBA:9203") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D014278") AnnotationAssertion(Annotation( "BIRNLEX:4096") "UMLS:C0040999") AnnotationAssertion( "Wikipedia:Trigeminal_nerve_nuclei") AnnotationAssertion( "neuronames:2021") @@ -201824,12 +201067,13 @@ AnnotationAssertion(Annotation( "UBERON:0007644") AnnotationAssertion(rdfs:label "thoracic lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (future meninx) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx.") AnnotationAssertion( "decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx") -AnnotationAssertion(Annotation( "MP:0009726") "the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d") AnnotationAssertion( "UBERON:0004065") AnnotationAssertion( "EHDAA2:0004453") AnnotationAssertion(Annotation( "EHDAA2:0004453") "primary meninx") @@ -201841,9 +201085,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "future meninx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endomeninx) @@ -201856,6 +201101,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf(Annotation( "ISBN:9781607950325") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectomeninx) @@ -201867,8 +201113,9 @@ AnnotationAssertion( "UBERON:0007647") AnnotationAssertion(rdfs:label "ectomeninx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ISBN:9781607950325") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:9781607950325") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical junction) @@ -201897,6 +201144,8 @@ AnnotationAssertion( "UBERON:0007652") AnnotationAssertion(rdfs:label "esophageal sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (uriniferous tubule) @@ -201906,20 +201155,20 @@ AnnotationAssertion( "UBERON:0007684") AnnotationAssertion(rdfs:label "uriniferous tubule") SubClassOf( ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (region of nephron tubule) -AnnotationAssertion(Annotation( "MA") "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts") AnnotationAssertion( "FMA:17692") AnnotationAssertion(Annotation( "FMA:17692") "renal tubule region") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FMA:17692") "region of renal tubule") AnnotationAssertion( "UBERON:0007685") AnnotationAssertion(rdfs:label "region of nephron tubule") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney field) @@ -201930,7 +201179,10 @@ AnnotationAssertion(Annotation( "UBERON:0007687") AnnotationAssertion(rdfs:label "kidney field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anlage) @@ -201939,7 +201191,6 @@ AnnotationAssertion( "AEO:0000170") AnnotationAssertion( "EFO:0001649") AnnotationAssertion( "EHDAA2:0003170") -AnnotationAssertion(Annotation( ) "FBbt:00005426") AnnotationAssertion( "Wikipedia:Anlage_(biology)") AnnotationAssertion( "developmental field") AnnotationAssertion( "uberon") @@ -201950,7 +201201,6 @@ AnnotationAssertion( "anlage") SubClassOf(Annotation( "FBbt") ) SubClassOf(Annotation( "AEO") Annotation( "FBbt") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (thyroid diverticulum) @@ -201970,8 +201220,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion( "EFO:0003626") AnnotationAssertion( "EHDAA2:0001457") AnnotationAssertion( "EHDAA:962") -AnnotationAssertion( "EMAPA:32754") -AnnotationAssertion( "FMA:293087") AnnotationAssertion( "TAO:0001104") AnnotationAssertion( "ZFA:0001104") AnnotationAssertion(Annotation( "EHDAA2:0001457") "early pharyngeal arch endoderm") @@ -201984,10 +201232,9 @@ AnnotationAssertion( "relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'") AnnotationAssertion(rdfs:label "early pharyngeal endoderm") AnnotationAssertion(rdfs:seeAlso "http://dev.biologists.org/content/128/22/4573.full"^^xsd:anyURI) -SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (gustatory pore) @@ -202004,6 +201251,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -202023,6 +201271,8 @@ AnnotationAssertion(Annotation( "UBERON:0007692") AnnotationAssertion(rdfs:label "nucleus of thalamus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tract of spinal cord) @@ -202035,6 +201285,8 @@ AnnotationAssertion( "UBERON:0007699") AnnotationAssertion(rdfs:label "tract of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (tract of brain) @@ -202048,6 +201300,8 @@ AnnotationAssertion(Annotation( "UBERON:0007702") AnnotationAssertion(rdfs:label "tract of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (bone of reproductive organ) @@ -202060,6 +201314,9 @@ AnnotationAssertion( "UBERON:0007719") AnnotationAssertion(rdfs:label "bone of reproductive organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interphalangeal joint of pes) @@ -202082,7 +201339,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interphalangeal joint of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "two in series") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectExactCardinality(2 )) # Class: (interphalangeal joint of manus) @@ -202108,7 +201368,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interphalangeal joint of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "two in series") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectExactCardinality(2 )) # Class: (epidermis gland) @@ -202122,6 +201385,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epidermis gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (umbilical vein endothelium) @@ -202132,6 +201397,7 @@ AnnotationAssertion( "UBERON:0007777") AnnotationAssertion(rdfs:label "umbilical vein endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (umbilical artery endothelium) @@ -202142,14 +201408,12 @@ AnnotationAssertion( "UBERON:0007778") AnnotationAssertion(rdfs:label "umbilical artery endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "BTO") ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (transudate) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/transudate") "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces.") -AnnotationAssertion( "transudative") -AnnotationAssertion( "characteristically low in protein and cellular content (unless there has been secondary concentration)") AnnotationAssertion( "FMA:12276") AnnotationAssertion( "GAID:1195") AnnotationAssertion( "MESH:D005122") @@ -202159,7 +201423,10 @@ AnnotationAssertion( "UBERON:0007779") AnnotationAssertion(rdfs:label "transudate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretion of serous gland) @@ -202172,14 +201439,15 @@ AnnotationAssertion( "UBERON:0007794") AnnotationAssertion(rdfs:label "secretion of serous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vascular system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Anatomical system that consists of all blood and lymph vessels.") AnnotationAssertion( "consider merging with vasculature") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ncithesaurus:Vascular_System") "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].") -AnnotationAssertion(Annotation( "MA") "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system") AnnotationAssertion( "BTO:0001085") AnnotationAssertion( "CALOHA:TS-2053") AnnotationAssertion( "EHDAA2:0004520") @@ -202219,6 +201487,8 @@ AnnotationAssertion( "UBERON:0007807") AnnotationAssertion(rdfs:label "connecting stalk vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (adipose tissue of abdominal region) @@ -202234,6 +201504,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adipose tissue of abdominal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (craniocervical region) @@ -202266,11 +201538,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010338") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001117") Annotation( "TAO") Annotation( "ZFIN:curator") "Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]") -AnnotationAssertion( "present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)") AnnotationAssertion( "AAO:0010338") -AnnotationAssertion( "EMAPA:16748") AnnotationAssertion( "MA:0000008") AnnotationAssertion( "NCIT:C77663") AnnotationAssertion( "TAO:0001117") @@ -202287,15 +201555,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "post-anal tail") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "possible exception in hemichordates") Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendage girdle region) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).") -AnnotationAssertion( "this encompasses non-skeletal tissue") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000303") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]") AnnotationAssertion( "UBERON:0007824") AnnotationAssertion( "girdle") AnnotationAssertion( "girdle region") @@ -202310,8 +201578,10 @@ AnnotationAssertion(Annotation( "UBERON:0007823") AnnotationAssertion(rdfs:label "appendage girdle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peritoneal mesentery) @@ -202324,13 +201594,13 @@ AnnotationAssertion( "UBERON:0007826") AnnotationAssertion(rdfs:label "peritoneal mesentery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (external nose) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "External part of the nose containing the external nares.") -AnnotationAssertion(Annotation( "FMA:59515") "Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37831") AnnotationAssertion( "FMA:59515") AnnotationAssertion( "NCIT:C32566") @@ -202342,6 +201612,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "external nose") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (girdle bone/zone) @@ -202353,8 +201627,8 @@ AnnotationAssertion( "UBERON:0007828") AnnotationAssertion(rdfs:label "girdle bone/zone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral girdle bone) @@ -202370,6 +201644,7 @@ AnnotationAssertion( "pectoral girdle bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic girdle bone/zone) @@ -202377,8 +201652,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone element or fused bone that is part of pelvic girdle.") AnnotationAssertion( "check sacrum, coccyx (MA does NOT include these)") AnnotationAssertion( ) -AnnotationAssertion( "typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone") -AnnotationAssertion( "EMAPA:18028") AnnotationAssertion( "MA:0000293") AnnotationAssertion( "NCIT:C33287") AnnotationAssertion( "SCTID:426214007") @@ -202392,18 +201665,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic girdle bone/zone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral girdle skeleton) AnnotationAssertion(Annotation( "Wikipedia:Pectoral_girdle") "A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000407") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000156") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000422") Annotation( "AAO") Annotation( "AAO:LAP") "Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001156") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18") Annotation( "http://bgee.unil.ch/") "The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]") -AnnotationAssertion(Annotation( "VSAO") "Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.") AnnotationAssertion( "AAO:0000422") AnnotationAssertion( "AAO:0000754") AnnotationAssertion( "EFO:0000946") @@ -202431,18 +201703,15 @@ AnnotationAssertion( "pectoral girdle skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic girdle skeleton) AnnotationAssertion(Annotation( "VSAO:0000155") Annotation( "Wikipedia:Pelvis") "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.") AnnotationAssertion( "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000426") Annotation( "AAO") Annotation( "AAO:LAP") "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000565") Annotation( "TAO") Annotation( "TAO:wd") "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000155") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000305") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333") Annotation( "http://bgee.unil.ch/") "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]") -AnnotationAssertion(Annotation( "VSAO") "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts") AnnotationAssertion( "AAO:0000426") AnnotationAssertion( "AAO:0000768") AnnotationAssertion( "EFO:0000947") @@ -202472,14 +201741,16 @@ AnnotationAssertion( "pelvic girdle skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:21455939") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (membrane bone) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000023") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/267") "Bone element that arises as a result of intramembranous ossification.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000023") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Bone element that arises as a result of intramembranous ossification.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001645") Annotation( "TAO") Annotation( "TAO:wd") "Intramembranous bone that forms deep in the organism.[TAO]") AnnotationAssertion( "AEO:0000085") AnnotationAssertion( "EHDAA2:0003085") AnnotationAssertion( "TAO:0001645") @@ -202496,10 +201767,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cartilage element) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000000") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal element that is composed of cartilage tissue and may be permanent or transient.") -AnnotationAssertion(Annotation( "TAO") "TAO still mixes tissue and element") AnnotationAssertion( "AAO:0011130") AnnotationAssertion( "CALOHA:TS-0118") -AnnotationAssertion( "EMAPA:32730") AnnotationAssertion( "FMA:55107") AnnotationAssertion( "VSAO:0000000") AnnotationAssertion( "XAO:0004013") @@ -202517,6 +201786,7 @@ EquivalentClasses( ObjectIntersec SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regular connective tissue) @@ -202526,6 +201796,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007845") AnnotationAssertion(rdfs:label "regular connective tissue") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -202535,8 +201806,6 @@ DisjointClasses( (dense regular connective tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000050") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000050") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]") -AnnotationAssertion(Annotation( "2012-08-29") Annotation( "FMA:64781") Annotation( "FMA") "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]") AnnotationAssertion( "FMA:64781") AnnotationAssertion( "NCIT:C33453") AnnotationAssertion( "SCTID:22560007") @@ -202581,7 +201850,8 @@ AnnotationAssertion( "sesamoid bone of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (sesamoid bone of pes) @@ -202594,7 +201864,8 @@ AnnotationAssertion( "sesamoid bone of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (irregular bone) @@ -202622,6 +201893,7 @@ AnnotationAssertion( "joint of girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -202634,12 +201906,13 @@ AnnotationAssertion( "UBERON:0008115") AnnotationAssertion(rdfs:label "surface of cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pneumatized bone) AnnotationAssertion(Annotation( "http://www.medilexicon.com/medicaldictionary.php?t=11303") "A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].") AnnotationAssertion( "subclasses of this should be checked for taxonomic consistency") -AnnotationAssertion( "Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]") AnnotationAssertion( "FMA:7478") AnnotationAssertion( "SCTID:333008005") AnnotationAssertion( "Wikipedia:Skeletal_pneumaticity") @@ -202651,12 +201924,12 @@ AnnotationAssertion( "UBERON:0008193") AnnotationAssertion(rdfs:label "pneumatized bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle of pectoral girdle) AnnotationAssertion(Annotation( "OBOL:automatic") "Any muscle organ that is part of a pectoral girdle region.") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate") -AnnotationAssertion( "EMAPA:17748") AnnotationAssertion( "FMA:37347") AnnotationAssertion(Annotation( "FMA:37347") "muscle of shoulder girdle") AnnotationAssertion(Annotation( "FMA:37347") "pectoral girdle muscle") @@ -202665,13 +201938,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle of pectoral girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nail plate) AnnotationAssertion(Annotation( "Wikipedia:Nail_plate") Annotation( "https://github.com/obophenotype/uberon/issues/20") Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8479/") "The nail plate is the hard and translucent portion of the nail, composed of keratin.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "in FMA, the nail is the nail plate") AnnotationAssertion( "EMAPA:35583") AnnotationAssertion( "MA:0002708") AnnotationAssertion( "NCIT:C34216") @@ -202683,15 +201956,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nail plate") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/9f/Fingernail_label.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of hip region) AnnotationAssertion( "todo - consider obsoletion") -AnnotationAssertion(Annotation( "MA") "in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37308") AnnotationAssertion( "FMA:42854") AnnotationAssertion( "MA:0000655") @@ -202720,12 +201992,13 @@ AnnotationAssertion( "pelvic cavity") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (craniocervical region musculature) AnnotationAssertion(Annotation( "ZFA:0000328") Annotation( "ZFA:curator") "Musculature system of the pharyngeal and head regions.") -AnnotationAssertion(Annotation( "MA") "in MA this is restricted to skeletal muscles") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37259") AnnotationAssertion( "MA:0000571") AnnotationAssertion( "TAO:0000328") @@ -202770,44 +202043,41 @@ AnnotationAssertion( "UBERON:0008243") AnnotationAssertion(rdfs:label "upper back muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (right clavicle) AnnotationAssertion(Annotation( "OBOL:automatic") "A clavicle that is in the right side of a entire appendicular skeleton.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:13322") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0008255") AnnotationAssertion(rdfs:label "right clavicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left clavicle) AnnotationAssertion(Annotation( "OBOL:automatic") "A clavicle that is in the left side of a entire appendicular skeleton.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:13323") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0008256") AnnotationAssertion(rdfs:label "left clavicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (periodontal ligament) AnnotationAssertion(Annotation( "BTO:0001020") Annotation( "Wikipedia:Periodontal_fiber") Annotation( "https://github.com/obophenotype/uberon/issues/1233") Annotation( "https://github.com/obophenotype/uberon/issues/21") "The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO].") -AnnotationAssertion(Annotation( "http://www.drugs.com/dict/desmodentium.html") "The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html].") -AnnotationAssertion(Annotation( "Wikipedia:Periodontal_fiber") "The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21].") -AnnotationAssertion(Annotation( "FMA") "FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA") AnnotationAssertion( "BTO:0001020") AnnotationAssertion( "CALOHA:TS-0763") AnnotationAssertion( "EMAPA:35679") AnnotationAssertion( "FMA:56665") AnnotationAssertion( "GAID:1259") AnnotationAssertion( "MA:0002467") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D010513") AnnotationAssertion( "SCTID:245775004") AnnotationAssertion( "Wikipedia:Periodontal_fiber") AnnotationAssertion(Annotation( "Wikipedia:Periodontal_ligament") Annotation( ) "fibra periodontalis") @@ -202837,8 +202107,8 @@ AnnotationAssertion(rdfs:seeAlso AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA-moved") ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:19767574") Annotation( "Wikipedia:Dental_follicle") ObjectSomeValuesFrom( )) # Class: (tooth bud) @@ -202885,13 +202155,14 @@ SubClassOf(Annotation( "BTO # Class: (heart endothelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An endothelium that is part of a heart [Automatically generated definition].") -AnnotationAssertion( "this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.") AnnotationAssertion( "BTO:0004293") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "BTO:0004293") "cardiac endothelium") AnnotationAssertion( "UBERON:0008307") AnnotationAssertion(rdfs:label "heart endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasopharyngeal gland) @@ -202903,6 +202174,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasopharyngeal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (erectile tissue) @@ -202924,11 +202198,13 @@ AnnotationAssertion(Annotation( "UBERON:0008331") AnnotationAssertion(rdfs:label "clitoral smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (plantar part of pes) AnnotationAssertion(Annotation( "Wikipedia:Sole_(foot)") "The sole is the bottom of the foot.") -AnnotationAssertion( "In humans is the sole of the foot anatomically referred to as the plantar aspect. The equivalent surface in ungulates is the hoof") AnnotationAssertion( "BTO:0005078") AnnotationAssertion( "CALOHA:TS-0379") AnnotationAssertion( "FMA:25000") @@ -202955,6 +202231,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/41/Soles2.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) # Class: (microvascular endothelium) @@ -202964,7 +202241,8 @@ AnnotationAssertion( "microvascular endothelium") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2186") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "BTO") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal villus of duodenum) @@ -202974,6 +202252,7 @@ AnnotationAssertion( "UBERON:0008342") AnnotationAssertion(rdfs:label "intestinal villus of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal villus of jejunum) @@ -202984,6 +202263,7 @@ AnnotationAssertion( "UBERON:0008343") AnnotationAssertion(rdfs:label "intestinal villus of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal villus of ileum) @@ -202994,6 +202274,7 @@ AnnotationAssertion( "UBERON:0008344") AnnotationAssertion(rdfs:label "intestinal villus of ileum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ileal epithelium) @@ -203010,6 +202291,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ileal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (duodenal epithelium) @@ -203027,6 +202309,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duodenal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (breast epithelium) @@ -203037,6 +202320,8 @@ AnnotationAssertion( "UBERON:0008367") AnnotationAssertion(rdfs:label "breast epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tracheobronchial epithelium) @@ -203048,6 +202333,8 @@ AnnotationAssertion(Annotation( "UBERON:0008397") AnnotationAssertion(rdfs:label "tracheobronchial epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal tubular epithelium) @@ -203064,6 +202351,8 @@ AnnotationAssertion(Annotation( "UBERON:0008404") AnnotationAssertion(rdfs:label "proximal tubular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal tubular epithelium) @@ -203075,15 +202364,13 @@ AnnotationAssertion(Annotation( "UBERON:0008408") AnnotationAssertion(rdfs:label "distal tubular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) # Class: (mammary ridge) AnnotationAssertion(Annotation( "GOC:dph") "A ridge of epidermal cells that will form the mammary placodes.") AnnotationAssertion( "consider splitting ridge (precursor) and milk line") -AnnotationAssertion( "These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development") -AnnotationAssertion( "The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission.") -AnnotationAssertion( "in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP]") AnnotationAssertion( "EMAPA:18541") AnnotationAssertion( "Wikipedia:Milk_line") AnnotationAssertion(Annotation( "http://dictionary.reference.com/browse/mammary+ridge") "mammary fold") @@ -203093,8 +202380,7 @@ AnnotationAssertion(Annotation( "Wikipedia:Milk_line") "milk line") AnnotationAssertion( "UBERON:0008425") AnnotationAssertion(rdfs:label "mammary ridge") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203108,6 +202394,9 @@ AnnotationAssertion( "UBERON:0008429") AnnotationAssertion(rdfs:label "cervical vertebral foramen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic vertebral foramen) @@ -203118,6 +202407,9 @@ AnnotationAssertion( "UBERON:0008432") AnnotationAssertion(rdfs:label "thoracic vertebral foramen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical vertebral arch) @@ -203129,6 +202421,10 @@ AnnotationAssertion( "UBERON:0008434") AnnotationAssertion(rdfs:label "cervical vertebral arch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic vertebral arch) @@ -203140,6 +202436,10 @@ AnnotationAssertion( "UBERON:0008436") AnnotationAssertion(rdfs:label "thoracic vertebral arch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intertarsal joint) @@ -203168,9 +202468,9 @@ AnnotationAssertion( "intertarsal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "two adjacent tarsals") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal muscle) @@ -203185,6 +202485,8 @@ AnnotationAssertion( "nasal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral girdle and thoracic body wall skeletal muscle) @@ -203210,6 +202512,10 @@ AnnotationAssertion( "UBERON:0008715") AnnotationAssertion(rdfs:label "muscle tissue of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal epiphysis of tibia) @@ -203228,11 +202534,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal epiphysis of tibia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal epiphysis of fibula) AnnotationAssertion(Annotation( "OBOL:automatic") "A proximal epiphysis that is part of a fibula.") -AnnotationAssertion(Annotation( "Wikipedia:Head_of_fibula") "The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37890") AnnotationAssertion( "FMA:33729") AnnotationAssertion( "NCIT:C32719") @@ -203250,6 +202557,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal epiphysis of fibula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (inner cell mass derived epiblast) @@ -203268,6 +202577,7 @@ AnnotationAssertion( "The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.") AnnotationAssertion(rdfs:label "inner cell mass derived epiblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) @@ -203305,6 +202615,8 @@ AnnotationAssertion( "UBERON:0008784") AnnotationAssertion(rdfs:label "lower limb segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper limb segment) @@ -203318,6 +202630,8 @@ AnnotationAssertion( "UBERON:0008785") AnnotationAssertion(rdfs:label "upper limb segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial fossa) @@ -203328,6 +202642,7 @@ AnnotationAssertion( "UBERON:0008789") AnnotationAssertion(rdfs:label "cranial fossa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (gingival groove) @@ -203346,16 +202661,16 @@ AnnotationAssertion( "gingival groove") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intromittent organ) AnnotationAssertion(Annotation( "Wikipedia:Intromittent_organ") "An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].") -AnnotationAssertion( "this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002036") Annotation( "TAO") Annotation( "TAO:wd") "Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]") AnnotationAssertion( "AAO:0010255") -AnnotationAssertion(Annotation( ) "FBbt:00004850") AnnotationAssertion( "HAO:0000091") AnnotationAssertion( "TAO:0002036") AnnotationAssertion( "TGMA:0000585") @@ -203368,9 +202683,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intromittent organ") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203401,13 +202714,14 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "OBOL:automatic") "A head that is part of a embryo.") AnnotationAssertion( "CALOHA:TS-0246") -AnnotationAssertion(Annotation( ) "FBbt:00000155") AnnotationAssertion( "FMA:293011") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0008816") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thymus primordium endoderm) @@ -203416,6 +202730,9 @@ AnnotationAssertion( "UBERON:0008817") AnnotationAssertion(rdfs:label "thymus primordium endoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) # Class: (neural tube derived brain) @@ -203429,8 +202746,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/338"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duct of epididymis) @@ -203447,17 +202765,17 @@ AnnotationAssertion( "UBERON:0008824") AnnotationAssertion(rdfs:label "duct of epididymis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary surfactant) AnnotationAssertion(Annotation( "Wikipedia:Pulmonary_surfactant") "A substance formed by type II alveolar cells composed of surface-active lipoprotein complex (phospholipoprotein).") -AnnotationAssertion( "surfactant") AnnotationAssertion( "EMAPA:36551") AnnotationAssertion( "FMA:62780") AnnotationAssertion( "MA:0002534") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D011663") AnnotationAssertion( "NCIT:C13273") AnnotationAssertion(Annotation( "ncithesaurus:Lung_Surfactant") "UMLS:C0034085") AnnotationAssertion( "Wikipedia:Pulmonary_surfactant") @@ -203469,13 +202787,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary surfactant") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic diverticulum) AnnotationAssertion(Annotation( "MP:MP") Annotation( "http://www.stembook.org/node/512") "An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.") -AnnotationAssertion( "in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10") -AnnotationAssertion( "The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.") AnnotationAssertion( "AAO:0011057") AnnotationAssertion( "EHDAA2:0000740") AnnotationAssertion( "EHDAA:1530") @@ -203490,10 +202808,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatic diverticulum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "caudal part") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (liver bud) @@ -203502,8 +202822,10 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0008836") AnnotationAssertion(rdfs:label "liver bud") +SubClassOf( ) SubClassOf(Annotation( "cjm") ) -SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "http://www.stembook.org/node/512") ObjectSomeValuesFrom( )) # Class: (palmar/plantar part of autopod) @@ -203517,8 +202839,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nonskeletal ligament) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A ligament that does not connect two skeletal elements.") -AnnotationAssertion(Annotation( "FMA:25625") "Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625].") -AnnotationAssertion(Annotation( "FMA") "this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus.") AnnotationAssertion( "FMA:25625") AnnotationAssertion( "MA:0003004") AnnotationAssertion( "SCTID:410746001") @@ -203534,8 +202854,6 @@ DisjointClasses( "GO_REF:0000034") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "http://orcid.org/0000-0002-6601-2165") "Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified].") AnnotationAssertion( "logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000072") Annotation( "VSAO") Annotation( "PSPUB:0000170") "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]") -AnnotationAssertion(Annotation( "FMA:25624") "Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624].") AnnotationAssertion(Annotation( "VSAO:0000072") Annotation( "ZFA:0001675") "ligament") AnnotationAssertion( "AAO:0010444") AnnotationAssertion( "AEO:0000090") @@ -203556,9 +202874,12 @@ AnnotationAssertion( "skeletal ligament") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AEO") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "bones or cartilage organs") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) # Class: (ectoplacental cavity) @@ -203572,12 +202893,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ectoplacental cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach muscularis externa) AnnotationAssertion(Annotation( "MP:0010779") "The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines.") -AnnotationAssertion(Annotation( "WP") "the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two") AnnotationAssertion( "FMA:14909") AnnotationAssertion( "SCTID:362132003") AnnotationAssertion(Annotation( "FMA:14909") "gastric muscularis") @@ -203590,11 +202912,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach muscularis externa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pyloric canal) @@ -203619,8 +202942,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cardiac gastric gland) AnnotationAssertion(Annotation( "MP:0010795") Annotation( "Wikipedia:Cardiac_glands") "A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP].") -AnnotationAssertion(Annotation( "Wikipedia:Cardiac_glands") "The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands].") -AnnotationAssertion(Annotation( "FMA") "Kardong places this in the glandular epithelium, FMA more generally in the mucosa") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37459") AnnotationAssertion( "FMA:14920") AnnotationAssertion( "SCTID:8894005") @@ -203637,9 +202958,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac gastric gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pyloric gastric gland) @@ -203662,9 +202983,9 @@ AnnotationAssertion( "pyloric gastric gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Tubular_gland") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203680,6 +203001,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary alveolar parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203704,6 +203027,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary acinus") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203724,6 +203048,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hypodermis skeletal muscle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP-def") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203744,6 +203072,7 @@ AnnotationAssertion( "UBERON:0008877") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epidermal-dermal junction") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203753,9 +203082,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (osteoid) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000046") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000046") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "PSPUB:0000170") "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]") -AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0010924") "Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n") -AnnotationAssertion(Annotation( "VSAO") "Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA.") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37923") AnnotationAssertion( "FMA:66830") AnnotationAssertion( "NCIT:C33228") @@ -203787,6 +203113,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right putamen) @@ -203799,12 +203127,13 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary vascular system) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Pulmonary_circulation") "The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") Annotation( "FMA:45621") "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]") AnnotationAssertion( "FMA:45621") AnnotationAssertion( "Wikipedia:Pulmonary_circulation") AnnotationAssertion(Annotation( "FMA:45621") "pulmonary circulatory system") @@ -203813,8 +203142,8 @@ AnnotationAssertion( "UBERON:0008886") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary vascular system") +SubClassOf( ) SubClassOf(Annotation( "Obol") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -203836,17 +203165,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (splanchnocranium) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Facial_skeleton") Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of endoskeleton derived from pharyngeal arches.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001216") Annotation( "TAO") Annotation( "ZFIN:curator") "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010157") Annotation( "AAO") Annotation( "AAO:EJS") "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000315") Annotation( "VHOG") Annotation( "http://bgee.unil.ch/") "The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000315") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235") Annotation( "http://bgee.unil.ch/") "The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]") -AnnotationAssertion(Annotation( "VSAO") "VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.") -AnnotationAssertion( "many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both") AnnotationAssertion( "AAO:0010157") AnnotationAssertion( "TAO:0001216") AnnotationAssertion( "VHOG:0000315") @@ -203871,17 +203195,15 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg"^^xsd:anyURI) SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/83") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "redundant") Annotation( "Grays") Annotation( "PMID:11237469") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (post-hyoid pharyngeal arch) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010362") Annotation( "AAO") Annotation( "AAO:EJS") "Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]") AnnotationAssertion( "AAO:0010362") AnnotationAssertion( "BTO:0002152") AnnotationAssertion( "EFO:0003694") -AnnotationAssertion( "SCTID:308766004") AnnotationAssertion( "TAO:0001597") AnnotationAssertion( "XAO:0000099") AnnotationAssertion( "ZFA:0001613") @@ -203899,17 +203221,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "post-hyoid pharyngeal arch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuromast) AnnotationAssertion(Annotation( "ZFIN:ZDB-PUB-961014-576") "Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0001004") Annotation( "AAO") Annotation( "AAO:EJS") "Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000243") Annotation( "TAO") Annotation( "ZFIN:curator") "Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0001004") Annotation( "AAO") "relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0001004") Annotation( "AAO") "relationship loss: subclass lateral line receptor (AAO:0010705)[AAO]") AnnotationAssertion(Annotation( "ZFA:0000243") "lateral line organ") AnnotationAssertion( "AAO:0001004") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006219") AnnotationAssertion( "EFO:0003513") AnnotationAssertion( "TAO:0000243") AnnotationAssertion( "ZFA:0000243") @@ -203920,21 +203239,17 @@ AnnotationAssertion( "UBERON:0008904") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuromast") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "DOI:10.1038/ncomms1502") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (lateral line nerve) AnnotationAssertion(Annotation( "ZFIN:curator") "Cranial nerves that carry afferent and efferent fibers for the lateral line system.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010077") Annotation( "AAO") Annotation( "AAO:SIQ") "Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010077") Annotation( "AAO") "relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010077") Annotation( "AAO") "relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO]") AnnotationAssertion( "AAO:0010077") AnnotationAssertion( "TAO:0001479") AnnotationAssertion( "ZFA:0001479") @@ -203943,14 +203258,16 @@ AnnotationAssertion( "UBERON:0008906") AnnotationAssertion(rdfs:label "lateral line nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NCBIBook:NBK53175") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermal bone) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000130") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/267") "Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001590") Annotation( "TAO") Annotation( "TAO:wd") "Intramembranous bone that forms superficially in the organism.[TAO]") -AnnotationAssertion( "other AOs are not yet in sync with this classification") AnnotationAssertion( "AAO:0010769") AnnotationAssertion( "TAO:0001590") AnnotationAssertion( "VSAO:0000130") @@ -203970,7 +203287,6 @@ SubClassOf(Annotation( "VSA AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000307") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Bone element that is adjacent to the notochord.") AnnotationAssertion( "We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001639") Annotation( "TAO") Annotation( "TAO:wd") "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]") AnnotationAssertion( "AAO:0010777") AnnotationAssertion( "TAO:0001639") AnnotationAssertion( "VSAO:0000307") @@ -203981,7 +203297,8 @@ AnnotationAssertion(Annotation( "UBERON:0008909") AnnotationAssertion(rdfs:label "perichordal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "not in VSAO") Annotation( "ZFA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (substratum of layer of retina) @@ -203989,6 +203306,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0008921") AnnotationAssertion(rdfs:label "substratum of layer of retina") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -204000,8 +203318,14 @@ AnnotationAssertion( "UBERON:0008922") AnnotationAssertion(rdfs:label "sublaminar layer S1") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sublaminar layer S2) @@ -204011,9 +203335,16 @@ AnnotationAssertion( "UBERON:0008923") AnnotationAssertion(rdfs:label "sublaminar layer S2") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sublaminar layer S3) @@ -204023,8 +203354,16 @@ AnnotationAssertion( "UBERON:0008924") AnnotationAssertion(rdfs:label "sublaminar layer S3") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sublaminar layer S4) @@ -204034,8 +203373,15 @@ AnnotationAssertion( "UBERON:0008925") AnnotationAssertion(rdfs:label "sublaminar layer S4") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sublaminar layer S5) @@ -204045,8 +203391,12 @@ AnnotationAssertion( "UBERON:0008926") AnnotationAssertion(rdfs:label "sublaminar layer S5") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sublaminar layers S1 or S2) @@ -204096,6 +203446,7 @@ AnnotationAssertion( "lung parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (respiratory primordium) @@ -204113,7 +203464,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (left lung lobe) AnnotationAssertion(Annotation( "OBOL:automatic") "A lobe of lung that is part of a left lung.") -AnnotationAssertion(Annotation( "ISBN:0123813611") "1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure") AnnotationAssertion( "EHDAA:2981") AnnotationAssertion( "NCIT:C48945") AnnotationAssertion( "SCTID:272655003") @@ -204124,6 +203474,8 @@ AnnotationAssertion( "UBERON:0008951") AnnotationAssertion(rdfs:label "left lung lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb bone) @@ -204139,6 +203491,9 @@ AnnotationAssertion( "UBERON:0008962") AnnotationAssertion(rdfs:label "forelimb bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dental follicle) @@ -204147,7 +203502,6 @@ AnnotationAssertion(Annotation( "BTO:0000337") AnnotationAssertion( "EMAPA:35275") AnnotationAssertion( "MA:0003121") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D003795") AnnotationAssertion( "NCIT:C34138") AnnotationAssertion( "SCTID:110975002") AnnotationAssertion( "Wikipedia:Dental_follicle") @@ -204157,20 +203511,18 @@ AnnotationAssertion(Annotation( "UBERON:0008969") AnnotationAssertion(rdfs:label "dental follicle") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:19767574") ObjectSomeValuesFrom( )) # Class: (apocrine gland) AnnotationAssertion(Annotation( "MGI:anna") "Any exocrine gland whose cells bud their secretions off through the plasma membrane producing membrane-bound vesicles in the lumen; the apical portion of the secretory cell of the gland pinches off and enters the lumen; it loses part of its cytoplasm in their secretions; apocrine secretion is functional during hormonal stress or puberty; an example of true apocrine glands are mammary glands, responsible for secreting breast milk.") AnnotationAssertion( ) -AnnotationAssertion( "apocrine") -AnnotationAssertion( "Mammary glands are modified apocrine glands present in both humans and mice; unlike humans, mice do not have axillary apocrine sweat glands[MGI:anna]") AnnotationAssertion( "BTO:0001162") AnnotationAssertion( "EMAPA:35141") AnnotationAssertion( "MA:0003040") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D001050") AnnotationAssertion( "SCTID:361698000") AnnotationAssertion( "Wikipedia:Apocrine") AnnotationAssertion( "true apocrine gland") @@ -204216,9 +203568,11 @@ AnnotationAssertion( "submucosal esophageal gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of brain) @@ -204239,7 +203593,8 @@ AnnotationAssertion( "UBERON:0008998") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of brain") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (periurethral tissue) @@ -204251,7 +203606,9 @@ AnnotationAssertion( "UBERON:0009010") AnnotationAssertion(rdfs:label "periurethral tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper back skin) @@ -204263,7 +203620,9 @@ AnnotationAssertion( "UBERON:0009015") AnnotationAssertion(rdfs:label "upper back skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vesical artery) @@ -204277,6 +203636,8 @@ AnnotationAssertion( "UBERON:0009027") AnnotationAssertion(rdfs:label "vesical artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pudendal vein) @@ -204291,12 +203652,11 @@ AnnotationAssertion( "UBERON:0009029") AnnotationAssertion(rdfs:label "pudendal vein") SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (left pulmonary vein) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Vein that drains left lung and returns blood to the heart.") -AnnotationAssertion(Annotation( "ncithesaurus:Left_Pulmonary_Vein") "A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37165") AnnotationAssertion( "MA:0002207") AnnotationAssertion( "NCIT:C48946") @@ -204306,11 +203666,12 @@ AnnotationAssertion( "UBERON:0009030") AnnotationAssertion(rdfs:label "left pulmonary vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right pulmonary vein) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Vein that drains right lung and returns blood to the heart.") -AnnotationAssertion(Annotation( "ncithesaurus:Right_Pulmonary_Vein") "A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37379") AnnotationAssertion( "MA:0002208") AnnotationAssertion( "NCIT:C48947") @@ -204320,6 +203681,8 @@ AnnotationAssertion( "UBERON:0009032") AnnotationAssertion(rdfs:label "right pulmonary vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal straight tubule) @@ -204356,6 +203719,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node germinal center") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (prostatic venous plexus) @@ -204373,57 +203737,60 @@ AnnotationAssertion( "prostatic venous plexus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner medulla vasa recta descending limb) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb") AnnotationAssertion( "KUPO:0001003") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009089") AnnotationAssertion(rdfs:label "inner medulla vasa recta descending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (outer medulla vasa recta descending limb) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb") AnnotationAssertion( "KUPO:0001004") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009090") AnnotationAssertion(rdfs:label "outer medulla vasa recta descending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (vasa recta ascending limb) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb") AnnotationAssertion( "KUPO:0001005") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009091") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasa recta ascending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (inner medulla vasa recta ascending limb) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb") AnnotationAssertion( "KUPO:0001006") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009092") AnnotationAssertion(rdfs:label "inner medulla vasa recta ascending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (outer medulla vasa recta ascending limb) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb") AnnotationAssertion( "KUPO:0001007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009093") AnnotationAssertion(rdfs:label "outer medulla vasa recta ascending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (tip of renal papilla) @@ -204443,7 +203810,6 @@ SubClassOf(Annotation( "KUP AnnotationAssertion(Annotation( "BTO:0004733") "An organism containing a developing embryo, fetus, or unborn offspring within the body.") AnnotationAssertion( "BTO:0004733") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "IDOMAL:0000443") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "BTO:0004733") "gravid") AnnotationAssertion(Annotation( "BTO:0004733") "pregnant adult") @@ -204453,6 +203819,8 @@ AnnotationAssertion(Annotation( "UBERON:0009097") AnnotationAssertion(rdfs:label "gravid organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -204468,20 +203836,23 @@ AnnotationAssertion( "UBERON:0009098") AnnotationAssertion(rdfs:label "gravid uterus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical thymus) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A mature thymus that is entirely part of the cervical region.") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125]") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009114") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic thymus) @@ -204491,7 +203862,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic thymus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA-modified") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (indifferent gonad) @@ -204512,7 +203884,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://www.ncbi.nlm.nih.gov/books/NBK53175/") "The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary.") AnnotationAssertion( "consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm") -AnnotationAssertion( "Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)") AnnotationAssertion( "EFO:0000229") AnnotationAssertion( "TAO:0001198") AnnotationAssertion( "XAO:0004208") @@ -204565,7 +203936,6 @@ SubClassOf(Annotation( "ZFA # Class: (epibranchial ganglion) AnnotationAssertion(Annotation( "PMID:20133851") Annotation( "ZFIN:curator") "Cranial ganglion which develops from an epibranchial placode.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006250") AnnotationAssertion( "TAO:0001555") AnnotationAssertion( "ZFA:0001555") AnnotationAssertion(Annotation( "ZFA:0001555") Annotation( ) "epibranchial ganglia") @@ -204575,6 +203945,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "epibranchial ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ObjectSomeValuesFrom( )) # Class: (lateral line placode) @@ -204582,7 +203953,6 @@ SubClassOf(Annotation( "NCB AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An ectodermal placode that will develop into the components of the lateral line system.") AnnotationAssertion( "TODO - compare with protoneuromast") AnnotationAssertion(Annotation( "http://tolweb.org/Amniota") ) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010718") Annotation( "AAO") Annotation( "AAO:SIQ") "Specialized series of dorsolateral ectodermal placodes.[AAO]") AnnotationAssertion( "AAO:0010718") AnnotationAssertion( "XAO:0000440") AnnotationAssertion( "uberon") @@ -204592,6 +203962,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ISBN:0471888893") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right atrium endocardium) @@ -204608,14 +203979,17 @@ AnnotationAssertion(Annotation( "UBERON:0009129") AnnotationAssertion(rdfs:label "right atrium endocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (pleuroperitoneal membrane) AnnotationAssertion(Annotation( "Wikipedia:Pleuroperitoneal") Annotation( "http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane") "A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000757") Annotation( "VHOG") Annotation( "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206") Annotation( "http://bgee.unil.ch/") "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]") AnnotationAssertion( "UBERON:0009146") AnnotationAssertion( "EHDAA2:0001483") AnnotationAssertion( "EMAPA:17709") @@ -204629,8 +204003,8 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0009133") AnnotationAssertion(rdfs:label "pleuroperitoneal membrane") -SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -204646,7 +204020,8 @@ AnnotationAssertion( "UBERON:0009141") AnnotationAssertion(rdfs:label "craniocervical region vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire embryonic mesenchyme) @@ -204686,8 +204061,12 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphenoid cartilage element) @@ -204698,8 +204077,11 @@ AnnotationAssertion( "UBERON:0009193") AnnotationAssertion(rdfs:label "sphenoid cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (indifferent external genitalia) @@ -204722,7 +204104,9 @@ AnnotationAssertion(Annotation( "UBERON:0009198") AnnotationAssertion(rdfs:label "craniofacial suture") EquivalentClasses( ObjectIntersectionOf( ObjectMinCardinality(2 ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial suture) @@ -204733,7 +204117,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectMinCardinality(2 ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "between two adjacent facial bones") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb epidermis) @@ -204743,6 +204127,8 @@ AnnotationAssertion( "UBERON:0009200") AnnotationAssertion(rdfs:label "limb epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (nephric duct) @@ -204754,20 +204140,21 @@ AnnotationAssertion( "pronephric duct or mesonephric duct") AnnotationAssertion(rdfs:label "nephric duct") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (vasa recta descending limb) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "CL") "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb") AnnotationAssertion( "KUPO:0001002") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009202") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasa recta descending limb") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (medial nasal process mesenchyme) @@ -204780,9 +204167,8 @@ AnnotationAssertion( "UBERON:0009204") AnnotationAssertion(rdfs:label "medial nasal process mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (lateral nasal process mesenchyme) @@ -204796,7 +204182,8 @@ AnnotationAssertion( "UBERON:0009205") AnnotationAssertion(rdfs:label "lateral nasal process mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral nasal process surface ectoderm) @@ -204808,14 +204195,14 @@ AnnotationAssertion( "UBERON:0009206") AnnotationAssertion(rdfs:label "lateral nasal process surface ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal membrane) AnnotationAssertion(Annotation( "http://musom.marshall.edu/anatomy/grosshom/z_devbranc.html") "A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001427") Annotation( "VHOG") Annotation( "ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]") AnnotationAssertion( "EMAPA:32749") AnnotationAssertion( "FMA:295758") AnnotationAssertion( "NCIT:C34251") @@ -204867,15 +204254,15 @@ AnnotationAssertion( "cartilaginous centrum of vertebra[PMID:11746457]") AnnotationAssertion(rdfs:label "cartilaginous vertebral centrum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic nasal process) -AnnotationAssertion(Annotation( "EHDAA2") "medial or lateral; in EHDAA2 also frontonasal or intermaxillary") AnnotationAssertion( "EHDAA2:0000581") AnnotationAssertion( "EHDAA:4776") AnnotationAssertion( "EMAPA:16680") -AnnotationAssertion( "FMA:293971") AnnotationAssertion( "SCTID:308881001") AnnotationAssertion( "uberon") AnnotationAssertion( "nasal placode") @@ -204902,7 +204289,6 @@ SubClassOf(Annotation( "FMA # Class: (axilla) AnnotationAssertion(Annotation( "Wikipedia:Axilla") "The axilla is the area directly under the joint where the forelimb connects to the shoulder.") -AnnotationAssertion( "axillary") AnnotationAssertion( "CALOHA:TS-2208") AnnotationAssertion( "EFO:0001395") AnnotationAssertion( "FMA:24864") @@ -204941,6 +204327,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "associated mesenchyme of otic placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectoderm of buccopharyngeal membrane) @@ -204953,6 +204341,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ectoderm of buccopharyngeal membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endoderm of buccopharyngeal membrane) @@ -204964,6 +204354,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endoderm of buccopharyngeal membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (associated mesenchyme of foregut-midgut junction) @@ -204975,11 +204367,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "associated mesenchyme of foregut-midgut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of foregut-midgut junction) AnnotationAssertion(Annotation( "OBOL:automatic") "A mesentery that is part of a foregut-midgut junction.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000430") Annotation( "VHOG") Annotation( "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11") Annotation( "http://bgee.unil.ch/") "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]") AnnotationAssertion( "EHDAA2:0000575") AnnotationAssertion( "EMAPA:16365") AnnotationAssertion( "VHOG:0000430") @@ -204989,6 +204382,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesentery of foregut-midgut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch mesenchymal region) @@ -205003,7 +204398,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch mesenchymal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -205018,7 +204415,10 @@ AnnotationAssertion( "epithelium of foregut-midgut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (periotic mesenchyme) @@ -205035,8 +204435,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "periotic mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of fronto-nasal process) @@ -205052,6 +204454,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of fronto-nasal process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of hindgut) @@ -205065,6 +204469,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of hindgut") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of trachea) @@ -205077,13 +204483,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of middle ear) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a developing middle ear.") -AnnotationAssertion(Annotation( "EHDAA2") "Also 1st arch maxillary mesenchyme in EHDAA2") AnnotationAssertion( "otic mesenchyme") AnnotationAssertion( "EHDAA2:0001182") AnnotationAssertion( "EMAPA:17001") @@ -205093,7 +204500,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of middle ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -205107,6 +204516,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anal membrane endodermal component") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral lingual swelling epithelium) @@ -205120,11 +204532,13 @@ AnnotationAssertion( "lateral lingual swelling epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme of handplate) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that is part of a handplate.") -AnnotationAssertion(Annotation( "EMAPA") "We group two EMAPA classes here but these may need to be separated") AnnotationAssertion( "EHDAA2:0000731") AnnotationAssertion( "EMAPA:17248") AnnotationAssertion( "EMAPA:17457") @@ -205135,6 +204549,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchyme of handplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (maxillary process mesenchyme) @@ -205150,6 +204566,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "maxillary process mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vascular element of left lung) @@ -205161,6 +204580,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vascular element of left lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vascular element of right lung) @@ -205172,6 +204594,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vascular element of right lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic sinusoid of left of lobe of liver) @@ -205185,6 +204610,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatic sinusoid of left of lobe of liver") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic sinusoid of right of lobe of liver) @@ -205199,6 +204626,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatic sinusoid of right of lobe of liver") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endoderm of foregut-midgut junction) @@ -205211,11 +204640,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endoderm of foregut-midgut junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal segment of digit) AnnotationAssertion(Annotation( "DOI:10.1038/nature10346") "A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).") -AnnotationAssertion( "Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "digit tip") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "distal digit segment") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "tip of digit") @@ -205223,6 +204653,10 @@ AnnotationAssertion( "UBERON:0009551") AnnotationAssertion(rdfs:label "distal segment of digit") EquivalentClasses(Annotation( "cjm") ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal segment of manual digit) @@ -205241,6 +204675,8 @@ AnnotationAssertion( "distal segment of manual digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal segment of pedal digit) @@ -205256,6 +204692,8 @@ AnnotationAssertion( "distal segment of pedal digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metacarpal/tarsal-phalangeal joint) @@ -205269,8 +204707,11 @@ AnnotationAssertion( "UBERON:0009559") AnnotationAssertion(rdfs:label "metacarpal/tarsal-phalangeal joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal limb integumentary appendage) @@ -205284,6 +204725,7 @@ AnnotationAssertion( "unguis") AnnotationAssertion( "UBERON:0009564") AnnotationAssertion(rdfs:label "distal limb integumentary appendage") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -205310,6 +204752,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nail of manual digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) @@ -205322,6 +204765,7 @@ AnnotationAssertion( "UBERON:0009566") AnnotationAssertion(rdfs:label "intestinal submucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (nail of pedal digit) @@ -205349,14 +204793,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nail of pedal digit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (trunk region of vertebral column) AnnotationAssertion(Annotation( "UBERONREF:0000006") "Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000612") Annotation( "AAO") Annotation( "AAO:Duellman_and_Trueb_1994") "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]") -AnnotationAssertion( "AAO:0000612") AnnotationAssertion( "FMA:72066") AnnotationAssertion( "NCIT:C92597") AnnotationAssertion( "SCTID:281699004") @@ -205376,6 +204819,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk region of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of trunk) @@ -205401,6 +204847,8 @@ AnnotationAssertion( "UBERON:0009570") AnnotationAssertion(rdfs:label "spinal cord sulcus limitans") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of central canal of spinal cord) @@ -205416,10 +204864,11 @@ AnnotationAssertion( "UBERON:0009572") AnnotationAssertion(rdfs:label "lumen of central canal of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA-modified") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medulla oblongata sulcus limitans) @@ -205430,6 +204879,8 @@ AnnotationAssertion( "UBERON:0009576") AnnotationAssertion(rdfs:label "medulla oblongata sulcus limitans") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (metencephalon sulcus limitans) @@ -205441,6 +204892,8 @@ AnnotationAssertion( "UBERON:0009577") AnnotationAssertion(rdfs:label "metencephalon sulcus limitans") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myelencephalon sulcus limitans) @@ -205450,6 +204903,8 @@ AnnotationAssertion( "UBERON:0009578") AnnotationAssertion(rdfs:label "myelencephalon sulcus limitans") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diencephalon mantle layer) @@ -205462,6 +204917,8 @@ AnnotationAssertion( "UBERON:0009580") AnnotationAssertion(rdfs:label "diencephalon mantle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain mantle layer) @@ -205475,6 +204932,8 @@ AnnotationAssertion(Annotation( "UBERON:0009581") AnnotationAssertion(rdfs:label "midbrain mantle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord mantle layer) @@ -205486,6 +204945,8 @@ AnnotationAssertion( "UBERON:0009583") AnnotationAssertion(rdfs:label "spinal cord mantle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch mandibular mesenchyme) @@ -205501,6 +204962,7 @@ AnnotationAssertion( "UBERON:0009584") AnnotationAssertion(rdfs:label "1st arch mandibular mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (left lung associated mesenchyme) @@ -205514,6 +204976,8 @@ AnnotationAssertion( "UBERON:0009602") AnnotationAssertion(rdfs:label "left lung associated mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung associated mesenchyme) @@ -205525,6 +204989,8 @@ AnnotationAssertion( "UBERON:0009603") AnnotationAssertion(rdfs:label "right lung associated mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain neural plate) @@ -205535,7 +205001,9 @@ AnnotationAssertion( "UBERON:0009610") AnnotationAssertion(rdfs:label "forebrain neural plate") EquivalentClasses(Annotation( "ZFA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain neural plate) @@ -205546,7 +205014,9 @@ AnnotationAssertion( "UBERON:0009611") AnnotationAssertion(rdfs:label "midbrain neural plate") EquivalentClasses(Annotation( "ZFA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain neural plate) @@ -205557,7 +205027,9 @@ AnnotationAssertion( "UBERON:0009614") AnnotationAssertion(rdfs:label "hindbrain neural plate") EquivalentClasses(Annotation( "ZFA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain hindbrain boundary neural plate) @@ -205571,7 +205043,7 @@ AnnotationAssertion( "midbrain hindbrain boundary neural plate") SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/438") Annotation( "Bgee:AN") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (presumptive midbrain) @@ -205593,14 +205065,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presumptive midbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head paraxial mesoderm) AnnotationAssertion(Annotation( "PMID:21610022") "Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.") -AnnotationAssertion( "A major contributor to neurocranium [PMID:16313393]") AnnotationAssertion( "EHDAA2:0000736") AnnotationAssertion( "EHDAA:364") AnnotationAssertion( "EMAPA:16171") @@ -205614,7 +205087,7 @@ AnnotationAssertion( "somitomeric mesoderm") AnnotationAssertion( "UBERON:0009617") AnnotationAssertion(rdfs:label "head paraxial mesoderm") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -205626,7 +205099,7 @@ AnnotationAssertion( "https://github.com/obophenotype/uberon/issues/30") "trunk paraxial mesenchyme") AnnotationAssertion( "UBERON:0009618") AnnotationAssertion(rdfs:label "trunk paraxial mesoderm") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -205640,6 +205113,8 @@ AnnotationAssertion( "UBERON:0009621") AnnotationAssertion(rdfs:label "tail somite") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pronephric proximal straight tubule) @@ -205651,20 +205126,19 @@ AnnotationAssertion(Annotation( "UBERON:0009622") AnnotationAssertion(rdfs:label "pronephric proximal straight tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (spinal nerve root) AnnotationAssertion(Annotation( "MESH:A08.800.800.720.725") "The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule.") -AnnotationAssertion(Annotation( "ZFA") "ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)") AnnotationAssertion( "BTO:0000883") AnnotationAssertion( "DHBA:146035120") AnnotationAssertion( "FMA:14060") AnnotationAssertion( "GAID:717") AnnotationAssertion( "MESH:D013126") AnnotationAssertion( "NCIT:C12791") -AnnotationAssertion( "SCTID:362436008") AnnotationAssertion(Annotation( "ncithesaurus:Spinal_Nerve_Root") "UMLS:C0037940") AnnotationAssertion( "ZFA:0005578") AnnotationAssertion(Annotation( "FMA:14060") "root of spinal nerve") @@ -205678,6 +205152,8 @@ EquivalentClasses( ObjectIntersec SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (root of thoracic nerve) @@ -205691,6 +205167,8 @@ AnnotationAssertion( "UBERON:0009630") AnnotationAssertion(rdfs:label "root of thoracic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (root of cervical nerve) @@ -205707,6 +205185,8 @@ AnnotationAssertion( "UBERON:0009632") AnnotationAssertion(rdfs:label "root of cervical nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (orbitosphenoid ossification center) @@ -205743,6 +205223,7 @@ AnnotationAssertion( "tympanic membrane epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) DisjointClasses( ) # Class: (eyelid subcutaneous connective tissue) @@ -205758,6 +205239,9 @@ AnnotationAssertion(Annotation( "UBERON:0009648") AnnotationAssertion(rdfs:label "eyelid subcutaneous connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nephron tubule basement membrane) @@ -205775,13 +205259,12 @@ AnnotationAssertion( "UBERON:0009651") AnnotationAssertion(rdfs:label "nephron tubule basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (bronchus basement membrane) AnnotationAssertion(Annotation( "OBOL:automatic") "A basement membrane that is part of a bronchus.") -AnnotationAssertion(Annotation( "MA") "MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37809") AnnotationAssertion( "MA:0001832") AnnotationAssertion( "NCIT:C49208") @@ -205791,6 +205274,8 @@ AnnotationAssertion( "UBERON:0009652") AnnotationAssertion(rdfs:label "bronchus basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (trachea basement membrane) @@ -205804,6 +205289,8 @@ AnnotationAssertion( "UBERON:0009653") AnnotationAssertion(rdfs:label "trachea basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MA-modified") ObjectSomeValuesFrom( )) @@ -205819,6 +205306,8 @@ AnnotationAssertion( "UBERON:0009655") AnnotationAssertion(rdfs:label "auricular artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (artery of lip) @@ -205831,6 +205320,8 @@ AnnotationAssertion( "UBERON:0009657") AnnotationAssertion(rdfs:label "artery of lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain nucleus) @@ -205842,6 +205333,8 @@ AnnotationAssertion( "UBERON:0009661") AnnotationAssertion(rdfs:label "midbrain nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain nucleus) @@ -205852,6 +205345,8 @@ AnnotationAssertion( "UBERON:0009662") AnnotationAssertion(rdfs:label "hindbrain nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (telencephalic nucleus) @@ -205862,6 +205357,8 @@ AnnotationAssertion( "UBERON:0009663") AnnotationAssertion(rdfs:label "telencephalic nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gut mesentery) @@ -205880,7 +205377,6 @@ SubClassOf(Annotation( "EHD # Class: (ventral mesentery) AnnotationAssertion(Annotation( "Wikipedia:Ventral_mesentery") "Ventral mesentery is the part of the peritoneum closest to the navel.") -AnnotationAssertion( "degenerates during development except foregut portion") AnnotationAssertion( "EHDAA2:0004569") AnnotationAssertion( "SCTID:361430000") AnnotationAssertion( "Wikipedia:Ventral_mesentery") @@ -205898,8 +205394,10 @@ AnnotationAssertion( "UBERON:0009669") AnnotationAssertion(rdfs:label "embryonic cloacal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rectal lumen) @@ -205913,9 +205411,11 @@ AnnotationAssertion( "UBERON:0009670") AnnotationAssertion(rdfs:label "rectal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (early telencephalic vesicle) @@ -205948,6 +205448,7 @@ AnnotationAssertion( "tooth row") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (set of lower jaw teeth) @@ -205964,6 +205465,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "set of lower jaw teeth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (set of upper jaw teeth) @@ -205980,6 +205483,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "set of upper jaw teeth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of appendix) @@ -205993,6 +205498,7 @@ AnnotationAssertion( "UBERON:0009697") AnnotationAssertion(rdfs:label "epithelium of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -206008,6 +205514,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal pancreas") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -206023,6 +205531,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ventral pancreas") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -206030,7 +205540,6 @@ SubClassOf(Annotation( "cjm # Class: (endocardium of right ventricle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any endocardium that is part of the right ventricle of the heart.") -AnnotationAssertion(Annotation( "FMA:9536") "Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.") AnnotationAssertion( "EHDAA2:0002188") AnnotationAssertion( "EMAPA:17341") AnnotationAssertion( "FMA:9536") @@ -206045,13 +205554,14 @@ AnnotationAssertion(Annotation( "UBERON:0009712") AnnotationAssertion(rdfs:label "endocardium of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (endocardium of left ventricle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any endocardium that is part of the left ventricle of the heart.") -AnnotationAssertion(Annotation( "FMA:9559") "Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.") AnnotationAssertion( "EHDAA2:0002182") AnnotationAssertion( "EMAPA:17338") AnnotationAssertion( "FMA:9559") @@ -206065,6 +205575,8 @@ AnnotationAssertion(Annotation( "UBERON:0009713") AnnotationAssertion(rdfs:label "endocardium of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (intermaxillary process) @@ -206082,7 +205594,7 @@ AnnotationAssertion(Annotation( "UBERON:0009714") AnnotationAssertion(rdfs:label "intermaxillary process") SubClassOf(Annotation( "EHDAA2-modified") ) -SubClassOf(Annotation( "inconsistent") Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (stomodeal lumen) @@ -206095,6 +205607,8 @@ AnnotationAssertion( "UBERON:0009715") AnnotationAssertion(rdfs:label "stomodeal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire pharyngeal arch endoderm) @@ -206105,10 +205619,11 @@ AnnotationAssertion( "EHDAA2:0004621") "pharyngeal arch endoderm") AnnotationAssertion( "UBERON:0009722") AnnotationAssertion(rdfs:label "entire pharyngeal arch endoderm") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (sublaminar layers S3 or S4) @@ -206188,7 +205703,10 @@ AnnotationAssertion( "UBERON:0009738") AnnotationAssertion(rdfs:label "border of sublaminar layers S1 and S2") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (border of sublaminar layers S3 and S4) @@ -206198,7 +205716,10 @@ AnnotationAssertion( "UBERON:0009739") AnnotationAssertion(rdfs:label "border of sublaminar layers S3 and S4") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (border between sublaminar layers) @@ -206206,6 +205727,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0009740") AnnotationAssertion(rdfs:label "border between sublaminar layers") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206246,7 +205768,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (limb mesenchyme) AnnotationAssertion(Annotation( "MP:0011261") "The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA mapping from TH") AnnotationAssertion( "EMAPA:32705") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "Geisha:syn") Annotation( "NCBITaxon:8782") "limb mesoderm") @@ -206254,6 +205775,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "limb mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac mesenchyme) @@ -206267,6 +205790,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas mesenchyme) @@ -206281,6 +205807,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pancreas mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adrenal gland cortex zone) @@ -206294,6 +205822,8 @@ AnnotationAssertion(Annotation( "UBERON:0009753") AnnotationAssertion(rdfs:label "adrenal gland cortex zone") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (abdominal ganglion) @@ -206304,6 +205834,8 @@ AnnotationAssertion( "UBERON:0009758") AnnotationAssertion(rdfs:label "abdominal ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal interphalangeal joint) @@ -206317,7 +205849,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "proximal interphalangeal joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (distal interphalangeal joint) @@ -206331,11 +205865,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "distal interphalangeal joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal tubule) AnnotationAssertion(Annotation( "DOI:10.1371/journal.pone.0099864") Annotation( "GO:0061333") Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.") -AnnotationAssertion( "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "renal tubule (generic)") AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "https://orcid.org/0000-0002-6601-2165") "tubule of excretory system") AnnotationAssertion( "uberon") @@ -206344,13 +205879,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal tubule") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pleural sac) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/86") "A serous sac that has the pleura and the pleural cavity as parts.") -AnnotationAssertion(Annotation( "EHDAA2") "despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac") AnnotationAssertion( "EHDAA2:0004737") AnnotationAssertion( "FMA:9690") AnnotationAssertion( "SCTID:361996004") @@ -206359,7 +205893,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pleural sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (upper rhombic lip) @@ -206378,7 +205917,7 @@ AnnotationAssertion(Annotation( "UBERON:0009841") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "upper rhombic lip") -SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ZFA-def") ObjectSomeValuesFrom( )) @@ -206386,7 +205925,6 @@ SubClassOf(Annotation( "ZFA # Class: (glandular acinus) AnnotationAssertion(Annotation( "Wikipedia:Acinus") "The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.") -AnnotationAssertion( "acinar") AnnotationAssertion(Annotation( "FMA:55588") "acinus") AnnotationAssertion( "FMA:55588") AnnotationAssertion( "Wikipedia:Acinus") @@ -206396,6 +205934,10 @@ AnnotationAssertion( "glandular acinus") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate epithelial cord) @@ -206407,6 +205949,8 @@ AnnotationAssertion( "Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204]") AnnotationAssertion(rdfs:label "prostate epithelial cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urogenital sinus lumen) @@ -206416,20 +205960,23 @@ AnnotationAssertion( "UBERON:0009844") AnnotationAssertion(rdfs:label "urogenital sinus lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urogenital sinus mesenchyme) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that surrounds primitive urogenital sinus.") -AnnotationAssertion( "Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth") AnnotationAssertion( "EMAPA:31500") AnnotationAssertion(Annotation( "PMID:18977204") Annotation( ) "UGM") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009845") AnnotationAssertion(rdfs:label "urogenital sinus mesenchyme") EquivalentClasses(Annotation( "PMID:18977204") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic cloacal epithelium) @@ -206440,7 +205987,10 @@ AnnotationAssertion( "UBERON:0009846") AnnotationAssertion(rdfs:label "embryonic cloacal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -206452,9 +206002,13 @@ AnnotationAssertion( "UBERON:0009847") AnnotationAssertion(rdfs:label "prostate field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PMID:18977204") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:18977204") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (border of sublaminar layers S4 and S5) @@ -206463,7 +206017,10 @@ AnnotationAssertion( "UBERON:0009851") AnnotationAssertion(rdfs:label "border of sublaminar layers S4 and S5") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (border of sublaminar layers S2 and S3) @@ -206472,12 +206029,14 @@ AnnotationAssertion( "UBERON:0009852") AnnotationAssertion(rdfs:label "border of sublaminar layers S2 and S3") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive tract diverticulum) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Branch or outpocketing of the digestive tract.") -AnnotationAssertion(Annotation( ) "FBbt:00100316") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FBbt:00100316") "diverticulum of gut") AnnotationAssertion( "intestinal pouch") @@ -206485,6 +206044,7 @@ AnnotationAssertion( "digestive tract diverticulum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (sac) @@ -206495,11 +206055,12 @@ AnnotationAssertion( "UBERON:0009856") AnnotationAssertion(rdfs:label "sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endosteum) AnnotationAssertion(Annotation( "Wikipedia:Endosteum") "A thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones.") -AnnotationAssertion( "endosteal") AnnotationAssertion( "FMA:32692") AnnotationAssertion( "NCIT:C13183") AnnotationAssertion( "SCTID:57487002") @@ -206534,12 +206095,12 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (nephrogenic zone) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Outer portion of the renal cortex. Site of formation of medullary and cortical elements.") -AnnotationAssertion( "see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.") AnnotationAssertion( "EMAPA:27721") AnnotationAssertion( "MA:0002996") AnnotationAssertion( "http://www.gudmap.org/Images/Organ_Summaries/Metanephros/NZ.png") @@ -206557,7 +206118,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MA:th") Annotation( "https://orcid.org/0000-0002-6601-2165") "Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region.") AnnotationAssertion( "considering adding 'acropodial region'") -AnnotationAssertion( "Naming conventions for pod terms under discussion within phenoscape group") AnnotationAssertion( "SCTID:370640001") AnnotationAssertion( "metacarpal or metatarsal part of limb") AnnotationAssertion( "metacarpus/metatarsus region") @@ -206570,15 +206130,14 @@ AnnotationAssertion( "UBERON:0009877") AnnotationAssertion(rdfs:label "metapodium region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "MA:th") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesopodial skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005022") Annotation( "VSAO") Annotation( "VSAO:NI") "Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005022") Annotation( "VSAO") "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]") AnnotationAssertion( "VSAO:0005022") AnnotationAssertion(Annotation( "VSAO:0005022") Annotation( "VSAO:NI") "basipodium skeleton") AnnotationAssertion( "carpal/tarsal skeleton") @@ -206591,18 +206150,17 @@ AnnotationAssertion(Annotation( "UBERON:0009878") AnnotationAssertion(rdfs:label "mesopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsal skeleton) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") Annotation( "VSAO:0005024") Annotation( "https://github.com/obophenotype/uberon/issues/94") "Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000220") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001160") Annotation( "VHOG") Annotation( "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)") Annotation( "http://bgee.unil.ch/") "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]") -AnnotationAssertion(Annotation( "PHENOSCAPE:ad") "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present") -AnnotationAssertion(Annotation( "MA") "we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.") AnnotationAssertion( "AAO:0000220") AnnotationAssertion( "EMAPA:19133") AnnotationAssertion( "FMA:71339") @@ -206630,19 +206188,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tarsal skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (carpal skeleton) AnnotationAssertion(Annotation( "PHENOSCAPE:ad") Annotation( "https://github.com/obophenotype/uberon/issues/93") "Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000201") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO]") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001161") Annotation( "VHOG") Annotation( "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)") Annotation( "http://bgee.unil.ch/") "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]") -AnnotationAssertion(Annotation( "Wikipedia:Carpus#Evolutionary_variations") "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad].") -AnnotationAssertion( "The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone") -AnnotationAssertion(Annotation( "MA") "we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.") AnnotationAssertion( "AAO:0000201") AnnotationAssertion( "FMA:71335") AnnotationAssertion( "MA:0000040") @@ -206667,8 +206222,10 @@ AnnotationAssertion( "carpal skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206682,7 +206239,8 @@ AnnotationAssertion( "UBERON:0009881") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anterior lateral plate mesoderm") -SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (anal column) @@ -206699,6 +206257,7 @@ AnnotationAssertion(Annotation( "UBERON:0009882") AnnotationAssertion(rdfs:label "anal column") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206707,8 +206266,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0011347") Annotation( "Wikipedia:Bone_marrow_of_ovaryry_ray_(anatomy)") "A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA says parenchyma, MP says cortex") -AnnotationAssertion( "Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla") AnnotationAssertion( "BTO:0001155") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37906") AnnotationAssertion( "FMA:74299") @@ -206730,7 +206287,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Interlobar_arteries") Annotation( "http://orcid.org/0000-0002-6601-2165") "An artery that supplies a renal lobe.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA only has the set term") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37091") AnnotationAssertion( "FMA:71637") AnnotationAssertion( "SCTID:62802007") @@ -206749,12 +206305,13 @@ AnnotationAssertion( "interlobar artery") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interlobar vein) AnnotationAssertion(Annotation( "Wikipedia:Interlobar_veins") "The interlobar veins are veins of the renal circulation which drain the renal lobes.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA only has the set term") AnnotationAssertion( "FMA:71631") AnnotationAssertion( "Wikipedia:Interlobar_veins") AnnotationAssertion(Annotation( "FMA:71631") "interlobar vein of kidney") @@ -206768,14 +206325,13 @@ AnnotationAssertion( "interlobar vein") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary heart field) AnnotationAssertion(Annotation( "GO:0003139") Annotation( "GOC:mtg_heart") Annotation( "GOC:rl") "A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).") -AnnotationAssertion(Annotation( "PMID:17276708") "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].") -AnnotationAssertion(Annotation( "PMID:17276708") "In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested") -AnnotationAssertion( "in mouse has left ventricular identity[PMID:22855565]") AnnotationAssertion( "XAO:0004186") AnnotationAssertion(Annotation( "PMID:17276708") "anterior heart field") AnnotationAssertion(Annotation( "Geisha:syn") Annotation( "NCBITaxon:8782") "anterior/second heart field") @@ -206784,6 +206340,9 @@ AnnotationAssertion( "XAO:0004186") "SHF") AnnotationAssertion( "UBERON:0009889") AnnotationAssertion(rdfs:label "secondary heart field") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "GO:0003129") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:17276708") ObjectSomeValuesFrom( )) @@ -206801,6 +206360,8 @@ AnnotationAssertion( "UBERON:0009891") AnnotationAssertion(rdfs:label "facial mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (root of optic nerve) @@ -206816,6 +206377,7 @@ AnnotationAssertion( "root of optic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobule) @@ -206847,7 +206409,6 @@ SubClassOf(Annotation( "cjm AnnotationAssertion(Annotation( "MP:0011381") Annotation( "Wikipedia:Renal_lobe") "The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].") AnnotationAssertion( "todo - add has_part relationships.") -AnnotationAssertion(Annotation( "MP") "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys") AnnotationAssertion( "FMA:17881") AnnotationAssertion( "NCIT:C32894") AnnotationAssertion(Annotation( "ncithesaurus:Kidney_Lower_Lobe") "UMLS:C0736382") @@ -206862,6 +206423,8 @@ AnnotationAssertion( "renal lobe") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal lobule) @@ -206886,6 +206449,7 @@ AnnotationAssertion( "Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis") AnnotationAssertion(rdfs:label "renal lobule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206901,6 +206465,9 @@ AnnotationAssertion( "UBERON:0009916") AnnotationAssertion(rdfs:label "wall of ureter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206913,7 +206480,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney corticomedullary boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (retrotrapezoid nucleus) @@ -206926,8 +206496,7 @@ AnnotationAssertion( "UBERON:0009918") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retrotrapezoid nucleus") -SubClassOf(Annotation( "cjm") ) -SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (ureter smooth muscle) @@ -206942,6 +206511,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureter smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -206952,6 +206522,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009920") AnnotationAssertion(rdfs:label "optic neural crest") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -206979,6 +206550,8 @@ AnnotationAssertion( "post-embryonic organism") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/667"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vomeronasal system) @@ -206995,8 +206568,6 @@ SubClassOf(Annotation( "Wik # Class: (neurogenic placode) AnnotationAssertion(Annotation( "PMID:11523831") Annotation( "http://orcid.org/0000-0002-6601-2165") "Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.") -AnnotationAssertion( "Includes: trigeminal, otic, lateral line and epibranchial placodes.") -AnnotationAssertion(Annotation( "NCBIBook:NBK53171") "While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)") AnnotationAssertion( "EFO:0003460") AnnotationAssertion( "TAO:0001309") AnnotationAssertion( "Wikipedia:Neurogenic_placodes") @@ -207011,6 +206582,9 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "cjm") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (bladder lumen) @@ -207028,8 +206602,10 @@ AnnotationAssertion( "UBERON:0009958") AnnotationAssertion(rdfs:label "bladder lumen") EquivalentClasses(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophagus smooth muscle circular layer) @@ -207044,13 +206620,14 @@ AnnotationAssertion(Annotation( "UBERON:0009960") AnnotationAssertion(rdfs:label "esophagus smooth muscle circular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (internodal tract) AnnotationAssertion(Annotation( "Wikipedia:Electrical_conduction_system_of_the_heart") "A conducting pathway in the conducting tissue of heart through which electrical activity spreads from the SA node to the AV node.") AnnotationAssertion( "include 3 subtypes?") -AnnotationAssertion(Annotation( "http://www.cvphysiology.com/Arrhythmias/A003.htm") "evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial") AnnotationAssertion( "FMA:9479") AnnotationAssertion( "interatrial conduction tract") AnnotationAssertion( "internodal conduction tract") @@ -207059,6 +206636,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0009966") AnnotationAssertion(rdfs:label "internodal tract") +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -207079,6 +206657,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen venous sinus") AnnotationAssertion(rdfs:seeAlso ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -207104,12 +206683,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of pancreatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (principal gastric gland) AnnotationAssertion(Annotation( "MP:0003892") Annotation( "http://www.drugs.com/dict/acid-gland.html") "One of the gastric glands that secretes the hydrochloric acid of the gastric juice[Stedman's].") -AnnotationAssertion(Annotation( "FMA") "FMA has this as part of both the fundus and the body, but these are largely spatially disjoint.") AnnotationAssertion(Annotation( "MP:0003892") "gastric gland") AnnotationAssertion( "FMA:14921") AnnotationAssertion( "FMA:14923") @@ -207140,7 +206721,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureteropelvic junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureterovesical junction) @@ -207160,7 +206744,10 @@ AnnotationAssertion( "ureterovesical junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of Rathke's pouch) @@ -207174,8 +206761,10 @@ AnnotationAssertion( "lumen of Rathke's pouch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-modified") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multicellular anatomical structure) @@ -207184,7 +206773,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "CARO:0010000") -AnnotationAssertion(Annotation( ) "FBbt:00100313") AnnotationAssertion(Annotation( "FBbt:00100313") "multicellular structure") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010000") @@ -207192,13 +206780,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multicellular anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell cluster organ) AnnotationAssertion(Annotation( "CARO:0010001") "A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function.") AnnotationAssertion( "CARO:0010001") -AnnotationAssertion(Annotation( ) "FBbt:00007229") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010001") AnnotationAssertion( ) @@ -207217,7 +206806,7 @@ AnnotationAssertion(Annotation( "UBERON:0010005") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "placental labyrinth villous") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -207225,7 +206814,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "NLXANAT:20090509") "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF].") AnnotationAssertion( "May be obsoleted.") -AnnotationAssertion( "FMA:256381") AnnotationAssertion( "NLXANAT:20090509") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FMA:256381") "set of nuclei of neuraxis") @@ -207233,27 +206821,26 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aggregate regional part of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of basal ganglia) AnnotationAssertion(Annotation( "BIRNLEX:826") "Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum.") AnnotationAssertion( "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001696") Annotation( "VHOG") Annotation( "DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)") Annotation( "http://bgee.unil.ch/") "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]") AnnotationAssertion( "BAMS:BG") AnnotationAssertion( "BIRNLEX:826") AnnotationAssertion( "BM:Tel-BG") -AnnotationAssertion( "DHBA:10331") AnnotationAssertion( "EMAPA:32673") AnnotationAssertion( "FMA:84013") AnnotationAssertion( "GAID:617") -AnnotationAssertion( "HBA:4275") AnnotationAssertion( "HBA:4276") AnnotationAssertion( "MA:0000184") AnnotationAssertion( "MBA:623") AnnotationAssertion( "MESH:D001479") AnnotationAssertion( "NCIT:C12447") -AnnotationAssertion( "PBA:128012596") AnnotationAssertion( "PBA:4001") AnnotationAssertion(Annotation( "ncithesaurus:Basal_Ganglia") "UMLS:C0004781") AnnotationAssertion( "VHOG:0001696") @@ -207280,7 +206867,6 @@ SubClassOf(Annotation( "MA" # Class: (tubotympanic recess epithelium) AnnotationAssertion(Annotation( "ISBN:0124020607") Annotation( "VHOG:0001297") "The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001297") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417") Annotation( "http://bgee.unil.ch/") "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0004115") AnnotationAssertion( "EHDAA:6772") AnnotationAssertion( "EMAPA:17002") @@ -207294,13 +206880,13 @@ AnnotationAssertion(Annotation( "UBERON:0010020") AnnotationAssertion(rdfs:label "tubotympanic recess epithelium") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") Annotation( "ISBN:0073040584") Annotation( "PMID:11237469") ObjectSomeValuesFrom( )) # Class: (dorsal part of pharyngeal pouch 3) -AnnotationAssertion(Annotation( "MP") "Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)") AnnotationAssertion( "EHDAA2:0000409") AnnotationAssertion( "EMAPA:16758") AnnotationAssertion(Annotation( "EHDAA2:0000409") "dorsal 3rd arch pharyngeal pouch endoderm") @@ -207313,12 +206899,12 @@ AnnotationAssertion( "dorsal pharyngeal pouch 3 endoderm") AnnotationAssertion( "UBERON:0010025") AnnotationAssertion(rdfs:label "dorsal part of pharyngeal pouch 3") -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (ventral part of pharyngeal pouch 3) -AnnotationAssertion(Annotation( "MP") "The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium") AnnotationAssertion( "EHDAA2:0002173") AnnotationAssertion( "EMAPA:16759") AnnotationAssertion(Annotation( "EHDAA2:0002173") "ventral 3rd arch pharyngeal pouch endoderm") @@ -207331,7 +206917,8 @@ AnnotationAssertion( "ventral pharyngeal pouch 3 endoderm") AnnotationAssertion( "UBERON:0010026") AnnotationAssertion(rdfs:label "ventral part of pharyngeal pouch 3") -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (dorsal part of pharyngeal pouch 4) @@ -207343,7 +206930,8 @@ AnnotationAssertion( "dorsal pharyngeal pouch 4 endoderm") AnnotationAssertion( "UBERON:0010027") AnnotationAssertion(rdfs:label "dorsal part of pharyngeal pouch 4") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventral part of pharyngeal pouch 4) @@ -207355,7 +206943,8 @@ AnnotationAssertion( "ventral pharyngeal pouch 4 endoderm") AnnotationAssertion( "UBERON:0010028") AnnotationAssertion(rdfs:label "ventral part of pharyngeal pouch 4") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (6th arch mesenchyme) @@ -207371,12 +206960,12 @@ AnnotationAssertion( "UBERON:0010031") AnnotationAssertion(rdfs:label "6th arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior part of tongue) AnnotationAssertion(Annotation( "Wikipedia:Anterior_tongue") "The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch.") -AnnotationAssertion( "The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue") -AnnotationAssertion(Annotation( "NCIT") "check NCIT") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37437") AnnotationAssertion( "FMA:229084") AnnotationAssertion( "NCIT:C32130") @@ -207396,6 +206985,9 @@ AnnotationAssertion( "anterior part of tongue") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg"^^xsd:anyURI) EquivalentClasses(Annotation( "ISBN:1607950324") ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fundic gastric gland) @@ -207417,15 +207009,15 @@ AnnotationAssertion( "fundic gastric gland") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) # Class: (food storage organ) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An organ of the digestive tract that is capable of retaining and storing food.") -AnnotationAssertion( "This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates") AnnotationAssertion( "BSA:0000123") AnnotationAssertion( "TADS:0000172") AnnotationAssertion( "TGMA:0001041") @@ -207434,7 +207026,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "food storage organ") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -207447,6 +207039,8 @@ AnnotationAssertion( "UBERON:0010042") AnnotationAssertion(rdfs:label "1st arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch maxillary mesenchyme) @@ -207460,6 +207054,8 @@ AnnotationAssertion( "UBERON:0010045") AnnotationAssertion(rdfs:label "1st arch maxillary mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire pharyngeal arch associated mesenchyme) @@ -207473,6 +207069,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0010046") AnnotationAssertion(rdfs:label "entire pharyngeal arch associated mesenchyme") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -207480,7 +207077,6 @@ SubClassOf(Annotation( "cjm # Class: (oral gland) AnnotationAssertion(Annotation( "ISBN:0073040584") "Gland of the epithelium lining the oral cavity. The most common are the salivary glands.") -AnnotationAssertion(Annotation( "EHDAA2") "Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa") AnnotationAssertion( "UBERON:0003293") AnnotationAssertion( "EHDAA2:0001327") AnnotationAssertion( "EHDAA:2181") @@ -207498,12 +207094,13 @@ AnnotationAssertion( "oral gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of dorsum of tongue) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a dorsum of tongue.") AnnotationAssertion( "check surface terms") -AnnotationAssertion( "develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324") AnnotationAssertion( "FMA:74871") AnnotationAssertion( "SCTID:245835003") AnnotationAssertion( "mucosa of dorsal surface of tongue") @@ -207511,6 +207108,8 @@ AnnotationAssertion( "UBERON:0010052") AnnotationAssertion(rdfs:label "mucosa of dorsum of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future tongue) @@ -207523,7 +207122,9 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypoglossal cord) @@ -207540,8 +207141,9 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010063") AnnotationAssertion(rdfs:label "tympanic cavity epithelium") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -207554,6 +207156,8 @@ AnnotationAssertion( "UBERON:0010064") AnnotationAssertion(rdfs:label "open anatomical space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (auditory meatus epithelium) @@ -207563,7 +207167,9 @@ AnnotationAssertion( "UBERON:0010065") AnnotationAssertion(rdfs:label "auditory meatus epithelium") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) # Class: (outer epithelial layer of tympanic membrane) @@ -207580,11 +207186,15 @@ AnnotationAssertion( "UBERON:0010069") AnnotationAssertion(rdfs:label "outer epithelial layer of tympanic membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intermediate layer of tympanic membrane) AnnotationAssertion(Annotation( "PMID:11237469") Annotation( "https://sourceforge.net/tracker/?func=detail&aid=3468783&group_id=76834&atid=1205376") "The intermediate fibrous layer of the tympanic membrane.") -AnnotationAssertion(Annotation( "MA") "check MA") AnnotationAssertion( "EMAPA:19063") AnnotationAssertion( "FMA:56830") AnnotationAssertion( "MA:0001223") @@ -207601,7 +207211,6 @@ SubClassOf(Annotation( "FMA # Class: (layer of tympanic membrane) -AnnotationAssertion( "In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer") AnnotationAssertion( "FMA:56732") AnnotationAssertion(Annotation( "FMA:56732") "tympanic membrane layer") AnnotationAssertion( "uberon") @@ -207614,7 +207223,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (chromaffin system) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Organ system subdivision that consists primarily of chromaffin cells and their supporting structures.") -AnnotationAssertion( "in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies") AnnotationAssertion( "FMA:79645") AnnotationAssertion( "MESH:D002838") AnnotationAssertion( "uberon") @@ -207622,9 +207230,9 @@ AnnotationAssertion(Annotation( "chromaffin tissue") AnnotationAssertion( "UBERON:0010074") AnnotationAssertion(rdfs:label "chromaffin system") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "CL") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sacral neural crest) @@ -207634,14 +207242,14 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010075") AnnotationAssertion(rdfs:label "sacral neural crest") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cuboidal epithelium) AnnotationAssertion(Annotation( "Wikipedia:Cuboidal_epithelium") "An epithelium consisting of cuboidal epithelial cells.") AnnotationAssertion( "TODO - coordinate with CL, add cuboidal cell") -AnnotationAssertion(Annotation( "NCIT") "in NCIT this is glandular") AnnotationAssertion( "NCIT:C32415") AnnotationAssertion(Annotation( "ncithesaurus:Cuboidal_Epithelium") "UMLS:C0682577") AnnotationAssertion( "Wikipedia:Cuboidal_epithelium") @@ -207658,8 +207266,12 @@ AnnotationAssertion( "UBERON:0010081") AnnotationAssertion(rdfs:label "future common hepatic duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future dermis) @@ -207670,9 +207282,11 @@ AnnotationAssertion( "UBERON:0010083") AnnotationAssertion(rdfs:label "future dermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "XAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future diaphragm) @@ -207682,9 +207296,11 @@ AnnotationAssertion( "UBERON:0010084") AnnotationAssertion(rdfs:label "future diaphragm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future hindbrain meninx) @@ -207695,8 +207311,12 @@ AnnotationAssertion( "UBERON:0010091") AnnotationAssertion(rdfs:label "future hindbrain meninx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future metencephalon) @@ -207706,7 +207326,9 @@ AnnotationAssertion( "UBERON:0010092") AnnotationAssertion(rdfs:label "future metencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future myelencephalon) @@ -207716,7 +207338,9 @@ AnnotationAssertion( "UBERON:0010096") AnnotationAssertion(rdfs:label "future myelencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future facial nucleus) @@ -207726,6 +207350,8 @@ AnnotationAssertion( "UBERON:0010123") AnnotationAssertion(rdfs:label "future facial nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future superior salivatory nucleus) @@ -207735,6 +207361,8 @@ AnnotationAssertion( "UBERON:0010125") AnnotationAssertion(rdfs:label "future superior salivatory nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (femur cartilage element) @@ -207746,7 +207374,10 @@ AnnotationAssertion( "UBERON:0010129") AnnotationAssertion(rdfs:label "femur cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -207760,7 +207391,9 @@ AnnotationAssertion( "UBERON:0010130") AnnotationAssertion(rdfs:label "embryonic autopod plate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (conducting tissue of heart) @@ -207784,6 +207417,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuroendocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -207819,6 +207454,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sensory circumventricular organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial sheet) @@ -207831,7 +207468,6 @@ SubClassOf( (primitive sex cord of indifferent gonad) AnnotationAssertion(Annotation( "OBOL:automatic") "A sex cord that is part of a indifferent gonad.") -AnnotationAssertion( "note that this represents the indifferent structure.") AnnotationAssertion( "EHDAA2:0004051") AnnotationAssertion( "indifferent sex cord") AnnotationAssertion(Annotation( "EHDAA2:0004051") "primitive sex cords") @@ -207839,14 +207475,14 @@ AnnotationAssertion( "UBERON:0010141") AnnotationAssertion(rdfs:label "primitive sex cord of indifferent gonad") EquivalentClasses(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (seminal vesicle fluid) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A bodily secretion that is produced by a seminal vesicle.") -AnnotationAssertion( "constitutes 60-70 % of the ejaculate in humans[MP]") -AnnotationAssertion( "important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP]") -AnnotationAssertion(Annotation( "ncit") "in ncit, seminal fluid is a subtype of seminal vesicle secretion") AnnotationAssertion( "vesicular fluid") AnnotationAssertion( "BTO:0002053") AnnotationAssertion( "FMA:62969") @@ -207863,6 +207499,7 @@ AnnotationAssertion( "seminal vesicle fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male accessory sex gland) @@ -207877,7 +207514,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male accessory sex gland") SubClassOf(Annotation( "BTO") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin mucus) @@ -207888,6 +207524,8 @@ AnnotationAssertion( "UBERON:0010152") AnnotationAssertion(rdfs:label "skin mucus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphenofrontal suture) @@ -207905,6 +207543,9 @@ AnnotationAssertion( "sphenofrontal suture") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of lymphatic vessel) @@ -207916,7 +207557,9 @@ AnnotationAssertion( "UBERON:0010160") AnnotationAssertion(rdfs:label "lumen of lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of blood vessel) @@ -207928,7 +207571,9 @@ AnnotationAssertion( "UBERON:0010161") AnnotationAssertion(rdfs:label "lumen of blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (post-anal tail tip) @@ -207943,7 +207588,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "post-anal tail tip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of hairs) @@ -207957,7 +207604,9 @@ AnnotationAssertion( "UBERON:0010164") AnnotationAssertion(rdfs:label "collection of hairs") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of hair on face) @@ -207971,6 +207620,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "collection of hair on face") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (strand of hair of face) @@ -207987,6 +207638,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "strand of hair of face") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver trabecula) @@ -207997,6 +207650,9 @@ AnnotationAssertion( "UBERON:0010183") AnnotationAssertion(rdfs:label "liver trabecula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male urethral gland) @@ -208018,6 +207674,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male urethral gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female urethral gland) @@ -208032,6 +207690,8 @@ AnnotationAssertion( "UBERON:0010187") AnnotationAssertion(rdfs:label "female urethral gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (protuberance) @@ -208047,7 +207707,6 @@ SubClassOf(Annotation( "FMA # Class: (right atrium venous valve) -AnnotationAssertion(Annotation( "EHDAA2") "part_of in EHDAA2. Only child in MA.") AnnotationAssertion( "EHDAA2:0001762") AnnotationAssertion( "EMAPA:17010") AnnotationAssertion( "EMAPA:17328") @@ -208057,21 +207716,8 @@ AnnotationAssertion(Annotation( "UBERON:0010189") AnnotationAssertion(rdfs:label "right atrium venous valve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (pair of dorsal aortae) - -AnnotationAssertion(Annotation( "ISBN:0-914294-08-3") Annotation( "MP:0004787") "The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation.") -AnnotationAssertion( "EHDAA2:0000410") -AnnotationAssertion( "EMAPA:18606") -AnnotationAssertion( "MA:0000476") -AnnotationAssertion(Annotation( "EHDAA2:0000410") "paired dorsal aortae") -AnnotationAssertion( "uberon") -AnnotationAssertion( "UBERON:0010190") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "pair of dorsal aortae") -SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (aortic system) @@ -208092,12 +207738,12 @@ AnnotationAssertion( "UBERON:0010192") AnnotationAssertion(rdfs:label "genital artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic portal system) AnnotationAssertion(Annotation( "ISBN:0073040584") "A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010225") Annotation( "AAO") Annotation( "AAO:BJB") "Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]") AnnotationAssertion( "AAO:0010225") AnnotationAssertion(Annotation( "AAO:0010225") "hepatic-portal system") AnnotationAssertion( "portal system of liver") @@ -208132,13 +207778,13 @@ AnnotationAssertion( "UBERON:0010202") AnnotationAssertion(rdfs:label "lateral line") SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail vasculature) AnnotationAssertion(Annotation( "OBOL:automatic") "A vasculature that is part of a post-anal tail.") -AnnotationAssertion(Annotation( "XAO") "isa blood vessel in XAO") AnnotationAssertion( "TAO:0005037") AnnotationAssertion( "XAO:0004151") AnnotationAssertion( "ZFA:0005037") @@ -208148,6 +207794,8 @@ AnnotationAssertion(Annotation( "UBERON:0010204") AnnotationAssertion(rdfs:label "tail vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood clot) @@ -208164,11 +207812,14 @@ AnnotationAssertion( "UBERON:0010210") AnnotationAssertion(rdfs:label "blood clot") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (laryngeal apparatus) @@ -208180,6 +207831,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0010212") AnnotationAssertion(rdfs:label "laryngeal apparatus") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -208190,8 +207842,8 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010213") AnnotationAssertion(rdfs:label "laryngeal pre-cartilage condensation") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abstracted") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abstracted") ObjectSomeValuesFrom( )) @@ -208202,6 +207854,7 @@ AnnotationAssertion( "UBERON:0010221") AnnotationAssertion(rdfs:comment "Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6?") AnnotationAssertion(rdfs:label "laryngeal associated mesenchyme") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -208218,7 +207871,7 @@ AnnotationAssertion( "UBERON:0010225") AnnotationAssertion(rdfs:label "thalamic complex") SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (future cardiac atrium) @@ -208232,15 +207885,13 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0010227") AnnotationAssertion(rdfs:label "future cardiac atrium") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyeball of camera-type eye) AnnotationAssertion(Annotation( "UBERON:cjm") "The core globe-shaped component of the camera-type eye.") -AnnotationAssertion( "See notes for camera-type eye") -AnnotationAssertion( ) AnnotationAssertion( "FMA:12513") AnnotationAssertion( "MIAA:0000283") AnnotationAssertion( "SCTID:244486005") @@ -208256,6 +207907,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eyeball of camera-type eye") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -208270,12 +207922,14 @@ AnnotationAssertion( "UBERON:0010233") AnnotationAssertion(rdfs:label "stroma of thyroid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (merocrine gland) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0013544") Annotation( "Wikipedia:Merocrine") "An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged.") -AnnotationAssertion( "merocrine") AnnotationAssertion( "BTO:0002324") AnnotationAssertion( "MA:0003041") AnnotationAssertion( "Wikipedia:Merocrine") @@ -208284,6 +207938,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "merocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch mandibular mesenchyme from neural crest) @@ -208293,6 +207949,7 @@ AnnotationAssertion( "UBERON:0010252") AnnotationAssertion(rdfs:label "1st arch mandibular mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "inferred") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208306,7 +207963,8 @@ AnnotationAssertion( "UBERON:0010253") AnnotationAssertion(rdfs:label "1st arch maxillary mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208322,7 +207980,9 @@ AnnotationAssertion( "UBERON:0010254") AnnotationAssertion(rdfs:label "2nd arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -208330,7 +207990,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (3rd arch mesenchyme from neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000571") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000083") AnnotationAssertion( "EMAPA:16404") AnnotationAssertion( "VHOG:0000571") @@ -208343,14 +208002,14 @@ AnnotationAssertion( "UBERON:0010255") AnnotationAssertion(rdfs:label "3rd arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2-inferred") ObjectSomeValuesFrom( )) # Class: (4th arch mesenchyme from neural crest) AnnotationAssertion(Annotation( "OBOL:automatic") "Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000580") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]") AnnotationAssertion( "EHDAA2:0000098") AnnotationAssertion( "EMAPA:16772") AnnotationAssertion( "VHOG:0000580") @@ -208363,10 +208022,11 @@ AnnotationAssertion( "UBERON:0010256") AnnotationAssertion(rdfs:label "4th arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2-inferred") ObjectSomeValuesFrom( )) # Class: (6th arch mesenchyme from neural crest) @@ -208379,10 +208039,11 @@ AnnotationAssertion( "UBERON:0010257") AnnotationAssertion(rdfs:label "6th arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2-inferred") ObjectSomeValuesFrom( )) # Class: (mesenchyme from rhombencephalic neural crest) @@ -208392,7 +208053,9 @@ AnnotationAssertion( "UBERON:0010258") AnnotationAssertion(rdfs:label "mesenchyme from rhombencephalic neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch mesenchyme from neural crest) @@ -208406,8 +208069,10 @@ AnnotationAssertion( "UBERON:0010259") AnnotationAssertion(rdfs:label "1st arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "EHDAA2-inferred") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (umbilical blood vessel) @@ -208424,14 +208089,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "umbilical blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hyoid apparatus) AnnotationAssertion(Annotation( "http://www.biology-online.org/dictionary/Hyoid_apparatus") "A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000225") Annotation( "AAO") Annotation( "AAO:LAP") "Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO]") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000225") Annotation( "AAO") "relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO]") -AnnotationAssertion( "In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).") AnnotationAssertion( "AAO:0000225") AnnotationAssertion( "AAO:0000682") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37600") @@ -208458,6 +208122,8 @@ AnnotationAssertion( "UBERON:0010273") AnnotationAssertion(rdfs:label "zone of hyoid bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (space in vertebral column) @@ -208469,11 +208135,12 @@ AnnotationAssertion( "UBERON:0010276") AnnotationAssertion(rdfs:label "space in vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal punctum) AnnotationAssertion(Annotation( "Wikipedia:Lacrimal_punctum") "A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi.") -AnnotationAssertion( "collect tears produced by the lacrimal glands") AnnotationAssertion( "FMA:59365") AnnotationAssertion( "SCTID:263344003") AnnotationAssertion( "Wikipedia:Lacrimal_punctum") @@ -208486,6 +208153,7 @@ AnnotationAssertion( "lacrimal punctum") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain basal plate) @@ -208515,7 +208183,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010286") AnnotationAssertion(rdfs:label "midbrain neural tube") -SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) # Class: (layer of sclera) @@ -208525,6 +208194,7 @@ AnnotationAssertion( "UBERON:0010291") AnnotationAssertion(rdfs:label "layer of sclera") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (scleral endothelium) @@ -208534,7 +208204,9 @@ AnnotationAssertion( "UBERON:0010294") AnnotationAssertion(rdfs:label "scleral endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ) +SubClassOf( ) # Class: (substantia propria of sclera) @@ -208552,17 +208224,19 @@ AnnotationAssertion( "UBERON:0010295") AnnotationAssertion(rdfs:label "substantia propria of sclera") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ) # Class: (scleral mesenchyme) AnnotationAssertion(Annotation( "PMID:16496288") Annotation( "https://orcid.org/0000-0002-6601-2165") "Mesenchyme surrounding the developing optic cup which develops into the sclera.") -AnnotationAssertion( "The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010299") AnnotationAssertion(rdfs:label "scleral mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (amnioserosa) @@ -208570,14 +208244,13 @@ AnnotationAssertion(Annotation( "May be obsoleted once added to insect ontology. Coordinate with cell type in CL") AnnotationAssertion( "BTO:0004800") AnnotationAssertion( "EFO:0000250") -AnnotationAssertion(Annotation( ) "FBbt:00000095") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "BTO:0004800") "amnion-serosa") AnnotationAssertion( "UBERON:0010302") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amnioserosa") SubClassOf(Annotation( "DOI:10.1073/pnas.0709145105") ) -SubClassOf(Annotation( "Cyclorrhapha") Annotation( "DOI:10.1073/pnas.0709145105") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic epithelium) @@ -208587,6 +208260,9 @@ AnnotationAssertion( "UBERON:0010303") AnnotationAssertion(rdfs:label "extraembryonic epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-keratinized stratified squamous epithelium) @@ -208616,12 +208292,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subdivision of conjunctiva") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (immature eye) AnnotationAssertion(Annotation( "ZFA:0001678") "Developing anatomical structure that develops into the eyeball and associated structures.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0002201") Annotation( "TAO") Annotation( "ZFIN:curator") "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]") AnnotationAssertion( "TAO:0002201") AnnotationAssertion( "ZFA:0001678") AnnotationAssertion( "future eye") @@ -208629,35 +208307,40 @@ AnnotationAssertion( "UBERON:0010312") AnnotationAssertion(rdfs:label "immature eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest-derived structure) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that develops from the neural crest.") -AnnotationAssertion( "Grouping term for query purposes") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010313") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural crest-derived structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (structure with developmental contribution from neural crest) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "An anatomical structure that has some part that develops from the neural crest.") -AnnotationAssertion( "Grouping term for query purposes") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010314") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "structure with developmental contribution from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (germ layer / neural crest) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010316") AnnotationAssertion(rdfs:label "germ layer / neural crest") -SubClassOf(Annotation( "GO") Annotation( "ZFA") ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal element of eye region) @@ -208670,16 +208353,15 @@ AnnotationAssertion( "UBERON:0010321") AnnotationAssertion(rdfs:label "skeletal element of eye region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:16496288") ObjectSomeValuesFrom( )) # Class: (cranial skeletal system) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000049") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.") AnnotationAssertion( "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)") -AnnotationAssertion( "that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000109") Annotation( "AAO") Annotation( "AAO:LAP") "Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0000737") Annotation( "TAO") Annotation( "ZFIN:curator") "Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]") AnnotationAssertion( "AAO:0000109") AnnotationAssertion( "AAO:0000971") AnnotationAssertion( "AAO:0010185") @@ -208704,6 +208386,8 @@ AnnotationAssertion( "UBERON:0010328") AnnotationAssertion(rdfs:label "limb bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired limb/fin bud mesenchyme) @@ -208712,6 +208396,8 @@ AnnotationAssertion( "UBERON:0010329") AnnotationAssertion(rdfs:label "paired limb/fin bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) # Class: (eyelid mesenchyme) @@ -208722,6 +208408,8 @@ AnnotationAssertion( "UBERON:0010330") AnnotationAssertion(rdfs:label "eyelid mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of handplate) @@ -208734,6 +208422,9 @@ AnnotationAssertion( "epithelium of handplate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (extraembryonic membrane mesenchyme) @@ -208743,6 +208434,10 @@ AnnotationAssertion( "UBERON:0010333") AnnotationAssertion(rdfs:label "extraembryonic membrane mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) # Class: (maxillary process mesenchyme from neural crest) @@ -208753,7 +208448,8 @@ AnnotationAssertion( "UBERON:0010334") AnnotationAssertion(rdfs:label "maxillary process mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208765,7 +208461,8 @@ AnnotationAssertion( "UBERON:0010335") AnnotationAssertion(rdfs:label "maxillary process mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208777,7 +208474,8 @@ AnnotationAssertion( "UBERON:0010336") AnnotationAssertion(rdfs:label "mandibular process mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208789,7 +208487,8 @@ AnnotationAssertion( "UBERON:0010337") AnnotationAssertion(rdfs:label "mandibular process mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -208801,9 +208500,9 @@ AnnotationAssertion( "UBERON:0010338") AnnotationAssertion(rdfs:label "1st arch maxillary mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (1st arch mandibular mesenchyme from head mesenchyme) @@ -208813,9 +208512,9 @@ AnnotationAssertion( "UBERON:0010339") AnnotationAssertion(rdfs:label "1st arch mandibular mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (1st arch mesenchyme from head mesenchyme) @@ -208826,7 +208525,9 @@ AnnotationAssertion( "UBERON:0010341") AnnotationAssertion(rdfs:label "1st arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (2nd arch mesenchyme from head mesenchyme) @@ -208842,9 +208543,10 @@ AnnotationAssertion( "UBERON:0010343") AnnotationAssertion(rdfs:label "2nd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (3rd arch mesenchyme from head mesenchyme) @@ -208859,9 +208561,10 @@ AnnotationAssertion( "UBERON:0010344") AnnotationAssertion(rdfs:label "3rd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (4th arch mesenchyme from head mesenchyme) @@ -208876,9 +208579,10 @@ AnnotationAssertion( "UBERON:0010345") AnnotationAssertion(rdfs:label "4th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (6th arch mesenchyme from head mesenchyme) @@ -208891,9 +208595,10 @@ AnnotationAssertion( "UBERON:0010347") AnnotationAssertion(rdfs:label "6th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (otic capsule pre-cartilage condensation) @@ -208904,7 +208609,8 @@ AnnotationAssertion( "UBERON:0010349") AnnotationAssertion(rdfs:label "otic capsule pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ossification center) @@ -208926,10 +208632,7 @@ SubClassOf(Annotation( "FMA # Class: (arch of centrum of vertebra) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001670") Annotation( "VHOG") Annotation( "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270") Annotation( "http://bgee.unil.ch/") "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]") -AnnotationAssertion(Annotation( "FMA") "Note that humans do not have hemal arches, so VA=NA for FMA") AnnotationAssertion( "EMAPA:36614") -AnnotationAssertion( "FMA:11946") AnnotationAssertion(Annotation( "FMA:11946") "arch of vertebra") AnnotationAssertion(Annotation( "FMA:11946") "arcus vertebrae (vertebralis)") AnnotationAssertion(Annotation( "MA:0001453") "vertebra arch") @@ -208952,6 +208655,9 @@ AnnotationAssertion( "Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme") AnnotationAssertion(rdfs:label "pharyngeal arch mesenchyme from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal arch mesenchyme from head mesenchyme) @@ -208964,11 +208670,15 @@ AnnotationAssertion( "Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme") AnnotationAssertion(rdfs:label "pharyngeal arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endoskeleton) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000037") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.") -AnnotationAssertion(Annotation( "Wikipedia:Endoskeleton") "An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t") AnnotationAssertion( "VSAO:0000037") AnnotationAssertion( "Wikipedia:Endoskeleton") AnnotationAssertion( "XAO:0004026") @@ -209012,8 +208722,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (odontoid tissue) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "PSPUB:0000170") Annotation( "VSAO:0000063") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla.") -AnnotationAssertion( "in many vertebrates, odontoid tissue is not restricted to the teeth") -AnnotationAssertion(Annotation( "FMA") "Classified as a portion of organism substance in FMA") AnnotationAssertion( "UBERON:0001973") AnnotationAssertion( "EMAPA:35872") AnnotationAssertion( "FMA:63001") @@ -209035,6 +208743,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "odontoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (conjunctival vasculature) @@ -209049,17 +208761,21 @@ AnnotationAssertion( "UBERON:0010366") AnnotationAssertion(rdfs:label "conjunctival vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (conjunctival vein) AnnotationAssertion(Annotation( "OBOL:automatic") "A vein that is part of a conjunctiva.") AnnotationAssertion( "conjunctival blood vessel") -AnnotationAssertion( "FMA:70887") AnnotationAssertion( "SCTID:149885003") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010367") AnnotationAssertion(rdfs:label "conjunctival vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary lobule) @@ -209072,13 +208788,14 @@ AnnotationAssertion( "UBERON:0010368") AnnotationAssertion(rdfs:label "pulmonary lobule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary pulmonary lobule) AnnotationAssertion(Annotation( "PMID:3259815") "A unit of lung supplied by three to five terminal bronchioles and contained by fibrous septa.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/secondary+pulmonary+lobule") "a pyramidal mass of lung tissue with sides that are bounded by the incomplete interlobular connective tissue septa and with a base, which is 1-2 cm in diameter, which usually faces the pleural surface of the lung; lobules that occupy a more central position in the lung are not well defined and are considered to consist of three to five pulmonary acini with proximate terminal bronchioles.") AnnotationAssertion( ) AnnotationAssertion( "FMA:7414") AnnotationAssertion(Annotation( "FMA:7414") Annotation( "FMA:TA") Annotation( ) "lobulus pulmonis secondarius") @@ -209102,7 +208819,7 @@ AnnotationAssertion( "UBERON:0010370") AnnotationAssertion(rdfs:label "tibial vein") SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (ecto-epithelium) @@ -209113,6 +208830,8 @@ AnnotationAssertion( "UBERON:0010371") AnnotationAssertion(rdfs:label "ecto-epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas dorsal primordium) @@ -209125,11 +208844,13 @@ AnnotationAssertion(Annotation( "UBERON:0010375") AnnotationAssertion(rdfs:label "pancreas dorsal primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas ventral primordium) -AnnotationAssertion( "Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')") AnnotationAssertion( "EHDAA2:0001387") AnnotationAssertion( "FMA:79794") AnnotationAssertion( "uberon") @@ -209137,7 +208858,10 @@ AnnotationAssertion(Annotation( "UBERON:0010376") AnnotationAssertion(rdfs:label "pancreas ventral primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme from somatopleure) @@ -209148,8 +208872,11 @@ AnnotationAssertion( "UBERON:0010377") AnnotationAssertion(rdfs:label "mesenchyme from somatopleure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme from splanchnopleure) @@ -209159,8 +208886,11 @@ AnnotationAssertion( "UBERON:0010378") AnnotationAssertion(rdfs:label "mesenchyme from splanchnopleure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enteric nerve) @@ -209172,6 +208902,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enteric nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (Peyer's patch follicle) @@ -209184,6 +208917,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Peyer's patch follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (Peyer's patch T cell area) @@ -209195,13 +208930,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Peyer's patch T cell area") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal segment of rib) AnnotationAssertion(Annotation( "MP:0000152") Annotation( "PMID:15906248") "The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37495") AnnotationAssertion( "MA:0001400") -AnnotationAssertion( "MA:0001414") AnnotationAssertion(Annotation( "PMID:15906248") "proximal part of rib") AnnotationAssertion(Annotation( "MA:0001400") "proximal rib") AnnotationAssertion( "proximal rib segment") @@ -209226,7 +208963,9 @@ AnnotationAssertion( "UBERON:0010390") AnnotationAssertion(rdfs:label "lumen of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (B cell domain) @@ -209235,6 +208974,8 @@ AnnotationAssertion( "UBERON:0010392") AnnotationAssertion(rdfs:label "B cell domain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (T cell domain) @@ -209243,6 +208984,8 @@ AnnotationAssertion( "UBERON:0010393") AnnotationAssertion(rdfs:label "T cell domain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphocyte domain) @@ -209252,8 +208995,12 @@ AnnotationAssertion( "lymphocyte domain") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/513"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node primary follicle) @@ -209269,6 +209016,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node primary follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (efferent lymphatic vessel) @@ -209291,7 +209040,6 @@ SubClassOf( "MP:0002354") Annotation( "Wikipedia:Trabecular_arteries") "One of the branches of the splenic artery[MP].") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia") Annotation( "Wikipedia:Trabecular_arteries") "When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]") AnnotationAssertion( "MA:0000759") AnnotationAssertion( "NCIT:C49775") AnnotationAssertion(Annotation( "ncithesaurus:Splenic_Trabecular_Artery") "UMLS:C1710159") @@ -209303,6 +209051,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen trabecular artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209310,7 +209061,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MP:0002228") Annotation( "Wikipedia:Trabecular_veins") "One of the veins that feed the splenic vein.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "Wikipedia") Annotation( "Wikipedia:Trabecular_veins") "The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]") AnnotationAssertion( "MA:0000760") AnnotationAssertion( "NCIT:C49779") AnnotationAssertion(Annotation( "ncithesaurus:Splenic_Trabecular_Vein") "UMLS:C1710160") @@ -209322,6 +209072,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen trabecular vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209338,11 +209090,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epidermis suprabasal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain marginal zone) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The part of the future brain that is derived from the mantle layer of the neural tube.") -AnnotationAssertion(Annotation( "MA") "not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here") AnnotationAssertion(Annotation( "MA:0000812") "brain marginal zone") AnnotationAssertion( "DHBA:10508") AnnotationAssertion( "EMAPA:32680") @@ -209368,6 +209123,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ocular surface region") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209383,6 +209139,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node B cell domain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) # Class: (lymph node T cell domain) @@ -209404,6 +209161,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) # Class: (urethral opening) @@ -209417,6 +209175,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urethral opening") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node germinal center mantle zone) @@ -209439,6 +209199,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node germinal center mantle zone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209463,6 +209224,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen B cell corona") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209470,7 +209233,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (primary nodular lymphoid tissue) AnnotationAssertion(Annotation( "CL:tm") "A lymphoid follicle containing naive B cells.") -AnnotationAssertion( "The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles") AnnotationAssertion( "FMA:55223") AnnotationAssertion( "primary lymphoid follicle") AnnotationAssertion(Annotation( "FMA:55223") "primary lymphoid nodule") @@ -209493,13 +209255,11 @@ AnnotationAssertion( "primary lymphoid nodule of tonsil") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (internal naris) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A naris that is located inside the nasal cavity and connects to the pharynx.") -AnnotationAssertion( "choanal") -AnnotationAssertion( "In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx") -AnnotationAssertion( ) AnnotationAssertion( "NCIT:C32856") AnnotationAssertion( "choana") AnnotationAssertion( "internal choana") @@ -209511,7 +209271,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "internal naris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliary processes) @@ -209534,13 +209296,12 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (flat bone) AnnotationAssertion(Annotation( "Wikipedia:Flat_bone") "A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.") -AnnotationAssertion( "In an adult mammal, most red blood cells are formed in flat bones") -AnnotationAssertion( "Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment") AnnotationAssertion( "FMA:7476") AnnotationAssertion( "NCIT:C32616") AnnotationAssertion( "SCTID:332907008") @@ -209558,8 +209319,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pseudostratified columnar epithelium) AnnotationAssertion(Annotation( "Wikipedia:Pseudostratified_columnar_epithelium") Annotation( "http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium") "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.") -AnnotationAssertion( "Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.") -AnnotationAssertion(Annotation( "NCIT") "glandular in NCIT; we consider the two NCIT terms synonymous") AnnotationAssertion( "FMA:45572") AnnotationAssertion( "NCIT:C33419") AnnotationAssertion( "NCIT:C49316") @@ -209582,6 +209341,8 @@ AnnotationAssertion( "UBERON:0010499") AnnotationAssertion(rdfs:label "pseudostratified ciliated columnar epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (electroreceptor organ) @@ -209592,6 +209353,8 @@ AnnotationAssertion( "UBERON:0010521") AnnotationAssertion(rdfs:label "electroreceptor organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (replacement element) @@ -209627,6 +209390,8 @@ AnnotationAssertion( "UBERON:0010527") AnnotationAssertion(rdfs:label "cavity of bone organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pneumatic cavity of bone) @@ -209640,12 +209405,10 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (metanephros induced blastemal cells) -AnnotationAssertion(Annotation( "EMAPA") "different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic.") AnnotationAssertion( "EHDAA2:0001143") AnnotationAssertion( "EHDAA:7007") AnnotationAssertion( "EHDAA:8105") AnnotationAssertion( "EMAPA:17953") -AnnotationAssertion( "EMAPA:27621") AnnotationAssertion( "MA:0002998") AnnotationAssertion( "VHOG:0001241") AnnotationAssertion(Annotation( "VHOG:0001241") "induced blastemal cells") @@ -209665,7 +209428,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (primitive nephron) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An epithelial tube that is fated to become a nephron.") -AnnotationAssertion(Annotation( "EHDAA2") "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells") AnnotationAssertion( "developing nephron") AnnotationAssertion( "primitive nephron") AnnotationAssertion( "future nephron") @@ -209674,7 +209436,8 @@ AnnotationAssertion( "UBERON:0010532") AnnotationAssertion(rdfs:label "primitive nephron") SubClassOf(Annotation( "EHDAA2-inferred") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209687,6 +209450,8 @@ AnnotationAssertion( "UBERON:0010533") AnnotationAssertion(rdfs:label "metanephros cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209700,6 +209465,8 @@ AnnotationAssertion( "UBERON:0010534") AnnotationAssertion(rdfs:label "primitive mesonephric nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (primitive metanephric nephron) @@ -209712,6 +209479,8 @@ AnnotationAssertion( "UBERON:0010535") AnnotationAssertion(rdfs:label "primitive metanephric nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (nephron progenitor) @@ -209731,6 +209500,9 @@ AnnotationAssertion( "UBERON:0010537") AnnotationAssertion(rdfs:label "mesonephric nephron progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired limb/fin segment) @@ -209741,6 +209513,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -209752,10 +209526,13 @@ AnnotationAssertion( "UBERON:0010540") AnnotationAssertion(rdfs:label "tarsus pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsus cartilage element) @@ -209765,10 +209542,13 @@ AnnotationAssertion( "UBERON:0010541") AnnotationAssertion(rdfs:label "tarsus cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acropodial skeleton) @@ -209789,17 +209569,18 @@ AnnotationAssertion( "UBERON:0010543") AnnotationAssertion(rdfs:label "acropodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (metacarpus skeleton) AnnotationAssertion(Annotation( "Wikipedia:Metacarpus") "The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted].") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000946") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]") AnnotationAssertion( "AAO:0000946") -AnnotationAssertion( "EMAPA:36158") AnnotationAssertion( "FMA:71336") AnnotationAssertion( "MESH:D050279") AnnotationAssertion( "VSAO:0005026") @@ -209825,16 +209606,16 @@ AnnotationAssertion( "metacarpus skeleton") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "many to one") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (metatarsus skeleton) AnnotationAssertion(Annotation( "Wikipedia:Metatarsus") "Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000221") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]") AnnotationAssertion( "AAO:0000221") AnnotationAssertion( "FMA:71340") AnnotationAssertion( "MESH:D008684") @@ -209858,17 +209639,15 @@ AnnotationAssertion( "metatarsus skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "many to one") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (metapodial skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005025") Annotation( "VSAO") Annotation( "VSAO:NI") "Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005025") Annotation( "VSAO") "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005025") Annotation( "VSAO") "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]") AnnotationAssertion( "VSAO:0005025") AnnotationAssertion( "metacarpal/metatarsal skeleton") AnnotationAssertion(Annotation( "VSAO:0005025") "metapodial skeleton") @@ -209880,8 +209659,11 @@ AnnotationAssertion(Annotation( "UBERON:0010546") AnnotationAssertion(rdfs:label "metapodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -209899,6 +209681,9 @@ AnnotationAssertion( "UBERON:0010585") AnnotationAssertion(rdfs:label "pedal digit phalanx pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (manual digit phalanx pre-cartilage condensation) @@ -209914,6 +209699,9 @@ AnnotationAssertion( "UBERON:0010586") AnnotationAssertion(rdfs:label "manual digit phalanx pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (pedal digit phalanx cartilage element) @@ -209925,6 +209713,9 @@ AnnotationAssertion( "UBERON:0010685") AnnotationAssertion(rdfs:label "pedal digit phalanx cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit phalanx cartilage element) @@ -209937,6 +209728,9 @@ AnnotationAssertion( "UBERON:0010686") AnnotationAssertion(rdfs:label "manual digit phalanx cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit metatarsal pre-cartilage condensation) @@ -209953,7 +209747,10 @@ AnnotationAssertion(Annotation( "UBERON:0010687") AnnotationAssertion(rdfs:label "pedal digit metatarsal pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (skeleton of manual acropodium) @@ -209977,6 +209774,7 @@ AnnotationAssertion(Annotation( "UBERON:0010688") AnnotationAssertion(rdfs:label "skeleton of manual acropodium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) @@ -209989,6 +209787,8 @@ AnnotationAssertion( "UBERON:0010695") AnnotationAssertion(rdfs:label "mesenchyme of tarsal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of pedal acropodium) @@ -210011,6 +209811,7 @@ AnnotationAssertion(Annotation( "UBERON:0010696") AnnotationAssertion(rdfs:label "skeleton of pedal acropodium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "PHENOSCAPE:ni") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -210025,6 +209826,8 @@ AnnotationAssertion(Annotation( "UBERON:0010697") AnnotationAssertion(rdfs:label "pedal digit metatarsal cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit metacarpus pre-cartilage condensation) @@ -210040,6 +209843,8 @@ AnnotationAssertion( "UBERON:0010698") AnnotationAssertion(rdfs:label "manual digit metacarpus pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (manual digit metacarpus cartilage element) @@ -210054,6 +209859,8 @@ AnnotationAssertion(Annotation( "UBERON:0010699") AnnotationAssertion(rdfs:label "manual digit metacarpus cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (phalanx pre-cartilage condensation) @@ -210063,6 +209870,8 @@ AnnotationAssertion( "UBERON:0010700") AnnotationAssertion(rdfs:label "phalanx pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (phalanx cartilage element) @@ -210073,6 +209882,8 @@ AnnotationAssertion( "UBERON:0010701") AnnotationAssertion(rdfs:label "phalanx cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digit mesenchyme) @@ -210086,12 +209897,13 @@ AnnotationAssertion(Annotation( "UBERON:0010702") AnnotationAssertion(rdfs:label "digit mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb zeugopod skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in an forelimb zeugopod region.") AnnotationAssertion( "adding proxinally_connected_to humerus causes inconsistencies - requires investigation") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000200") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the forearm corresponding to the radius and ulna.[AAO]") AnnotationAssertion( "AAO:0000200") AnnotationAssertion( "FMA:71199") AnnotationAssertion( "VSAO:0005011") @@ -210112,17 +209924,16 @@ AnnotationAssertion( "UBERON:0010703") AnnotationAssertion(rdfs:label "forelimb zeugopod skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (appendage girdle complex) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton") Annotation( "https://orcid.org/0000-0002-6601-2165") "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).") AnnotationAssertion( "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000214") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]") -AnnotationAssertion(Annotation( "2012-09-06") Annotation( "VSAO:0000214") Annotation( "VSAO") Annotation( "Curator") "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]") -AnnotationAssertion(Annotation( "FMA") "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)") AnnotationAssertion( ) AnnotationAssertion( "2012-04-23T10:46:51Z") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37858") @@ -210138,6 +209949,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "appendage girdle complex") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -210145,8 +209957,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (pectoral complex) AnnotationAssertion(Annotation( "VSAO:0000213") "Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000213") Annotation( "VSAO") Annotation( "VSAO:MAH") "Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]") -AnnotationAssertion(Annotation( "FMA") "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37860") AnnotationAssertion( "FMA:7183") AnnotationAssertion( "SCTID:110716002") @@ -210162,14 +209972,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pectoral complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic complex) AnnotationAssertion(Annotation( "VSAO:0000215") "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000215") Annotation( "VSAO") Annotation( "VSAO:MAH") "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]") -AnnotationAssertion(Annotation( "FMA") "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37863") AnnotationAssertion( "FMA:7184") AnnotationAssertion( "SCTID:416631005") @@ -210185,6 +209994,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb skeleton subdivision) @@ -210196,7 +210007,9 @@ AnnotationAssertion( "UBERON:0010712") AnnotationAssertion(rdfs:label "limb skeleton subdivision") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac cartilage element) @@ -210210,15 +210023,13 @@ AnnotationAssertion( "iliac cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (girdle skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The subdivision of the skeleton of either the pectoral or pelvic girdle.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000302") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal subdivision that is part of the appendage girdle region.[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000302") Annotation( "VSAO") "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000302") Annotation( "VSAO") "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]") AnnotationAssertion( "AAO:0010686") AnnotationAssertion( "VSAO:0000302") AnnotationAssertion( "skeleton of girdle") @@ -210226,14 +210037,15 @@ AnnotationAssertion( "UBERON:0010719") AnnotationAssertion(rdfs:label "girdle skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb zeugopod skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000216") Annotation( "AAO") Annotation( "AAO:LAP") "Segment of the leg corresponding to the tibia and fibula.[AAO]") AnnotationAssertion( "AAO:0000216") AnnotationAssertion( "VSAO:0005014") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "crural skeleton") @@ -210249,7 +210061,9 @@ AnnotationAssertion(Annotation( "UBERON:0010720") AnnotationAssertion(rdfs:label "hindlimb zeugopod skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphenoid lesser wing pre-cartilage condensation) @@ -210261,8 +210075,13 @@ AnnotationAssertion( "sphenoid lesser wing pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of appendage girdle complex) @@ -210276,15 +210095,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of appendage girdle complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "UBERONREF:0000003") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of pectoral complex) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.") AnnotationAssertion( "considering adding pectoral and pelvic complex skeleton classes") -AnnotationAssertion(Annotation( "MA") "note that the MA class includes girdle parts so it belongs here;") -AnnotationAssertion( "EMAPA:32623") AnnotationAssertion( "EMAPA:35933") AnnotationAssertion( "MA:0000612") AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( ) "wing bone") @@ -210295,13 +210114,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of pectoral complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of pelvic complex) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.") -AnnotationAssertion(Annotation( "MA") "the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle") -AnnotationAssertion( "EMAPA:32633") AnnotationAssertion( "EMAPA:35934") AnnotationAssertion( "MA:0000660") AnnotationAssertion( "uberon") @@ -210311,15 +210129,12 @@ AnnotationAssertion( "bone of pelvic complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meningeal cluster) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all meningeal layers that line a central nervous system.") -AnnotationAssertion( "meningeal") -AnnotationAssertion( "In some primitive organisms, the meningeal cluster includes only the primitive meninx") AnnotationAssertion( "EHDAA2:0004661") -AnnotationAssertion( "EMAPA:32660") AnnotationAssertion( "FMA:231572") AnnotationAssertion( "NCIT:C12349") AnnotationAssertion( "SCTID:362879001") @@ -210334,7 +210149,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "meningeal cluster") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node follicle) @@ -210348,7 +210167,8 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "issues/7") Annotation( "MP-def") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node secondary follicle) @@ -210363,6 +210183,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node secondary follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -210374,7 +210195,6 @@ AnnotationAssertion( "EV:0100051") AnnotationAssertion( "MESH:D018858") AnnotationAssertion( "NCIT:C13337") -AnnotationAssertion( "SCTID:64626006") AnnotationAssertion(Annotation( "ncithesaurus:Germinal_Center") "UMLS:C0282491") AnnotationAssertion( "Wikipedia:Germinal_center") AnnotationAssertion(Annotation( "CL:tm") "central zone of follice") @@ -210407,11 +210227,13 @@ AnnotationAssertion( "UBERON:0010755") AnnotationAssertion(rdfs:label "secondary follicle corona") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of organism along appendicular axis) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.") -AnnotationAssertion(Annotation( ) "FBbt:00007018") AnnotationAssertion(Annotation( "FBbt:00007018") "appendage segment") AnnotationAssertion( "appendicular segment") AnnotationAssertion( "uberon") @@ -210424,25 +210246,27 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (clavicle cartilage element) AnnotationAssertion(Annotation( "OBOL:automatic") "A cartilaginous condensation that has the potential to develop into a clavicle.") -AnnotationAssertion(Annotation( "ISBN:978-0-12-319060-4") "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.") AnnotationAssertion( "EMAPA:18342") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010843") AnnotationAssertion(rdfs:label "clavicle cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (clavicle pre-cartilage condensation) AnnotationAssertion(Annotation( "OBOL:automatic") "A pre-cartilage condensation that has the potential to develop into a clavicle.") -AnnotationAssertion(Annotation( "ISBN:978-0-12-319060-4") "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.") AnnotationAssertion( "EMAPA:18026") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010844") AnnotationAssertion(rdfs:label "clavicle pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tibia cartilage element) @@ -210452,8 +210276,9 @@ AnnotationAssertion( "UBERON:0010849") AnnotationAssertion(rdfs:label "tibia cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tibia pre-cartilage condensation) @@ -210464,8 +210289,11 @@ AnnotationAssertion( "UBERON:0010850") AnnotationAssertion(rdfs:label "tibia pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibula cartilage element) @@ -210478,7 +210306,8 @@ AnnotationAssertion(Annotation( "UBERON:0010851") AnnotationAssertion(rdfs:label "fibula cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -210493,8 +210322,11 @@ AnnotationAssertion( "UBERON:0010852") AnnotationAssertion(rdfs:label "fibula pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb cartilage element) @@ -210503,6 +210335,8 @@ AnnotationAssertion( "UBERON:0010881") AnnotationAssertion(rdfs:label "limb cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb bone pre-cartilage condensation) @@ -210512,6 +210346,8 @@ AnnotationAssertion( "UBERON:0010882") AnnotationAssertion(rdfs:label "limb bone pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb cartilage element) @@ -210524,6 +210360,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb bone pre-cartilage condensation) @@ -210536,6 +210374,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "forelimb bone pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (hindlimb cartilage element) @@ -210546,6 +210386,8 @@ AnnotationAssertion( "UBERON:0010885") AnnotationAssertion(rdfs:label "hindlimb cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb pre-cartilage condensation) @@ -210557,11 +210399,12 @@ AnnotationAssertion( "UBERON:0010886") AnnotationAssertion(rdfs:label "hindlimb pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (pelvic complex muscle) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Muscles of the pelvic girdle, hindlimb or pelvic fin.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000218") Annotation( "AAO") Annotation( "AAO:EJS") "Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]") AnnotationAssertion( "AAO:0000218") AnnotationAssertion( "EMAPA:32634") AnnotationAssertion( "FMA:9622") @@ -210577,13 +210420,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pelvic complex muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (pectoral complex muscle) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A muscle of a pectoral girdle, pectoral fin or anterior limb.") AnnotationAssertion( "the MA class belongs here, based on its current child classes") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010687") Annotation( "AAO") Annotation( "AAO:EJS") "Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]") AnnotationAssertion( "AAO:0010687") AnnotationAssertion( "EMAPA:32624") AnnotationAssertion( "FMA:9621") @@ -210597,6 +210440,7 @@ AnnotationAssertion( "UBERON:0010891") AnnotationAssertion(rdfs:label "pectoral complex muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (median external naris) @@ -210613,6 +210457,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "median external naris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (keratinous tooth) @@ -210625,7 +210471,9 @@ AnnotationAssertion( "The hagfish's jawless mouth contains two parallel rows of pointed keratinous teeth") AnnotationAssertion(rdfs:label "keratinous tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (synchronous hermaphroditic organism) @@ -210642,6 +210490,8 @@ AnnotationAssertion( "synchronous hermaphroditic organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "CARO") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (clavicle bone primordium) @@ -210653,9 +210503,11 @@ AnnotationAssertion( "lateral part derives from a fish dermal bone while the medial part comes from a spur off the manubrium endochondral bone[JB]") AnnotationAssertion(rdfs:label "clavicle bone primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "mah") Annotation( "shown in mouse") Annotation( "PMC1352163") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ossicle) @@ -210673,7 +210525,6 @@ SubClassOf(Annotation( "VSA # Class: (subdivision of skeleton) AnnotationAssertion(Annotation( "UBERONREF:0000003") Annotation( "https://orcid.org/0000-0002-6601-2165") "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000042") Annotation( "incorrect") Annotation( "VSAO") Annotation( "VSAO:curator") "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]") AnnotationAssertion( "FMA:23879") AnnotationAssertion( "SCTID:129140006") AnnotationAssertion( "VSAO:0000042") @@ -210690,10 +210541,6 @@ SubClassOf(Annotation( "VSA # Class: (vertebral element) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000184") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "https://github.com/obophenotype/uberon/issues/294") "Skeletal element that forms around the notochord and is part of the vertebral column.") -AnnotationAssertion( "we include a distinct subclass for bony vertebra") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001143") Annotation( "VHOG") Annotation( "DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)") Annotation( "http://bgee.unil.ch/") "In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]") -AnnotationAssertion( "vertebral") -AnnotationAssertion( "Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage") AnnotationAssertion( "UBERON:0015005") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern") "vertebra skeletal element") AnnotationAssertion( "VHOG:0001143") @@ -210722,6 +210569,9 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "cleidooccipital muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sternooccipital muscle) @@ -210736,6 +210586,8 @@ AnnotationAssertion( "sternooccipital muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trapezius pre-muscle mass) @@ -210744,6 +210596,8 @@ AnnotationAssertion( "UBERON:0010955") AnnotationAssertion(rdfs:label "trapezius pre-muscle mass") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -210758,6 +210612,7 @@ AnnotationAssertion( "UBERON:0010959") AnnotationAssertion(rdfs:label "craniocervical muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (trunk and cervical myotome group) @@ -210767,6 +210622,7 @@ AnnotationAssertion( "UBERON:0010963") AnnotationAssertion(rdfs:comment "isa row in EHDAA2") AnnotationAssertion(rdfs:label "trunk and cervical myotome group") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -210776,6 +210632,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010982") AnnotationAssertion(rdfs:label "latissimus dorsi pre-muscle mass") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -210786,6 +210643,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010983") AnnotationAssertion(rdfs:label "levator scapulae pre-muscle mass") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -210796,6 +210654,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0010984") AnnotationAssertion(rdfs:label "pectoral pre-muscle mass") +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -210847,7 +210706,6 @@ SubClassOf(Annotation( "Wik # Class: (pharyngeal arch cartilage) AnnotationAssertion(Annotation( "OBOL:automatic") "A cartilage element that is part of a splanchnocranium.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006051") AnnotationAssertion( "EFO:0003689") AnnotationAssertion( "TAO:0001460") AnnotationAssertion( "ZFA:0001460") @@ -210866,7 +210724,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "MESH:A09.246.631.246.280") Annotation( "Wikipedia:Perilymphatic_duct") "A channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space.") AnnotationAssertion( "relationship to FMA class unclear") -AnnotationAssertion(Annotation( "ZFA:0005461, ZFIN:curator") "Duct that contains perilymph[ZFA:0005461, ZFIN:curator].") AnnotationAssertion( "AAO:0000136") AnnotationAssertion( "EMAPA:35677") AnnotationAssertion( "FMA:77822") @@ -210882,16 +210739,15 @@ AnnotationAssertion(Annotation( "UBERON:0011060") AnnotationAssertion(rdfs:label "perilymphatic channel") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (palatoquadrate arch) AnnotationAssertion(Annotation( "VHOG:0000511") Annotation( "https://github.com/obophenotype/uberon/issues/153") "The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG].") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0000511") Annotation( "VHOG") Annotation( "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)") Annotation( "http://bgee.unil.ch/") "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]") AnnotationAssertion( "EFO:0003659") AnnotationAssertion( "TAO:0001272") -AnnotationAssertion( "VHOG:0000511") AnnotationAssertion( "ZFA:0001272") AnnotationAssertion(Annotation( "ZFA:0001272") "dorsal visceral arch 1") AnnotationAssertion(Annotation( "ZFA:0001272") "upper pharyngeal jaw") @@ -210905,6 +210761,7 @@ AnnotationAssertion(Annotation( "UBERON:0011085") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "palatoquadrate arch") +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) @@ -210921,6 +210778,7 @@ AnnotationAssertion( "ligament of knee joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of right pelvic girdle) @@ -210930,6 +210788,8 @@ AnnotationAssertion( "UBERON:0011090") AnnotationAssertion(rdfs:label "skeleton of right pelvic girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of left pelvic girdle) @@ -210939,36 +210799,38 @@ AnnotationAssertion( "UBERON:0011091") AnnotationAssertion(rdfs:label "skeleton of left pelvic girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right pelvic girdle region) AnnotationAssertion(Annotation( "OBOL:automatic") "A pelvic girdle region that is in the right side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:16582") AnnotationAssertion(Annotation( "FMA:16582") Annotation( ) "right pelvic girdle") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011092") AnnotationAssertion(rdfs:label "right pelvic girdle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left pelvic girdle region) AnnotationAssertion(Annotation( "OBOL:automatic") "A pelvic girdle region that is in the left side of a multicellular organism.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:16583") AnnotationAssertion(Annotation( "FMA:16583") Annotation( ) "left pelvic girdle") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011093") AnnotationAssertion(rdfs:label "left pelvic girdle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebra cartilage element) AnnotationAssertion(Annotation( "GO_REF:0000034") Annotation( "VSAO:0000184") Annotation( "http://dx.plos.org/10.1371/journal.pone.0051070") Annotation( "http://orcid.org/0000-0002-6601-2165") "The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.") -AnnotationAssertion(Annotation( "vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist") Annotation( "PMC3157150") ) -AnnotationAssertion(Annotation( "EHDAA2") "This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups") AnnotationAssertion( "EMAPA:32669") AnnotationAssertion( "VHOG:0000584") AnnotationAssertion(Annotation( "VHOG:0000584") "vertebral cartilage condensation") @@ -210976,6 +210838,7 @@ AnnotationAssertion( "UBERON:0011094") AnnotationAssertion(rdfs:label "vertebra cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -210990,8 +210853,9 @@ AnnotationAssertion( "UBERON:0011095") AnnotationAssertion(rdfs:label "vertebra pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "EHDAA2-abduced") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal nerve) @@ -211005,6 +210869,9 @@ AnnotationAssertion( "UBERON:0011096") AnnotationAssertion(rdfs:label "lacrimal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (synovial joint of pelvic girdle) @@ -211019,12 +210886,14 @@ AnnotationAssertion( "UBERON:0011107") AnnotationAssertion(rdfs:label "synovial joint of pelvic girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (synovial joint of pectoral girdle) AnnotationAssertion(Annotation( "OBOL:automatic") "A synovial joint that is part of a pectoral girdle region.") -AnnotationAssertion(Annotation( "FMA") "in FMA, these are part of the bony pectoral girdle") AnnotationAssertion( "FMA:35243") AnnotationAssertion( "SCTID:303080001") AnnotationAssertion( "joint of shoulder girdle") @@ -211033,7 +210902,9 @@ AnnotationAssertion( "UBERON:0011108") AnnotationAssertion(rdfs:label "synovial joint of pectoral girdle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tibiofibular joint) @@ -211051,6 +210922,10 @@ AnnotationAssertion( "tibiofibular joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsometatarsal joint) @@ -211071,8 +210946,9 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carpometacarpal joint) @@ -211080,7 +210956,6 @@ AnnotationAssertion(Annotation( "Wikipedia:Carpometacarpal_joint") "CMJ") AnnotationAssertion(Annotation( "Wikipedia:Carpometacarpal_joint") "carpometacarpal") AnnotationAssertion( "FMA:35287") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D052737") AnnotationAssertion( "NCIT:C32265") AnnotationAssertion( "SCTID:361842002") AnnotationAssertion(Annotation( "ncithesaurus:Carpometacarpal_Joint") "UMLS:C0224620") @@ -211092,8 +210967,9 @@ AnnotationAssertion( "carpometacarpal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (laryngeal joint) @@ -211107,6 +210983,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intermetacarpal joint) @@ -211120,15 +210997,14 @@ AnnotationAssertion(Annotation( "UBERON:0011131") AnnotationAssertion(rdfs:label "intermetacarpal joint") EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "two adjacent metacarpals") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intercarpal joint) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A skeletal joint that connects two carpal bones.") AnnotationAssertion( "FMA:35292") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D050824") AnnotationAssertion( "NCIT:C32264") AnnotationAssertion( "SCTID:182176003") AnnotationAssertion(Annotation( "ncithesaurus:Carpal_Joint") "UMLS:C1262468") @@ -211142,14 +211018,13 @@ AnnotationAssertion( "intercarpal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "two adjacent carpals") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intermetatarsal joint) AnnotationAssertion(Annotation( "Wikipedia:Intermetatarsal_articulations") "A joint that connects two adjacent metatarsals.") -AnnotationAssertion(Annotation( "WP") "In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb") AnnotationAssertion( "FMA:35219") AnnotationAssertion( "SCTID:361868009") AnnotationAssertion( "Wikipedia:Intermetatarsal_articulations") @@ -211158,9 +211033,9 @@ AnnotationAssertion( "intermetatarsal joint") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "two adjacent metatarsals") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nonsynovial joint) @@ -211175,7 +211050,6 @@ SubClassOf(Annotation( "FMA # Class: (intervertebral cartilage) AnnotationAssertion(Annotation( "ISBN:0073040584") "A cartilage element that lies between two successive vertebral centra.") -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0000795") Annotation( "AAO") Annotation( "AAO:Trueb_1973") "Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]") AnnotationAssertion( "AAO:0000795") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011135") @@ -211183,7 +211057,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "MA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "between two centra") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ligament of vertebral column) @@ -211197,7 +211071,9 @@ AnnotationAssertion( "UBERON:0011136") AnnotationAssertion(rdfs:label "ligament of vertebral column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axial skeletal system) @@ -211209,7 +211085,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton"^^xsd:anyURI) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (postcranial axial skeletal system) @@ -211234,6 +211109,7 @@ AnnotationAssertion( "Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses.") AnnotationAssertion(rdfs:label "synovial limb joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (appendicular ossicle) @@ -211247,6 +211123,8 @@ AnnotationAssertion( "Examples of appendicular ossicles include the patella and meniscus of the knee joint.") AnnotationAssertion(rdfs:label "appendicular ossicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axial ossicle) @@ -211260,6 +211138,8 @@ AnnotationAssertion( "Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column.") AnnotationAssertion(rdfs:label "axial ossicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper urinary tract) @@ -211275,6 +211155,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "upper urinary tract") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -211290,7 +211171,9 @@ AnnotationAssertion( "UBERON:0011148") AnnotationAssertion(rdfs:label "submucosal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "perforates") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial skeleton) @@ -211311,9 +211194,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facial skeleton") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:11523816") ObjectSomeValuesFrom( )) # Class: (primary subdivision of skull) @@ -211348,25 +211231,27 @@ AnnotationAssertion( "UBERON:0011164") AnnotationAssertion(rdfs:label "neurocranium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (joint connecting upper and lower jaws) AnnotationAssertion(Annotation( "http://evolution.berkeley.edu/evolibrary/article/evograms_05") Annotation( "https://orcid.org/0000-0002-6601-2165") "Synovial joint that articulates bones of upper and lower jaw.") -AnnotationAssertion(Annotation( "http://evolution.berkeley.edu") "Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long") AnnotationAssertion( "jaw joint") -AnnotationAssertion( "NCIT:C32888") AnnotationAssertion( "craniomandibular joint") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011171") AnnotationAssertion(rdfs:label "joint connecting upper and lower jaws") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "abduced") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of crypt of Lieberkuhn) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a crypt of Lieberkuhn.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "FMA has classes for subdivisions of this epithelium") AnnotationAssertion( "crypt epithelium") AnnotationAssertion( "NCIT:C83191") AnnotationAssertion(Annotation( "ncithesaurus:Crypt_Epithelium") "UMLS:C2826787") @@ -211376,6 +211261,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of crypt of Lieberkuhn") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrointestinal sphincter) @@ -211386,6 +211273,9 @@ AnnotationAssertion( "UBERON:0011185") AnnotationAssertion(rdfs:label "gastrointestinal sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of large intestine) @@ -211402,7 +211292,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lamina propria of large intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (ophthalmic vein) @@ -211452,6 +211342,9 @@ AnnotationAssertion( "parathyroid epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2-abduced") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -211469,6 +211362,7 @@ AnnotationAssertion( "UBERON:0011198") AnnotationAssertion(rdfs:label "muscle layer of large intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (muscle layer of small intestine) @@ -211488,12 +211382,12 @@ AnnotationAssertion( "UBERON:0011201") AnnotationAssertion(rdfs:label "muscle layer of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (root of vagus nerve) AnnotationAssertion(Annotation( "OBOL:automatic") "A root of cranial nerve that is part of a vagus nerve.") -AnnotationAssertion(Annotation( "FMA") "FMA distinguishes between roots and rootlets - we mix the two here") AnnotationAssertion(Annotation( "ZFA:0007011") "rX") AnnotationAssertion( "BIRNLEX:1456") AnnotationAssertion( "DHBA:12888") @@ -211509,6 +211403,8 @@ AnnotationAssertion(Annotation( "UBERON:0011213") AnnotationAssertion(rdfs:label "root of vagus nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of midbrain tectum) @@ -211520,6 +211416,8 @@ AnnotationAssertion( "UBERON:0011214") AnnotationAssertion(rdfs:label "nucleus of midbrain tectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central nervous system cell part cluster) @@ -211532,6 +211430,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "central nervous system cell part cluster") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (organ system subdivision) @@ -211540,7 +211441,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "FBbt:00007330") AnnotationAssertion( "FMA:67509") AnnotationAssertion( "SCTID:91690000") AnnotationAssertion( "uberon") @@ -211554,7 +211454,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (intra-ocular muscle) -AnnotationAssertion(Annotation( "2012-06-20") Annotation( "AAO:0010038") Annotation( "AAO") Annotation( "AAO:EJS") "Muscles within the eye (bulbus oculi).[AAO]") AnnotationAssertion( "AAO:0010038") AnnotationAssertion( "EMAPA:18808") AnnotationAssertion( "FMA:49150") @@ -211563,8 +211462,8 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0011222") AnnotationAssertion(rdfs:label "intra-ocular muscle") -SubClassOf(Annotation( "organ component in FMA") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (synovial membrane of synovial tendon sheath) @@ -211579,6 +211478,8 @@ AnnotationAssertion( "Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]") AnnotationAssertion(rdfs:label "synovial membrane of synovial tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibrous membrane of synovial tendon sheath) @@ -211587,11 +211488,14 @@ AnnotationAssertion( "UBERON:0011234") AnnotationAssertion(rdfs:label "fibrous membrane of synovial tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ethmoid region) AnnotationAssertion(Annotation( "UBERONREF:0000007") Annotation( "http://palaeos.com/vertebrates/bones/braincase/ethmoid.html") "The most anterior region of the braincase. Provides structural support for peripheral olfactory organ.") -AnnotationAssertion( "currently this is not restricted to skeletal elements, unlike UBERONREF:0000007") AnnotationAssertion( "AAO:0000986") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011241") @@ -211603,9 +211507,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (appendicular skeletal system) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000306") Annotation( "VSAO") Annotation( "https://orcid.org/0000-0002-6601-2165") "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]") AnnotationAssertion( "FMA:7484") -AnnotationAssertion( "VHOG:0001666") AnnotationAssertion( "VSAO:0000306") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011249") @@ -211618,18 +211520,17 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (autopod bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011250") AnnotationAssertion(rdfs:label "autopod bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal trunk) AnnotationAssertion(Annotation( "UBERONREF:0000006") Annotation( "Wikipedia:Human_back") "The part of the trunk that is in the dorsum[cjm].") -AnnotationAssertion( "In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]") AnnotationAssertion( "EMAPA:35162") AnnotationAssertion( "FMA:25056") AnnotationAssertion( "MA:0000020") @@ -211654,6 +211555,7 @@ AnnotationAssertion(Annotation( "UBERON:0011272") AnnotationAssertion(rdfs:label "embryonic skin basal layer") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211670,6 +211572,7 @@ AnnotationAssertion( "pharyngobasilar fascia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of uterine tube) @@ -211684,11 +211587,14 @@ AnnotationAssertion( "UBERON:0011298") AnnotationAssertion(rdfs:label "submucosa of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of telencephalon) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum.") -AnnotationAssertion(Annotation( "ZFA:0000597") "CNS white matter that is part of the telencephalon[ZFA:0000597].") AnnotationAssertion( "UBERON:0013202") AnnotationAssertion( "UBERON:0022550") AnnotationAssertion( "BIRNLEX:1075") @@ -211705,6 +211611,8 @@ AnnotationAssertion( "UBERON:0011299") AnnotationAssertion(rdfs:label "white matter of telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter of telencephalon) @@ -211717,6 +211625,8 @@ AnnotationAssertion( "UBERON:0011300") AnnotationAssertion(rdfs:label "gray matter of telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extrinsic tongue pre-muscle mass) @@ -211725,26 +211635,28 @@ AnnotationAssertion( "UBERON:0011332") AnnotationAssertion(rdfs:label "extrinsic tongue pre-muscle mass") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Reissner's fiber) AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "Wikipedia:Reissner's_fiber") "An acellular strand that runs from subcommissural organ caudally through the ventricular system and central canal to the ampulla caudalis. Develops from glycoproteins secreted into CSF.") AnnotationAssertion(Annotation( "ISBN:0471888893") ) -AnnotationAssertion( "Reissner's fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner's fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]") AnnotationAssertion( "NLX:151878") AnnotationAssertion( "Wikipedia:Reissner's_fiber") AnnotationAssertion( "Reissner's fibre") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011357") AnnotationAssertion(rdfs:label "Reissner's fiber") +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial blood vasculature) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood vasculature that is part of a head.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0005297") Annotation( "TAO") Annotation( "ZFIN:curator") "Blood vessel part of cranial vasculature.[TAO]") AnnotationAssertion( "TAO:0005297") AnnotationAssertion( "ZFA:0005297") AnnotationAssertion(Annotation( "ZFA:0005297") "cranial blood vessel") @@ -211754,6 +211666,8 @@ AnnotationAssertion(Annotation( "UBERON:0011362") AnnotationAssertion(rdfs:label "cranial blood vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cranial lymph vasculature) @@ -211770,6 +211684,8 @@ AnnotationAssertion(Annotation( "UBERON:0011363") AnnotationAssertion(rdfs:label "cranial lymph vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (transverse process of atlas) @@ -211781,20 +211697,22 @@ AnnotationAssertion( "UBERON:0011370") AnnotationAssertion(rdfs:label "transverse process of atlas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) # Class: (prepuce) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present.") -AnnotationAssertion( "this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue") -AnnotationAssertion( "preputial") AnnotationAssertion( "NCIT:C12323") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0011374") AnnotationAssertion(rdfs:label "prepuce") +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -211808,7 +211726,9 @@ AnnotationAssertion( "UBERON:0011375") AnnotationAssertion(rdfs:label "skin of prepuce of clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of gastrointestinal system) @@ -211843,8 +211763,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lumen of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesonephric duct lumen) @@ -211856,11 +211778,12 @@ AnnotationAssertion( "UBERON:0011574") AnnotationAssertion(rdfs:label "mesonephric duct lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired limb/fin skeleton) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The collection of all skeletal elements in an individual limb or fin.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000301") Annotation( "VSAO") Annotation( "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070") "Skeletal subdivision that is part of the paired limb/fin.[VSAO]") AnnotationAssertion( "VSAO:0000301") AnnotationAssertion(Annotation( "VSAO:0000301") "limb/fin skeleton") AnnotationAssertion( "skeletal parts of limb/fin") @@ -211870,17 +211793,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780878932504") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stylopodial skeleton) AnnotationAssertion(Annotation( "VSAO:0005007") "Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0005007") Annotation( "VSAO") Annotation( "VSAO:NI") "Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]") -AnnotationAssertion( "propodial") -AnnotationAssertion( "stylopodial") AnnotationAssertion( "VSAO:0005007") AnnotationAssertion( "stylopodium skeleton") AnnotationAssertion( "uberon") @@ -211893,14 +211815,15 @@ AnnotationAssertion( "UBERON:0011583") AnnotationAssertion(rdfs:label "stylopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (zeugopodial skeleton) AnnotationAssertion(Annotation( "VSAO:0005010") "Section of the forelimb skeleton located between the stylopodium and the autopodium.") -AnnotationAssertion( "zeugopodial") -AnnotationAssertion( "zygopodial") AnnotationAssertion( "VSAO:0005010") AnnotationAssertion( "epipodial skeleton") AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "skeleton of zeugopod") @@ -211913,8 +211836,11 @@ AnnotationAssertion(Annotation( "UBERON:0011584") AnnotationAssertion(rdfs:label "zeugopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell condensation) @@ -211941,8 +211867,6 @@ AnnotationAssertion( "UBERON:0011587") AnnotationAssertion(rdfs:label "pre-dentine") SubClassOf(Annotation( "VSAO") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "text definition") ObjectSomeValuesFrom( )) # Class: (pre-enamel) @@ -211978,6 +211902,8 @@ AnnotationAssertion( "UBERON:0011591") AnnotationAssertion(rdfs:label "tract of diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future upper lip) @@ -211987,19 +211913,16 @@ AnnotationAssertion( "UBERON:0011592") AnnotationAssertion(rdfs:label "future upper lip") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "fusion") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "fusion") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dentary tooth) AnnotationAssertion(Annotation( "TAO:0001628") "Tooth that is attached to a dentary/mandible[TAO,modified].") AnnotationAssertion( "Note that we treat dentary tooth and mandibular tooth as equivalent") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001628") Annotation( "TAO") Annotation( "TAO:wd") "Tooth that is attached to the dentary.[TAO]") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001628") Annotation( "TAO") "relationship loss: part_of dentary tooth row (TAO:0001952)[TAO]") AnnotationAssertion( "AAO:0000125") AnnotationAssertion( "AAO:0000641") -AnnotationAssertion( "FMA:321647") AnnotationAssertion( "SCTID:245547003") AnnotationAssertion( "TAO:0001628") AnnotationAssertion( "uberon") @@ -212009,7 +211932,8 @@ AnnotationAssertion( "UBERON:0011594") AnnotationAssertion(rdfs:label "dentary tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jaw region) @@ -212021,8 +211945,11 @@ AnnotationAssertion( "jaw region") AnnotationAssertion(rdfs:seeAlso "http://eol.org/collections/11578"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") Annotation( "FMA-abduced") Annotation( "ZFA-abduced") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future lower lip) @@ -212032,7 +211959,7 @@ AnnotationAssertion( "UBERON:0011596") AnnotationAssertion(rdfs:label "future lower lip") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia:Mandibular_prominence") ObjectSomeValuesFrom( )) # Class: (bone of upper jaw) @@ -212045,6 +211972,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gingiva of upper jaw) @@ -212066,6 +211994,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gingiva of upper jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gingiva of lower jaw) @@ -212087,6 +212017,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gingiva of lower jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (oral epithelium from ectoderm) @@ -212097,6 +212029,9 @@ AnnotationAssertion( "oral epithelium from ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (iliofemoralis muscle) @@ -212107,6 +212042,9 @@ AnnotationAssertion( "UBERON:0011645") AnnotationAssertion(rdfs:label "iliofemoralis muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jaw muscle) @@ -212142,7 +212080,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (trunk vertebra) AnnotationAssertion(Annotation( "UBERONREF:0000006") "A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly.") -AnnotationAssertion( ) AnnotationAssertion( "thoracolumbar vertebra") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "presacral vertebra") @@ -212150,7 +212087,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trunk vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal tarsal bone) @@ -212159,6 +212099,9 @@ AnnotationAssertion( "UBERON:0011679") AnnotationAssertion(rdfs:label "proximal tarsal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic portion of umbilical artery) @@ -212187,6 +212130,8 @@ AnnotationAssertion( "UBERON:0011695") AnnotationAssertion(rdfs:label "embryonic cardiovascular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left extraembryonic umbilical artery) @@ -212206,7 +212151,6 @@ AnnotationAssertion( "UBERON:0011697") AnnotationAssertion(rdfs:label "right extraembryonic umbilical artery") SubClassOf( ) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (differentiated genital tubercle) @@ -212226,7 +212170,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (left recurrent laryngeal nerve) -AnnotationAssertion( "The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]") AnnotationAssertion( "EMAPA:25350") AnnotationAssertion( "FMA:14469") AnnotationAssertion( "MA:0001107") @@ -212239,6 +212182,9 @@ AnnotationAssertion( "left recurrent laryngeal nerve") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right recurrent laryngeal nerve) @@ -212253,6 +212199,9 @@ AnnotationAssertion( "UBERON:0011767") AnnotationAssertion(rdfs:label "right recurrent laryngeal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cartilaginous projection) @@ -212264,6 +212213,8 @@ AnnotationAssertion( "UBERON:0011769") AnnotationAssertion(rdfs:label "cartilaginous projection") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lower jaw opening) @@ -212273,7 +212224,9 @@ AnnotationAssertion( "UBERON:0011772") AnnotationAssertion(rdfs:label "lower jaw opening") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper jaw opening) @@ -212283,7 +212236,9 @@ AnnotationAssertion( "UBERON:0011773") AnnotationAssertion(rdfs:label "upper jaw opening") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vagus nerve nucleus) @@ -212303,7 +212258,9 @@ AnnotationAssertion(Annotation( "UBERON:0011775") AnnotationAssertion(rdfs:label "vagus nerve nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleus of spinal cord) @@ -212315,6 +212272,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of head region) @@ -212326,6 +212285,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nerve of head region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-neurogenic ectodermal placode) @@ -212344,9 +212305,11 @@ AnnotationAssertion( "UBERON:0011817") AnnotationAssertion(rdfs:label "skin appendage placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NCBIBook:NBK53175") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (atrioventricular region) @@ -212364,6 +212327,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "atrioventricular region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (irregular connective tissue) @@ -212377,7 +212345,6 @@ SubClassOf(Annotation( "FMA # Class: (dense irregular connective tissue) AnnotationAssertion(Annotation( "FMA:20109") Annotation( "Wikipedia:Dense_irregular_connective_tissue") "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.") -AnnotationAssertion(Annotation( "2012-08-29") Annotation( "ncithesaurus:Irregular_Dense_Connective_Tissue") Annotation( "NCIT") "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]") AnnotationAssertion( "FMA:20109") AnnotationAssertion( "NCIT:C32882") AnnotationAssertion(Annotation( "ncithesaurus:Irregular_Dense_Connective_Tissue") "UMLS:C0738366") @@ -212390,12 +212357,12 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dense connective tissue) AnnotationAssertion(Annotation( "Wikipedia:Dense_connective_tissue") "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets.") AnnotationAssertion( "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.") -AnnotationAssertion(Annotation( "2012-08-29") Annotation( "ncithesaurus:Dense_Connective_Tissue") Annotation( "NCIT") "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]") AnnotationAssertion( "AAO:0000121") AnnotationAssertion( "NCIT:C32450") AnnotationAssertion(Annotation( "ncithesaurus:Dense_Connective_Tissue") "UMLS:C1511770") @@ -212404,6 +212371,9 @@ AnnotationAssertion( "UBERON:0011823") AnnotationAssertion(rdfs:label "dense connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (fibrous connective tissue) @@ -212439,6 +212409,9 @@ AnnotationAssertion( "UBERON:0011845") AnnotationAssertion(rdfs:label "duct of sebaceous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acinus of sebaceous gland) @@ -212449,6 +212422,9 @@ AnnotationAssertion( "UBERON:0011846") AnnotationAssertion(rdfs:label "acinus of sebaceous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acinus of salivary gland) @@ -212459,6 +212435,8 @@ AnnotationAssertion( "UBERON:0011850") AnnotationAssertion(rdfs:label "acinus of salivary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acinus of lactiferous gland) @@ -212469,6 +212447,8 @@ AnnotationAssertion( "UBERON:0011856") AnnotationAssertion(rdfs:label "acinus of lactiferous gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (acinus of lacrimal gland) @@ -212480,6 +212460,9 @@ AnnotationAssertion( "UBERON:0011857") AnnotationAssertion(rdfs:label "acinus of lacrimal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acinus of exocrine gland) @@ -212489,10 +212472,11 @@ AnnotationAssertion( "UBERON:0011858") AnnotationAssertion(rdfs:label "acinus of exocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of collagen fibrils) -AnnotationAssertion(Annotation( "FMA") "the FMA class specifically refers to ureter") AnnotationAssertion( "FMA:63212") AnnotationAssertion( "MESH:D024022") AnnotationAssertion( "NCIT:C32339") @@ -212501,6 +212485,7 @@ AnnotationAssertion( "UBERON:0011860") AnnotationAssertion(rdfs:label "collection of collagen fibrils") AnnotationAssertion(rdfs:seeAlso ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -212513,6 +212498,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aorta collagen fibril") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary collagen fibril) @@ -212523,6 +212511,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary collagen fibril") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone collagen fibril) @@ -212533,6 +212524,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone collagen fibril") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tendon collagen fibril) @@ -212542,6 +212535,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tendon collagen fibril") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (corneal stroma collagen fibril) @@ -212552,6 +212547,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "corneal stroma collagen fibril") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ligament of sternoclavicular joint) @@ -212565,11 +212563,12 @@ AnnotationAssertion( "UBERON:0011875") AnnotationAssertion(rdfs:label "ligament of sternoclavicular joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of esophagus) AnnotationAssertion(Annotation( "OBOL:automatic") "A muscle layer that is part of a wall of esophagus.") -AnnotationAssertion(Annotation( "WP") "In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle") AnnotationAssertion( "FMA:62998") AnnotationAssertion(Annotation( "FMA:62998") "muscle coat of esophagus") AnnotationAssertion(Annotation( "FMA:62998") "muscular coat of oesophagus") @@ -212581,8 +212580,9 @@ AnnotationAssertion( "UBERON:0011878") AnnotationAssertion(rdfs:label "muscle layer of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "upper part") Annotation( "Wikipedia:Muscular_layer") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior uvea) @@ -212603,8 +212603,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anterior uvea") SubClassOf(Annotation( "ZFA") ) +SubClassOf( ) SubClassOf(Annotation( "MP") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -212619,11 +212619,12 @@ AnnotationAssertion( "UBERON:0011894") AnnotationAssertion(rdfs:label "lumen of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epimysium) AnnotationAssertion(Annotation( "Wikipedia:Epimysium") "Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.") -AnnotationAssertion( "The Epimysium also protects muscles from friction against other muscles and bones") AnnotationAssertion( "FMA:9726") AnnotationAssertion( "NCIT:C32527") AnnotationAssertion(Annotation( "ncithesaurus:Epimysium") "UMLS:C0504096") @@ -212633,6 +212634,7 @@ AnnotationAssertion( "Wikipedia:Epimysium") Annotation( ) "epimysia") AnnotationAssertion( "UBERON:0011899") AnnotationAssertion(rdfs:label "epimysium") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -212650,11 +212652,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "yolk sac blood island") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (connecting stalk blood islands) -AnnotationAssertion(Annotation( "EHDAA2") "in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels") AnnotationAssertion( "EHDAA2:0003242") AnnotationAssertion(Annotation( "Wikipedia:Blood_island") "blood island of umbilical vesicle") AnnotationAssertion(Annotation( "Wikipedia:Blood_island") "insula sanguinea vesiculae umbilicalis") @@ -212662,6 +212666,8 @@ AnnotationAssertion( "UBERON:0011921") AnnotationAssertion(rdfs:label "connecting stalk blood islands") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -212676,6 +212682,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cochlear basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (preganglionic autonomic fiber) @@ -212690,7 +212699,10 @@ AnnotationAssertion( "UBERON:0011925") AnnotationAssertion(rdfs:label "preganglionic autonomic fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (preganglionic sympathetic fiber) @@ -212703,6 +212715,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (preganglionic parasympathetic fiber) @@ -212715,6 +212728,7 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal hair) @@ -212730,6 +212744,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nasal hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pilosebaceous unit) @@ -212746,6 +212762,7 @@ AnnotationAssertion(Annotation( "UBERON:0011932") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pilosebaceous unit") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "ISBN:0123813611") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -212770,6 +212787,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureter luminal urothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endometrium luminal epithelium) @@ -212783,6 +212802,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endometrium luminal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland luminal epithelium) @@ -212794,6 +212816,8 @@ AnnotationAssertion( "UBERON:0011950") AnnotationAssertion(rdfs:label "mammary gland luminal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (prostate luminal epithelium) @@ -212805,6 +212829,8 @@ AnnotationAssertion( "UBERON:0011951") AnnotationAssertion(rdfs:label "prostate luminal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") Annotation( "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships") ObjectSomeValuesFrom( )) # Class: (stomach glandular region) @@ -212822,6 +212848,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach glandular region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left hepatic vein) @@ -212836,6 +212865,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left hepatic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right hepatic vein) @@ -212850,6 +212881,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right hepatic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (articular capsule of glenohumeral joint) @@ -212866,6 +212899,8 @@ AnnotationAssertion(Annotation( "UBERON:0011960") AnnotationAssertion(rdfs:label "articular capsule of glenohumeral joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (saddle joint) @@ -212897,7 +212932,10 @@ AnnotationAssertion( "UBERON:0011972") AnnotationAssertion(rdfs:label "medial ligament of ankle joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of phalanx of pes) @@ -212908,6 +212946,8 @@ AnnotationAssertion( "UBERON:0011973") AnnotationAssertion(rdfs:label "epiphysis of phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of proximal phalanx of pes) @@ -212918,6 +212958,9 @@ AnnotationAssertion( "UBERON:0011974") AnnotationAssertion(rdfs:label "epiphysis of proximal phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of middle phalanx of pes) @@ -212928,6 +212971,9 @@ AnnotationAssertion( "UBERON:0011975") AnnotationAssertion(rdfs:label "epiphysis of middle phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of distal phalanx of pes) @@ -212938,6 +212984,9 @@ AnnotationAssertion( "UBERON:0011976") AnnotationAssertion(rdfs:label "epiphysis of distal phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of proximal phalanx of manus) @@ -212949,6 +212998,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epiphysis of proximal phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of middle phalanx of manus) @@ -212959,6 +213010,8 @@ AnnotationAssertion( "UBERON:0011978") AnnotationAssertion(rdfs:label "epiphysis of middle phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiphysis of distal phalanx of manus) @@ -212970,11 +213023,12 @@ AnnotationAssertion( "UBERON:0011979") AnnotationAssertion(rdfs:label "epiphysis of distal phalanx of manus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (crurotarsal joint) AnnotationAssertion(Annotation( "Wikipedia:Crurotarsal") "A joint that connects the bones of the crus to the proximal tarsal bones.") -AnnotationAssertion(Annotation( "http://palaeos.com/vertebrates/glossary/glossaryCr.html#Crurotarsal%20joint") "an ankle joint that passes between the astragalus and calcaneum[Palaeos].") AnnotationAssertion( "Wikipedia:Crurotarsal") AnnotationAssertion( "uberon") AnnotationAssertion( "crurotarsal") @@ -212983,13 +213037,13 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "crurotarsal joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (coelom) AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Body_cavity") Annotation( "Wikipedia:Coelom") "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.") AnnotationAssertion( "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.") AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) -AnnotationAssertion( "coelomic") AnnotationAssertion( "EHDAA2:0004731") AnnotationAssertion( "Wikipedia:Coelom") AnnotationAssertion(Annotation( "NCBITaxon:33511") "enterocoelom") @@ -213006,13 +213060,14 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (myocoele) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/myocoele") "The cavity within a myotome.") -AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001283") Annotation( "VHOG") Annotation( "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6") Annotation( "http://bgee.unil.ch/") "The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]") AnnotationAssertion( "EMAPA:31134") AnnotationAssertion( "VHOG:0001283") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012054") AnnotationAssertion(rdfs:label "myocoele") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium-associated lymphoid tissue) @@ -213030,12 +213085,12 @@ AnnotationAssertion( "UBERON:0012070") AnnotationAssertion(rdfs:label "palatal tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (palate bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Any bone that is part of a palate.") -AnnotationAssertion( "this is distinct (but not disjoint) from palatine bone") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37930") AnnotationAssertion( "NCIT:C33248") AnnotationAssertion(Annotation( "ncithesaurus:Palate_Bone") "UMLS:C1518857") @@ -213045,6 +213100,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "palate bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (palatal part of dermatocranium) @@ -213061,8 +213118,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (replacement bone) AnnotationAssertion(Annotation( "ZFA:0001628") "Bone that forms as a replacement of another structural tissue.") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "TAO:0001637") Annotation( "TAO") Annotation( "TAO:wd") "Bone that forms as a replacement of another structural tissue.[TAO]") -AnnotationAssertion(Annotation( "ZFA") "This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.") AnnotationAssertion( "AAO:0010768") AnnotationAssertion( "TAO:0001637") AnnotationAssertion( "ZFA:0001628") @@ -213082,9 +213137,13 @@ AnnotationAssertion( "UBERON:0012080") AnnotationAssertion(rdfs:label "patella cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (patella pre-cartilage condensation) @@ -213094,8 +213153,12 @@ AnnotationAssertion( "UBERON:0012081") AnnotationAssertion(rdfs:label "patella pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchial lumen) @@ -213108,7 +213171,9 @@ AnnotationAssertion( "UBERON:0012082") AnnotationAssertion(rdfs:label "bronchial lumen") EquivalentClasses(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of secondary bronchus) @@ -213121,7 +213186,9 @@ AnnotationAssertion( "UBERON:0012084") AnnotationAssertion(rdfs:label "lumen of secondary bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of tertiary bronchus) @@ -213133,68 +213200,58 @@ AnnotationAssertion( "UBERON:0012085") AnnotationAssertion(rdfs:label "lumen of tertiary bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (dermatological-muscosal system) - -AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/53") "Anatomical system that consists of the integumental system plus all mucosae and submucosae.") -AnnotationAssertion( "uberon") -AnnotationAssertion(Annotation( "OBI:MC") "dermatological system") -AnnotationAssertion( "UBERON:0012125") -AnnotationAssertion(rdfs:label "dermatological-muscosal system") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (segment of autopod) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012139") AnnotationAssertion(rdfs:label "segment of autopod") -SubClassOf(Annotation( "may be revised") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digitopodium region) AnnotationAssertion(Annotation( "PHENOSCAPE:ni") Annotation( "https://github.com/obophenotype/uberon/issues/131") "A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion( "acropodium (Wagner)") AnnotationAssertion( "UBERON:0012140") AnnotationAssertion(rdfs:label "digitopodium region") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digitopodium region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012141") AnnotationAssertion(rdfs:label "manual digitopodium region") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digitopodium region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012142") AnnotationAssertion(rdfs:label "pedal digitopodium region") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of digitopodium) AnnotationAssertion(Annotation( "PHENOSCAPE:ni") "A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "PHENOSCAPE:ni") "digitopodium") AnnotationAssertion(Annotation( ) "skeleton of digits") @@ -213202,32 +213259,35 @@ AnnotationAssertion( "skeleton of digitopodium") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of manual digitopodium) AnnotationAssertion(Annotation( "PHENOSCAPE:ni") Annotation( "https://orcid.org/0000-0002-6601-2165") "A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion( "manual digitopodium") AnnotationAssertion( "UBERON:0012151") AnnotationAssertion(rdfs:label "skeleton of manual digitopodium") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (skeleton of pedal digitopodium) AnnotationAssertion(Annotation( "PHENOSCAPE:ni") Annotation( "https://orcid.org/0000-0002-6601-2165") "A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton.") -AnnotationAssertion( "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod") AnnotationAssertion( "uberon") AnnotationAssertion( "pedal digitopodium") AnnotationAssertion( "UBERON:0012152") AnnotationAssertion(rdfs:label "skeleton of pedal digitopodium") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -213248,7 +213308,9 @@ AnnotationAssertion( "Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]") AnnotationAssertion(rdfs:label "umbilical cord blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach primordium) @@ -213262,14 +213324,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acoustico-facial VII-VIII ganglion complex) AnnotationAssertion( "EHDAA2:0000494") AnnotationAssertion( "EMAPA:16794") AnnotationAssertion( "SCTID:361514006") -AnnotationAssertion( "VHOG:0000715") AnnotationAssertion( "acousticofacial ganglion") AnnotationAssertion( "facio-acoustic ganglion") AnnotationAssertion(Annotation( "EMAPA:16794") "facio-acoustic ganglion complex VII-VIII") @@ -213279,6 +213342,7 @@ AnnotationAssertion(Annotation( "UBERON:0012175") AnnotationAssertion(rdfs:label "acoustico-facial VII-VIII ganglion complex") SubClassOf(Annotation( "cjm") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) @@ -213292,6 +213356,8 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "skin apocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "MA") ) +SubClassOf( ) +SubClassOf( ) # Class: (head or neck skin) @@ -213304,6 +213370,8 @@ AnnotationAssertion( "UBERON:0012180") AnnotationAssertion(rdfs:label "head or neck skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (phrenic vein) @@ -213316,6 +213384,8 @@ AnnotationAssertion( "UBERON:0012193") AnnotationAssertion(rdfs:label "phrenic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urinary bladder vasculature) @@ -213332,6 +213402,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urinary bladder vasculature") EquivalentClasses(Annotation( "EMAPA") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethral meatus) @@ -213355,11 +213428,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "urethral meatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male urethral meatus) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "Wikipedia:External_urethral_orifice_(male)") "A urethral meatus that is part of a male urethra[Automatically generated definition].") -AnnotationAssertion(Annotation( "Wikipedia:External_urethral_orifice_(male)") "The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis.") AnnotationAssertion( "EMAPA:36434") AnnotationAssertion( "FMA:85265") AnnotationAssertion( "MA:0002642") @@ -213376,6 +213453,8 @@ AnnotationAssertion(Annotation( "UBERON:0012241") AnnotationAssertion(rdfs:label "male urethral meatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -213399,12 +213478,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "internal urethral orifice") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical gland) AnnotationAssertion(Annotation( "http://www.thefreedictionary.com/cervical+glands") "Mucus-secreting glands in the mucosa of the uterine cervix.") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "NCIT:C32296") AnnotationAssertion( "SCTID:280836000") AnnotationAssertion(Annotation( "ncithesaurus:Cervical_Gland") "UMLS:C2724437") @@ -213414,7 +213497,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical mucosa) @@ -213425,12 +213508,13 @@ AnnotationAssertion( "UBERON:0012248") AnnotationAssertion(rdfs:label "cervical mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectocervix) AnnotationAssertion(Annotation( "BTO:0001850") Annotation( "Wikipedia:Vaginal_portion_of_cervix") "The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "FMA") "distinction between two FMA classes not clear - we merge them here") AnnotationAssertion( "UBERON:0010182") AnnotationAssertion( "BTO:0001850") AnnotationAssertion( "CALOHA:TS-1098") @@ -213451,15 +213535,18 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ectocervix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "BTO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervix glandular epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "A glandular epithelium that is part of a uterine cervix.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx") "The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium.") AnnotationAssertion( "NCIT:C54414") AnnotationAssertion(Annotation( "ncithesaurus:Cervix_Columnar_Epithelium") "UMLS:C1707350") AnnotationAssertion( "uberon") @@ -213468,6 +213555,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervix glandular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (ectocervical epithelium) @@ -213478,6 +213567,8 @@ AnnotationAssertion( "UBERON:0012251") AnnotationAssertion(rdfs:label "ectocervical epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocervical epithelium) @@ -213491,7 +213582,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocervical epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical squamo-columnar junction) @@ -213506,6 +213598,9 @@ AnnotationAssertion( "Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia.") AnnotationAssertion(rdfs:label "cervical squamo-columnar junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal aorta artery) @@ -213518,6 +213613,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "abdominal aorta artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (columnar epithelium) @@ -213539,6 +213636,8 @@ AnnotationAssertion( "UBERON:0012275") AnnotationAssertion(rdfs:label "meso-epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (endometrium glandular epithelium) @@ -213554,7 +213653,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endometrium glandular epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "Wikipedia") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of nasal mucosa) @@ -213573,7 +213675,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gland of nasal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (chromaffin paraganglion) @@ -213604,8 +213710,13 @@ AnnotationAssertion( "UBERON:0012287") AnnotationAssertion(rdfs:label "Rathkes pouch epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic cloacal fold) @@ -213634,6 +213745,9 @@ AnnotationAssertion( "UBERON:0012299") AnnotationAssertion(rdfs:label "mucosa of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch maxillary ectoderm) @@ -213644,6 +213758,9 @@ AnnotationAssertion( "UBERON:0012313") AnnotationAssertion(rdfs:label "1st arch maxillary ectoderm") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -213659,9 +213776,8 @@ AnnotationAssertion( "primordium of face") AnnotationAssertion( "UBERON:0012314") AnnotationAssertion(rdfs:label "embryonic facial prominence") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vagina orifice) @@ -213684,6 +213800,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vagina orifice") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical artery) @@ -213696,6 +213816,8 @@ AnnotationAssertion( "UBERON:0012320") AnnotationAssertion(rdfs:label "cervical artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (deep cervical artery) @@ -213710,14 +213832,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "deep cervical artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (transverse cervical artery) AnnotationAssertion(Annotation( "Wikipedia:Transverse_cervical_artery") "The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "MA") "Unclear if MA class belongs here or in parent") AnnotationAssertion( "FMA:10664") AnnotationAssertion( "MA:0001936") AnnotationAssertion( "SCTID:244224008") @@ -213745,6 +213867,8 @@ AnnotationAssertion( "UBERON:0012329") AnnotationAssertion(rdfs:label "keratinized stratified squamous epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nasal-associated lymphoid tissue) @@ -213759,6 +213883,9 @@ AnnotationAssertion( "UBERON:0012330") AnnotationAssertion(rdfs:label "nasal-associated lymphoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (broad ligament of uterus) @@ -213779,6 +213906,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "broad ligament of uterus") SubClassOf(Annotation( "MESH") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -213798,7 +213926,6 @@ SubClassOf(Annotation( "MA" # Class: (acropodium region) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The segment of the autopod that is distal to the metapodial region and consists of the digits.") -AnnotationAssertion( "class refers to an entire limb segment, not just the bones") AnnotationAssertion( "acropodial limb segment") AnnotationAssertion( "acropodial region") AnnotationAssertion( "acropodial segment of autopod") @@ -213807,13 +213934,14 @@ AnnotationAssertion( "UBERON:0012354") AnnotationAssertion(rdfs:label "acropodium region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual acropodium region) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers).") -AnnotationAssertion( "class refers to an entire limb segment, not just the bones") AnnotationAssertion( "FMA:75592") AnnotationAssertion( "acropodial hindlimb segment") AnnotationAssertion( "acropodial region of manus") @@ -213835,13 +213963,14 @@ AnnotationAssertion( "UBERON:0012355") AnnotationAssertion(rdfs:label "manual acropodium region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal acropodium region) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes).") -AnnotationAssertion( "class refers to an entire limb segment, not just the bones") AnnotationAssertion( "FMA:70664") AnnotationAssertion( "SCTID:362835004") AnnotationAssertion( "acropodial forelimb segment") @@ -213857,41 +213986,45 @@ AnnotationAssertion(Annotation( "UBERON:0012356") AnnotationAssertion(rdfs:label "pedal acropodium region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digitopodium bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.") -AnnotationAssertion( ) AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( ) "digit bone") AnnotationAssertion( "UBERON:0012357") AnnotationAssertion(rdfs:label "digitopodium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digitopodium bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton.") -AnnotationAssertion( ) AnnotationAssertion( "SCTID:265809008") AnnotationAssertion( "bone of forelimb digitopodium") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012358") AnnotationAssertion(rdfs:label "manual digitopodium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digitopodium bone) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton.") -AnnotationAssertion( ) AnnotationAssertion( "bone of hindlimb digitopodium") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012359") AnnotationAssertion(rdfs:label "pedal digitopodium bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone of jaw) @@ -213907,6 +214040,7 @@ AnnotationAssertion( "bone of jaw") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (internal anal region) @@ -213929,6 +214063,7 @@ AnnotationAssertion( "UBERON:0012367") AnnotationAssertion(rdfs:label "muscle layer of intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (circular muscle layer of muscular coat) @@ -213943,9 +214078,8 @@ AnnotationAssertion(Annotation( "FMA:62899") "inner muscularis layer") AnnotationAssertion( "UBERON:0012368") AnnotationAssertion(rdfs:label "circular muscle layer of muscular coat") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (longitudinal muscle layer of muscular coat) @@ -213959,9 +214093,8 @@ AnnotationAssertion(Annotation( "FMA:62900") "outer muscularis layer") AnnotationAssertion( "UBERON:0012369") AnnotationAssertion(rdfs:label "longitudinal muscle layer of muscular coat") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (sympathetic nerve plexus) @@ -213974,6 +214107,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sympathetic nerve plexus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subserosa) @@ -213990,7 +214125,10 @@ AnnotationAssertion( "Contains nerves, blood vessels, lymphatics and lymph nodes") AnnotationAssertion(rdfs:label "subserosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of jejunum) @@ -214006,6 +214144,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle layer of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of urinary bladder) @@ -214027,6 +214167,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle layer of urinary bladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -214043,6 +214185,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "large intestine smooth muscle circular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (large intestine smooth muscle longitudinal layer) @@ -214057,6 +214202,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "large intestine smooth muscle longitudinal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (small intestine smooth muscle circular layer) @@ -214077,6 +214225,9 @@ AnnotationAssertion( "UBERON:0012401") AnnotationAssertion(rdfs:label "small intestine smooth muscle circular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (small intestine smooth muscle longitudinal layer) @@ -214098,6 +214249,9 @@ AnnotationAssertion( "UBERON:0012402") AnnotationAssertion(rdfs:label "small intestine smooth muscle longitudinal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (respiratory system arterial smooth muscle) @@ -214110,6 +214264,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system arterial smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system venous smooth muscle) @@ -214122,6 +214279,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory system venous smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (taenia coli) @@ -214139,16 +214298,12 @@ AnnotationAssertion(Annotation( "UBERON:0012419") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "taenia coli") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of microvilli) AnnotationAssertion(Annotation( "GO:0005902") Annotation( "Wikipedia:Microvillus") "A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified].") -AnnotationAssertion( "a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction") -AnnotationAssertion( "increases the surface area of a cell lining whilst minimizing increase in volume") -AnnotationAssertion(Annotation( "FMA") "FMA class represents an individual microvillus.") AnnotationAssertion( "FMA:67296") AnnotationAssertion( "MESH:D008871") AnnotationAssertion( "NCIT:C33112") @@ -214165,7 +214320,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (striated border microvillus layer) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/striated+border") Annotation( "http://orcid.org/0000-0002-6601-2165") "A microvillus layer that is striated and found in the intestine.") -AnnotationAssertion(Annotation( "FMA") "FMA class represents an individual microvillus") AnnotationAssertion( "FMA:70978") AnnotationAssertion( "NCIT:C33634") AnnotationAssertion( "uberon") @@ -214178,7 +214332,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (hematopoietic tissue) AnnotationAssertion(Annotation( "http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue") "Blood-forming tissue, consisting of reticular fibers and cells.") -AnnotationAssertion( "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue") AnnotationAssertion( "CALOHA:TS-2142") AnnotationAssertion( "FMA:14073") AnnotationAssertion( "NCIT:C13051") @@ -214192,8 +214345,10 @@ AnnotationAssertion( "UBERON:0012429") AnnotationAssertion(rdfs:label "hematopoietic tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "defitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tunica fibrosa of eyeball) @@ -214209,7 +214364,10 @@ AnnotationAssertion(Annotation( "Wikipedia:Fibrous_tunic_of_eyeball") "fibrous tunic") AnnotationAssertion( "UBERON:0012430") AnnotationAssertion(rdfs:label "tunica fibrosa of eyeball") +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -214225,11 +214383,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endothelium of peritubular capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal lumen) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical space that is enclosed by a cloaca.") -AnnotationAssertion(Annotation( "ZFA") "the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/") AnnotationAssertion( "TAO:0000330") AnnotationAssertion( "ZFA:0000330") AnnotationAssertion(Annotation( "ZFA:0000330") "cloaca lumen") @@ -214238,8 +214398,10 @@ AnnotationAssertion( "UBERON:0012463") AnnotationAssertion(rdfs:label "cloacal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal vent) @@ -214251,16 +214413,19 @@ AnnotationAssertion( "UBERON:0012464") AnnotationAssertion(rdfs:label "cloacal vent") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of terminal part of digestive tract) AnnotationAssertion(Annotation( "OBOL:automatic") "An anatomical space that is enclosed by a terminal part of digestive tract.") -AnnotationAssertion( "includes the cloacal lumen, in species where this is present") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0012465") AnnotationAssertion(rdfs:label "lumen of terminal part of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic cavity) @@ -214272,6 +214437,8 @@ AnnotationAssertion(Annotation( "UBERON:0012466") AnnotationAssertion(rdfs:label "extraembryonic cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enclosed anatomical space) @@ -214282,6 +214449,8 @@ AnnotationAssertion( "UBERON:0012467") AnnotationAssertion(rdfs:label "enclosed anatomical space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anal tooth) @@ -214294,6 +214463,8 @@ AnnotationAssertion( "UBERON:0012468") AnnotationAssertion(rdfs:label "anal tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (external anal region) @@ -214320,8 +214491,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeleton of pectoral complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeleton of pelvic complex) @@ -214338,13 +214511,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeleton of pelvic complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal part of neck) AnnotationAssertion(Annotation( "MP:0012723") "The posterior region of the neck, including the suboccipital region.") -AnnotationAssertion( "nuchal") AnnotationAssertion(Annotation( "BTO:0000957") "nape") AnnotationAssertion( "BTO:0000957") AnnotationAssertion( "FMA:24189") @@ -214365,7 +214539,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dorsal part of neck") SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -214376,6 +214549,8 @@ AnnotationAssertion( "UBERON:0012478") AnnotationAssertion(rdfs:label "cloacal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal mucosa) @@ -214394,11 +214569,12 @@ AnnotationAssertion( "UBERON:0012480") AnnotationAssertion(rdfs:label "cloacal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal epithelium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An epithelium that is part of a cloaca.") -AnnotationAssertion(Annotation( "EMAPA:27577") "cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium.") AnnotationAssertion( "EMAPA:27577") AnnotationAssertion( "EMAPA:36070") AnnotationAssertion( "ZFA:0005783") @@ -214407,7 +214583,9 @@ AnnotationAssertion(Annotation( "UBERON:0012481") AnnotationAssertion(rdfs:label "cloacal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of cloaca) @@ -214418,6 +214596,8 @@ AnnotationAssertion( "UBERON:0012482") AnnotationAssertion(rdfs:label "submucosa of cloaca") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of cloaca) @@ -214431,6 +214611,8 @@ AnnotationAssertion( "UBERON:0012483") AnnotationAssertion(rdfs:label "serosa of cloaca") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal villus) @@ -214439,6 +214621,8 @@ AnnotationAssertion( "UBERON:0012485") AnnotationAssertion(rdfs:label "cloacal villus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of cloaca) @@ -214449,6 +214633,8 @@ AnnotationAssertion( "UBERON:0012486") AnnotationAssertion(rdfs:label "muscle layer of cloaca") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vaginal sphincter) @@ -214460,6 +214646,10 @@ AnnotationAssertion( "UBERON:0012487") AnnotationAssertion(rdfs:label "vaginal sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of duodenum) @@ -214474,6 +214664,8 @@ AnnotationAssertion(Annotation( "UBERON:0012488") AnnotationAssertion(rdfs:label "muscle layer of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of colon) @@ -214494,6 +214686,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle layer of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of anal canal) @@ -214510,6 +214704,9 @@ AnnotationAssertion( "UBERON:0012490") AnnotationAssertion(rdfs:label "muscle layer of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of appendix) @@ -214526,6 +214723,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serosa of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of uterine tube) @@ -214543,6 +214742,9 @@ AnnotationAssertion( "UBERON:0012499") AnnotationAssertion(rdfs:label "serosa of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosa of fundus of stomach) @@ -214554,6 +214756,8 @@ AnnotationAssertion( "UBERON:0012503") AnnotationAssertion(rdfs:label "serosa of fundus of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (adventitia of esophagus) @@ -214571,6 +214775,8 @@ AnnotationAssertion( "UBERON:0012504") AnnotationAssertion(rdfs:label "adventitia of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (umbilical smooth muscle) @@ -214580,6 +214786,9 @@ AnnotationAssertion( "UBERON:0012615") AnnotationAssertion(rdfs:label "umbilical smooth muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastroduodenal junction) @@ -214590,7 +214799,10 @@ AnnotationAssertion( "UBERON:0012650") AnnotationAssertion(rdfs:label "gastroduodenal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of gastroduodenal junction) @@ -214601,14 +214813,14 @@ AnnotationAssertion( "UBERON:0012651") AnnotationAssertion(rdfs:label "mucosa of gastroduodenal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sulcus of brain) AnnotationAssertion(Annotation( "Wikipedia:Sulcus_(neuroanatomy)") Annotation( "https://github.com/obophenotype/uberon/issues/315") "A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals.") AnnotationAssertion( "sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class") -AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://neurolex.org/wiki/Cumbo_terms") "Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)") AnnotationAssertion(Annotation( "HBA:9352") Annotation( ) "sulci & spaces") AnnotationAssertion(Annotation( "NLX:144078") "sulcus") AnnotationAssertion( "DHBA:10610") @@ -214626,6 +214838,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sulcus of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -214641,12 +214855,14 @@ AnnotationAssertion( "UBERON:0013121") AnnotationAssertion(rdfs:label "proximal epiphysis of phalanx of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein of abdomen) AnnotationAssertion(Annotation( "OBOL:automatic") "A vein that is part of a abdomen.") AnnotationAssertion( "TODO mirror representation of abdominal aorta") -AnnotationAssertion( "this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein") AnnotationAssertion( "SCTID:281473003") AnnotationAssertion( "abdominal vein") AnnotationAssertion( "uberon") @@ -214654,11 +214870,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vein of abdomen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (pulmonary venous system) AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Pulmonary_venous_system") "The part of the venous system that drains the lungs[Kardong].") -AnnotationAssertion(Annotation( "Wikipedia:Pulmonary_circulation") "Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung.") AnnotationAssertion( "Wikipedia:Pulmonary_venous_system") AnnotationAssertion( "pulmonary venous circulatory system") AnnotationAssertion( "uberon") @@ -214680,6 +214897,8 @@ AnnotationAssertion( "UBERON:0013136") AnnotationAssertion(rdfs:label "vein of lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (ligament of liver) @@ -214695,6 +214914,11 @@ AnnotationAssertion( "UBERON:0013139") AnnotationAssertion(rdfs:label "ligament of liver") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (systemic vein) @@ -214708,6 +214932,8 @@ AnnotationAssertion( "UBERON:0013140") AnnotationAssertion(rdfs:label "systemic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain vesicle) @@ -214724,7 +214950,6 @@ SubClassOf(Annotation( "EHD # Class: (future brain vesicle) AnnotationAssertion( "consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html).") -AnnotationAssertion( "Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'") AnnotationAssertion( "NCIT:C34259") AnnotationAssertion( "SCTID:360409004") AnnotationAssertion( "neuronames:2499") @@ -214737,7 +214962,6 @@ AnnotationAssertion( "UBERON:0013150") AnnotationAssertion(rdfs:label "future brain vesicle") SubClassOf(Annotation( "EHDAA2") ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -214753,6 +214977,8 @@ AnnotationAssertion( "UBERON:0013151") AnnotationAssertion(rdfs:label "choroidal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (1st arch mandibular endoderm) @@ -214762,11 +214988,11 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0013156") AnnotationAssertion(rdfs:label "1st arch mandibular endoderm") -SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (foregut-midgut junction gland) @@ -214778,6 +215004,8 @@ AnnotationAssertion( "UBERON:0013158") AnnotationAssertion(rdfs:label "foregut-midgut junction gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithalamus mantle layer) @@ -214791,6 +215019,8 @@ AnnotationAssertion( "UBERON:0013159") AnnotationAssertion(rdfs:label "epithalamus mantle layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithalamus ventricular layer) @@ -214805,11 +215035,12 @@ AnnotationAssertion( "UBERON:0013160") AnnotationAssertion(rdfs:label "epithalamus ventricular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lateral ventricle) AnnotationAssertion(Annotation( "OBOL:automatic") "A telencephalic ventricle that is in_the_left_side_of a telencephalon.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:78450") AnnotationAssertion( "SCTID:368593005") AnnotationAssertion( "left telencephalic ventricle") @@ -214817,12 +215048,14 @@ AnnotationAssertion( "UBERON:0013161") AnnotationAssertion(rdfs:label "left lateral ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lateral ventricle) AnnotationAssertion(Annotation( "OBOL:automatic") "A telencephalic ventricle that is in_the_right_side_of a telencephalon.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:78449") AnnotationAssertion( "SCTID:368571000") AnnotationAssertion( "right telencephalic ventricle") @@ -214830,7 +215063,10 @@ AnnotationAssertion( "UBERON:0013162") AnnotationAssertion(rdfs:label "right lateral ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian cortex) @@ -214848,12 +215084,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ovarian cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian medulla) AnnotationAssertion(Annotation( "MGI:anna") "Highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles.") -AnnotationAssertion(Annotation( "NCIT") "composed of loose connective tissue that contains blood vessels, lymph vessels and nerves") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37928") AnnotationAssertion( "FMA:18616") AnnotationAssertion( "NCIT:C33245") @@ -214867,6 +215104,28 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ovarian medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anal sac gland secretion) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A bodily secretion that is produced by a gland of anal sac.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "NCBITaxon:29132") Annotation( ) "castoreum") +AnnotationAssertion(Annotation( "NCBITaxon:9673") Annotation( ) "civet") +AnnotationAssertion( "uberon") +AnnotationAssertion( "anal gland secretion") +AnnotationAssertion(Annotation( "Wikipedia:Hyena_butter") Annotation( ) "hyena butter") +AnnotationAssertion(Annotation( "NCBITaxon:30533") "musk") +AnnotationAssertion( "odorous sac") +AnnotationAssertion( "UBERON:0013212") +AnnotationAssertion(rdfs:label "anal sac gland secretion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sweat gland of eyelid) @@ -214884,6 +215143,9 @@ AnnotationAssertion( "UBERON:0013228") AnnotationAssertion(rdfs:label "sweat gland of eyelid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (eyelid gland) @@ -214894,6 +215156,10 @@ AnnotationAssertion( "UBERON:0013229") AnnotationAssertion(rdfs:label "eyelid gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebaceous gland of eyelid) @@ -214902,6 +215168,8 @@ AnnotationAssertion( "UBERON:0013231") AnnotationAssertion(rdfs:label "sebaceous gland of eyelid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (serous acinus) @@ -214912,6 +215180,8 @@ AnnotationAssertion( "UBERON:0013232") AnnotationAssertion(rdfs:label "serous acinus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (future glans) @@ -214933,6 +215203,7 @@ AnnotationAssertion( "UBERON:0013239") AnnotationAssertion(rdfs:label "future glans penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (future glans clitoris) @@ -214944,12 +215215,12 @@ AnnotationAssertion( "UBERON:0013240") AnnotationAssertion(rdfs:label "future glans clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (embryonic urethral groove) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The precursor of the urethra.") -AnnotationAssertion(Annotation( "Wikipedia:Urethral_groove") "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week") AnnotationAssertion( "SCTID:361531004") AnnotationAssertion( "Wikipedia:Urethral_groove") AnnotationAssertion(Annotation( "Wikipedia:Urethral_groove") Annotation( ) "sulcus urethralis primarius") @@ -214973,13 +215244,15 @@ AnnotationAssertion(Annotation( "UBERON:0013247") AnnotationAssertion(rdfs:label "male paramesonephric duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (diaphysis of fibula) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "Wikipedia:Body_of_fibula") "A diaphysis that is part of a fibula[Automatically generated definition].") -AnnotationAssertion(Annotation( "Wikipedia:Body_of_fibula") "The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37892") AnnotationAssertion( "FMA:33738") AnnotationAssertion( "SCTID:302528006") @@ -214992,11 +215265,13 @@ AnnotationAssertion( "UBERON:0013279") AnnotationAssertion(rdfs:label "diaphysis of fibula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diaphysis of tibia) AnnotationAssertion(Annotation( "OBOL:automatic") Annotation( "Wikipedia:Body_of_tibia") "A diaphysis that is part of a tibia.") -AnnotationAssertion(Annotation( "Wikipedia:Body_of_tibia") "The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia].") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37770") AnnotationAssertion( "FMA:33125") AnnotationAssertion( "MA:0003049") @@ -215012,6 +215287,9 @@ AnnotationAssertion(Annotation( "UBERON:0013280") AnnotationAssertion(rdfs:label "diaphysis of tibia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial cavity) @@ -215032,12 +215310,13 @@ AnnotationAssertion( "cranial cavity") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cecal tonsil) AnnotationAssertion(Annotation( "ISBN:0824754077") "A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus.") -AnnotationAssertion( "In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil") AnnotationAssertion( "SCTID:14239003") AnnotationAssertion( "caecal tonsil") AnnotationAssertion( "uberon") @@ -215045,6 +215324,7 @@ AnnotationAssertion( "UBERON:0013478") AnnotationAssertion(rdfs:label "cecal tonsil") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215058,6 +215338,9 @@ AnnotationAssertion(Annotation( "UBERON:0013479") AnnotationAssertion(rdfs:label "lung endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (crypt of Lieberkuhn of ileum) @@ -215072,6 +215355,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "crypt of Lieberkuhn of ileum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of duodenum) @@ -215086,6 +215370,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "crypt of Lieberkuhn of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of jejunum) @@ -215100,6 +215385,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "crypt of Lieberkuhn of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of colon) @@ -215114,6 +215400,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "crypt of Lieberkuhn of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (crypt of Lieberkuhn of appendix) @@ -215126,6 +215413,7 @@ AnnotationAssertion( "UBERON:0013486") AnnotationAssertion(rdfs:label "crypt of Lieberkuhn of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vestibulo-cochlear VIII ganglion complex) @@ -215140,6 +215428,8 @@ AnnotationAssertion(Annotation( "UBERON:0013498") AnnotationAssertion(rdfs:label "vestibulo-cochlear VIII ganglion complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal sphincter) @@ -215152,6 +215442,8 @@ AnnotationAssertion( "the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938).") AnnotationAssertion(rdfs:label "cloacal sphincter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (5th arch mesenchyme) @@ -215163,6 +215455,8 @@ AnnotationAssertion( "UBERON:0013502") AnnotationAssertion(rdfs:label "5th arch mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (caudal vertebra cartilage element) @@ -215177,7 +215471,9 @@ AnnotationAssertion( "UBERON:0013503") AnnotationAssertion(rdfs:label "caudal vertebra cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215192,7 +215488,8 @@ AnnotationAssertion( "UBERON:0013504") AnnotationAssertion(rdfs:label "caudal vertebra pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (cervical vertebra cartilage element) @@ -215203,6 +215500,10 @@ AnnotationAssertion( "UBERON:0013505") AnnotationAssertion(rdfs:label "cervical vertebra cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215213,6 +215514,8 @@ AnnotationAssertion( "UBERON:0013506") AnnotationAssertion(rdfs:label "cervical vertebra pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (thoracic vertebra cartilage element) @@ -215223,7 +215526,9 @@ AnnotationAssertion( "UBERON:0013507") AnnotationAssertion(rdfs:label "thoracic vertebra cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215234,7 +215539,8 @@ AnnotationAssertion( "UBERON:0013508") AnnotationAssertion(rdfs:label "thoracic vertebra pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (space surrounding organism) @@ -215245,11 +215551,12 @@ AnnotationAssertion( "UBERON:0013514") AnnotationAssertion(rdfs:label "space surrounding organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of oviduct) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A section through the tube or network of tubes that connects the ovaries to the outside of the body.") -AnnotationAssertion(Annotation( "FMA") "FMA class may only represent the uterine portion") AnnotationAssertion( "FMA:18302") AnnotationAssertion(Annotation( "FMA:18302") "subdivision of oviduct") AnnotationAssertion( "subdivision of uterine tube") @@ -215261,7 +215568,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subdivision of oviduct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of tube) @@ -215277,7 +215587,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (stomach lumen) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The anatomical space that is enclosed by a stomach.") -AnnotationAssertion(Annotation( "FMA:14585") "Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].") AnnotationAssertion( "EMAPA:18395") AnnotationAssertion( "FMA:14585") AnnotationAssertion(Annotation( "FMA:14585") "cavity of stomach") @@ -215286,7 +215595,9 @@ AnnotationAssertion(Annotation( "UBERON:0013525") AnnotationAssertion(rdfs:label "stomach lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (otocyst lumen) @@ -215298,9 +215609,11 @@ AnnotationAssertion( "UBERON:0013526") AnnotationAssertion(rdfs:label "otocyst lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of lateral geniculate body) @@ -215308,6 +215621,9 @@ AnnotationAssertion( "UBERON:0013605") AnnotationAssertion(rdfs:label "layer of lateral geniculate body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (magnocellular layer of dorsal nucleus of lateral geniculate body) @@ -215323,7 +215639,9 @@ AnnotationAssertion( "Rods; necessary for the perception of movement, depth, and small differences in brightness[WP]") AnnotationAssertion(rdfs:label "magnocellular layer of dorsal nucleus of lateral geniculate body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parvocellular layer of dorsal nucleus of lateral geniculate body) @@ -215337,7 +215655,9 @@ AnnotationAssertion( "Cones; long- and medium-wavelength (\"red\" and \"green\" cones); necessary for the perception of color and form (fine details).[WP]") AnnotationAssertion(rdfs:label "parvocellular layer of dorsal nucleus of lateral geniculate body") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (koniocellular layer of dorsal nucleus of lateral geniculate body) @@ -215387,6 +215707,8 @@ AnnotationAssertion( "UBERON:0013632") AnnotationAssertion(rdfs:label "sesamoid cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (epithelium of intestinal villus) @@ -215399,12 +215721,13 @@ AnnotationAssertion( "UBERON:0013636") AnnotationAssertion(rdfs:label "epithelium of intestinal villus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (prostate gland lateral lobe) AnnotationAssertion(Annotation( "ncithesaurus:Lateral_Lobe_of_the_Prostate") "The prostate gland lobe that is located on the lateral side of the organ.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "EMAPA:29822") AnnotationAssertion( "FMA:19577") AnnotationAssertion( "MA:0003125") @@ -215417,11 +215740,13 @@ AnnotationAssertion(Annotation( "UBERON:0013637") AnnotationAssertion(rdfs:label "prostate gland lateral lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left dorsal thalamus) AnnotationAssertion(Annotation( "OBOL:automatic") "A dorsal thalamus that is in_the_left_side_of a diencephalon.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "FMA:258716") "left thalamus") AnnotationAssertion( "FMA:258716") AnnotationAssertion( "uberon") @@ -215429,11 +215754,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left dorsal thalamus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right dorsal thalamus) AnnotationAssertion(Annotation( "OBOL:automatic") "A dorsal thalamus that is in_the_right_side_of a diencephalon.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(Annotation( "FMA:258714") "right thalamus") AnnotationAssertion( "FMA:258714") AnnotationAssertion( "uberon") @@ -215441,6 +215768,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right dorsal thalamus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (foramen of skull) @@ -215456,6 +215786,8 @@ AnnotationAssertion(Annotation( "UBERON:0013685") AnnotationAssertion(rdfs:label "foramen of skull") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical conduit space) @@ -215482,13 +215814,14 @@ AnnotationAssertion( "UBERON:0013687") AnnotationAssertion(rdfs:label "pericranium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tonsil germinal center) AnnotationAssertion(Annotation( "OBOL:automatic") "A germinal center that is part of a tonsil.") AnnotationAssertion( "consider adding related terms, e.g. secondary lymphoid tissue of tonsil") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "TS-1288") "The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288].") AnnotationAssertion( "CALOHA:TS-1288") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "CALOHA:TS-1288") "tonsil reaction center") @@ -215496,6 +215829,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil germinal center") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendix lymphoid tissue) @@ -215508,6 +215843,8 @@ AnnotationAssertion(Annotation( "UBERON:0013689") AnnotationAssertion(rdfs:label "appendix lymphoid tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain endothelium) @@ -215520,6 +215857,9 @@ AnnotationAssertion(Annotation( "UBERON:0013694") AnnotationAssertion(rdfs:label "brain endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colon endothelium) @@ -215535,6 +215875,8 @@ AnnotationAssertion(Annotation( "UBERON:0013695") AnnotationAssertion(rdfs:label "colon endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (tonsil epithelium) @@ -215548,6 +215890,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (exocrine pancreas epithelium) @@ -215559,11 +215903,12 @@ AnnotationAssertion(Annotation( "UBERON:0013697") AnnotationAssertion(rdfs:label "exocrine pancreas epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (strand of axillary hair) AnnotationAssertion(Annotation( "OBOL:automatic") "A strand of hair that is part of a axilla.") -AnnotationAssertion( ) AnnotationAssertion( "FMA:54253") AnnotationAssertion( "SCTID:280911007") AnnotationAssertion( "axilla hair") @@ -215574,6 +215919,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "strand of axillary hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axial musculature) @@ -215584,6 +215931,9 @@ AnnotationAssertion( "UBERON:0013700") AnnotationAssertion(rdfs:label "axial musculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (main body axis) @@ -215598,10 +215948,8 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (body proper) AnnotationAssertion(Annotation( "AEO:0000103") "The region of the organism associated with the visceral organs.") -AnnotationAssertion(Annotation( "FMA:231424") "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].") AnnotationAssertion( "AEO:0000103") AnnotationAssertion( "BTO:0001489") -AnnotationAssertion( "EMAPA:36031") AnnotationAssertion( "FMA:231424") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "AEO:0000103") "body") @@ -215620,6 +215968,7 @@ AnnotationAssertion( "UBERON:0013703") AnnotationAssertion(rdfs:label "integumentary projection") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (notochordal canal) @@ -215633,6 +215982,9 @@ AnnotationAssertion( "UBERON:0013704") AnnotationAssertion(rdfs:label "notochordal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (notochordal fluid) @@ -215644,6 +215996,9 @@ AnnotationAssertion( "Distinct feature of coelocanths") AnnotationAssertion(rdfs:label "notochordal fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metaphysis of humerus) @@ -215656,6 +216011,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metaphysis of humerus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metaphysis of tibia) @@ -215669,6 +216027,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "metaphysis of tibia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diaphysis of metacarpal bone) @@ -215683,6 +216044,9 @@ AnnotationAssertion( "UBERON:0013752") AnnotationAssertion(rdfs:label "diaphysis of metacarpal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (integumentary system layer) @@ -215695,11 +216059,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integumentary system layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arterial blood) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood that is part of a artery.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006188") AnnotationAssertion( "FMA:83066") AnnotationAssertion(Annotation( "FMA:83066") "arterial blood") AnnotationAssertion(Annotation( "FMA:83066") "blood in artery") @@ -215709,11 +216074,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous blood) AnnotationAssertion(Annotation( "OBOL:automatic") "A blood that is part of a vein.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006187") AnnotationAssertion( "FMA:83067") AnnotationAssertion(Annotation( "FMA:83067") "blood in vein") AnnotationAssertion(Annotation( "FMA:83067") "portion of venous blood") @@ -215722,6 +216088,8 @@ AnnotationAssertion( "UBERON:0013756") AnnotationAssertion(rdfs:label "venous blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (capillary blood) @@ -215735,6 +216103,8 @@ AnnotationAssertion( "UBERON:0013757") AnnotationAssertion(rdfs:label "capillary blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical os) @@ -215746,11 +216116,13 @@ AnnotationAssertion( "UBERON:0013758") AnnotationAssertion(rdfs:label "cervical os") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (external cervical os) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Opening of uterine cervix into the vagina.") -AnnotationAssertion(Annotation( "Wikipedia:External_orifice_of_the_uterus") "The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus].") AnnotationAssertion( "FMA:76836") AnnotationAssertion( "NCIT:C32491") AnnotationAssertion( "SCTID:362255005") @@ -215765,7 +216137,9 @@ AnnotationAssertion( "external cervical os") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215789,6 +216163,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive system element) @@ -215803,6 +216179,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "digestive system element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (great vessel of heart) @@ -215832,11 +216210,12 @@ AnnotationAssertion( "UBERON:0013769") AnnotationAssertion(rdfs:label "uterine lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left nipple) AnnotationAssertion(Annotation( "OBOL:automatic") "A nipple that is in_the_left_side_of a body proper.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:223695") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0013772") @@ -215844,11 +216223,13 @@ AnnotationAssertion( "left nipple") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right nipple) AnnotationAssertion(Annotation( "OBOL:automatic") "A nipple that is in_the_right_side_of a body proper.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( "FMA:223693") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0013773") @@ -215856,6 +216237,9 @@ AnnotationAssertion( "right nipple") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (diaphysis of metatarsal bone) @@ -215870,6 +216254,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diaphysis of metatarsal bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of palmar/plantar part of autopod) @@ -215878,6 +216265,8 @@ AnnotationAssertion( "UBERON:0013776") AnnotationAssertion(rdfs:label "skin of palmar/plantar part of autopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of sole of pes) @@ -215892,6 +216281,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of sole of pes") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (piriform cortex layer 3) @@ -215904,6 +216296,7 @@ AnnotationAssertion( "NLXANAT:091009") "layer 3 of piriform cortex") AnnotationAssertion( "UBERON:0014283") AnnotationAssertion(rdfs:label "piriform cortex layer 3") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -215921,8 +216314,10 @@ AnnotationAssertion( "paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP]") AnnotationAssertion(rdfs:label "future telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of hairs on head or neck) @@ -215931,6 +216326,8 @@ AnnotationAssertion( "UBERON:0014382") AnnotationAssertion(rdfs:label "collection of hairs on head or neck") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme derived from neural crest) @@ -215944,11 +216341,12 @@ AnnotationAssertion( "UBERON:0014387") AnnotationAssertion(rdfs:label "mesenchyme derived from neural crest") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (kidney collecting duct epithelium) AnnotationAssertion(Annotation( "MGI:anna") Annotation( "MP:0011843") "The simple cuboidal epithelium lining the lumen of kidney collecting ducts.") -AnnotationAssertion( "In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37885") AnnotationAssertion( "collecting duct of renal tubule epithelium") AnnotationAssertion( "epithelium of collecting duct of renal tubule") @@ -215959,12 +216357,13 @@ AnnotationAssertion( "kidney collecting duct epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gustatory papilla of tongue) AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0006256") "A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae.") -AnnotationAssertion( "FMA:54822") AnnotationAssertion( "gustatory papilla") AnnotationAssertion( "taste papilla") AnnotationAssertion( "uberon") @@ -215973,6 +216372,8 @@ AnnotationAssertion(Annotation( "UBERON:0014389") AnnotationAssertion(rdfs:label "gustatory papilla of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle layer of ileum) @@ -215987,11 +216388,12 @@ AnnotationAssertion(Annotation( "UBERON:0014390") AnnotationAssertion(rdfs:label "muscle layer of ileum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (palmar/plantar sweat gland) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A sweat gland that is part of the skin of the palmar part of the manus or plantar part of the pes.") -AnnotationAssertion(Annotation( "MP:0000675") "in mice these are the only sweat glands present") AnnotationAssertion( "palm sweat gland") AnnotationAssertion( "palmar eccrine sweat gland") AnnotationAssertion( "sweat gland of palmar part of manus") @@ -216003,11 +216405,11 @@ AnnotationAssertion( "palmar/plantar sweat gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sweat of palm) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Sweat that is produced by the glands on the palmar and plantar surfaces.") -AnnotationAssertion( "serves a purpose of increasing friction on the palms of hands or the pads of paws[WP]") AnnotationAssertion( "FMA:63084") AnnotationAssertion(Annotation( "FMA:63084") "palm sweat") AnnotationAssertion(Annotation( "FMA:63084") "palmar sweat") @@ -216015,6 +216417,8 @@ AnnotationAssertion( "UBERON:0014392") AnnotationAssertion(rdfs:label "sweat of palm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sweat of axilla) @@ -216025,6 +216429,8 @@ AnnotationAssertion( "UBERON:0014393") AnnotationAssertion(rdfs:label "sweat of axilla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal mesopodial bone) @@ -216033,19 +216439,20 @@ AnnotationAssertion( "UBERON:0014395") AnnotationAssertion(rdfs:label "proximal mesopodial bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory muscle) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Muscle that is part of the respiratory system.") -AnnotationAssertion( "this class may be merged with 'respiratory system muscle'; check intercostals") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D012132") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0014398") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sinusoidal space) @@ -216058,7 +216465,9 @@ AnnotationAssertion( "UBERON:0014399") AnnotationAssertion(rdfs:label "sinusoidal space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic sinusoidal space) @@ -216069,11 +216478,12 @@ AnnotationAssertion( "UBERON:0014400") AnnotationAssertion(rdfs:label "hepatic sinusoidal space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal venous blood vessel) AnnotationAssertion(Annotation( "MGI:csmith") "Any member of the network of tubes that return blood from the renal tissues to the systemic circulation.") -AnnotationAssertion(Annotation( "MA") "we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta") AnnotationAssertion( "EMAPA:31450") AnnotationAssertion( "MA:0002591") AnnotationAssertion(Annotation( "MA:0002591") "kidney venous blood vessel") @@ -216084,6 +216494,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal venous blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (sex-specific anatomical structure) @@ -216097,6 +216509,8 @@ AnnotationAssertion( "UBERON:0014402") AnnotationAssertion(rdfs:label "sex-specific anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male anatomical structure) @@ -216109,6 +216523,8 @@ AnnotationAssertion(Annotation( "UBERON:0014403") AnnotationAssertion(rdfs:label "male anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female anatomical structure) @@ -216118,6 +216534,8 @@ AnnotationAssertion( "UBERON:0014404") AnnotationAssertion(rdfs:label "female anatomical structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tongue taste bud) @@ -216129,6 +216547,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tongue taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gustatory epithelium of tongue) @@ -216141,6 +216561,8 @@ AnnotationAssertion( "UBERON:0014452") AnnotationAssertion(rdfs:label "gustatory epithelium of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (gustatory epithelium of palate) @@ -216150,12 +216572,14 @@ AnnotationAssertion( "UBERON:0014453") AnnotationAssertion(rdfs:label "gustatory epithelium of palate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral abdominal adipose tissue) AnnotationAssertion(Annotation( "CALOHA:paula") Annotation( "MGI:csmith") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/259") "Subcutaneous adipose tissue that is located in the peritoneal cavity.") -AnnotationAssertion(Annotation( "BTO:0004041") "Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041].") AnnotationAssertion( "BTO:0004041") AnnotationAssertion( "CALOHA:TS-2405") AnnotationAssertion( "uberon") @@ -216168,6 +216592,9 @@ AnnotationAssertion(Annotation( "UBERON:0014454") AnnotationAssertion(rdfs:label "visceral abdominal adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcutaneous abdominal adipose tissue) @@ -216180,12 +216607,13 @@ AnnotationAssertion( "UBERON:0014455") AnnotationAssertion(rdfs:label "subcutaneous abdominal adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cardiac ganglion) AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0003685") "Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/cardiac+ganglion") "Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion].") AnnotationAssertion( "EMAPA:36644") AnnotationAssertion( "FMA:77582") AnnotationAssertion( "SCTID:57098005") @@ -216200,7 +216628,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subarachnoid fissure) @@ -216256,6 +216685,9 @@ AnnotationAssertion( "UBERON:0014530") AnnotationAssertion(rdfs:label "white matter lamina of neuraxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter lamina of diencephalon) @@ -216266,6 +216698,8 @@ AnnotationAssertion( "UBERON:0014531") AnnotationAssertion(rdfs:label "white matter lamina of diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter lamina of cerebral hemisphere) @@ -216276,6 +216710,8 @@ AnnotationAssertion( "UBERON:0014532") AnnotationAssertion(rdfs:label "white matter lamina of cerebral hemisphere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subdivision of spinal cord central canal) @@ -216287,7 +216723,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "subdivision of spinal cord central canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter lamina of cerebellum) @@ -216311,6 +216750,8 @@ AnnotationAssertion(Annotation( "UBERON:0014540") AnnotationAssertion(rdfs:label "white matter lamina of cerebellum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic division of spinal cord central canal) @@ -216328,6 +216769,7 @@ AnnotationAssertion( "thoracic division of spinal cord central canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "NIFSTD") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical division of cord spinal central canal) @@ -216342,6 +216784,7 @@ AnnotationAssertion( "cervical division of cord spinal central canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "NIFSTD") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic spinal cord dorsal horn) @@ -216357,6 +216800,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic spinal cord dorsal horn") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic spinal cord ventral horn) @@ -216373,6 +216818,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic spinal cord ventral horn") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical spinal cord gray matter) @@ -216387,6 +216834,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical spinal cord gray matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical spinal cord white matter) @@ -216401,6 +216850,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical spinal cord white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (accessory nerve root) @@ -216430,6 +216881,8 @@ AnnotationAssertion(Annotation( "UBERON:0014615") AnnotationAssertion(rdfs:label "accessory nerve root") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical spinal cord dorsal horn) @@ -216445,13 +216898,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical spinal cord dorsal horn") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical spinal cord ventral horn) AnnotationAssertion(Annotation( "OBOL:automatic") "A ventral horn of spinal cord that is part of a cervical spinal cord.") AnnotationAssertion( ) AnnotationAssertion( "BIRNLEX:1680") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D066151") AnnotationAssertion( "SCTID:174363005") AnnotationAssertion(Annotation( "BIRNLEX:1680") "UMLS:C0228615") AnnotationAssertion(Annotation( "BIRNLEX:1680") "UMLS:C1278740") @@ -216462,6 +216916,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cervical spinal cord ventral horn") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal nerve root of cervical spinal cord) @@ -216475,7 +216931,9 @@ AnnotationAssertion(Annotation( "UBERON:0014635") AnnotationAssertion(rdfs:label "dorsal nerve root of cervical spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "NIFSTD") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic spinal cord gray matter) @@ -216490,6 +216948,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic spinal cord gray matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic spinal cord white matter) @@ -216505,6 +216965,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "thoracic spinal cord white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontal sulcus) @@ -216518,6 +216980,8 @@ AnnotationAssertion( "UBERON:0014639") AnnotationAssertion(rdfs:label "frontal sulcus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of medulla oblongata) @@ -216535,6 +216999,9 @@ AnnotationAssertion(Annotation( "UBERON:0014649") AnnotationAssertion(rdfs:label "white matter of medulla oblongata") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (angular vein) @@ -216547,8 +217014,8 @@ AnnotationAssertion( "UBERON:0014686") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "angular vein") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (temporal sulcus) @@ -216563,6 +217030,8 @@ AnnotationAssertion( "UBERON:0014687") AnnotationAssertion(rdfs:label "temporal sulcus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deep auricular artery) @@ -216576,6 +217045,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "deep auricular artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -216589,6 +217060,7 @@ AnnotationAssertion( "UBERON:0014699") AnnotationAssertion(rdfs:label "extraembryonic venous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VHOG") ) # Class: (extraembryonic vascular system) @@ -216601,6 +217073,9 @@ AnnotationAssertion( "UBERON:0014701") AnnotationAssertion(rdfs:label "extraembryonic vascular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontonasal process epithelium) @@ -216612,6 +217087,9 @@ AnnotationAssertion( "frontonasal process epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (anal membrane ectodermal component) @@ -216623,6 +217101,9 @@ AnnotationAssertion( "UBERON:0014703") AnnotationAssertion(rdfs:label "anal membrane ectodermal component") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pleuroperitoneal canal lumen) @@ -216634,7 +217115,9 @@ AnnotationAssertion( "UBERON:0014704") AnnotationAssertion(rdfs:label "pleuroperitoneal canal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (median lingual swelling epithelium) @@ -216647,6 +217130,10 @@ AnnotationAssertion( "median lingual swelling epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (primitive renal collecting duct system) @@ -216659,6 +217146,7 @@ AnnotationAssertion( "UBERON:0014706") AnnotationAssertion(rdfs:label "primitive renal collecting duct system") SubClassOf(Annotation( "EHDAA2") ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (interlobular duct) @@ -216674,6 +217162,8 @@ AnnotationAssertion( "interlobular duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucous acinus) @@ -216685,6 +217175,8 @@ AnnotationAssertion( "UBERON:0014717") AnnotationAssertion(rdfs:label "mucous acinus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intralobular duct) @@ -216698,6 +217190,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intralobular duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interlobar duct) @@ -216708,60 +217202,8 @@ AnnotationAssertion( "interlobar duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) - -# Class: (crus of diaphragm) - -AnnotationAssertion(Annotation( "PMID:23586979") "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta.") -AnnotationAssertion( "EHDAA2:0000597") -AnnotationAssertion( "EMAPA:17703") -AnnotationAssertion( "SCTID:244668003") -AnnotationAssertion( "VHOG:0001546") -AnnotationAssertion( "Wikipedia:Crus_of_diaphragm") -AnnotationAssertion(Annotation( "PMID:23586979") "crural diaphragm") -AnnotationAssertion( "uberon") -AnnotationAssertion(Annotation( "Wikipedia:Crus_of_diaphragm") "crura of the diaphragm") -AnnotationAssertion(Annotation( "Wikipedia:Crus_of_diaphragm") "crus of the diaphragm") -AnnotationAssertion(Annotation( ) "diaphragm crura") -AnnotationAssertion(Annotation( "Wikipedia:Crus_of_diaphragm") "diaphragmatic crura") -AnnotationAssertion( "UBERON:0014765") -AnnotationAssertion(rdfs:comment "Classification notes: May be considered an external sphincter[PMID:8224664]") -AnnotationAssertion(rdfs:label "crus of diaphragm") -SubClassOf( ) -SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (right crus of diaphragm) - -AnnotationAssertion(Annotation( "OBOL:automatic") "A crus of diaphragm that is in_the_right_side_of a diaphragm.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "FMA:58286") -AnnotationAssertion( "SCTID:362690009") -AnnotationAssertion(Annotation( "FMA:58286") Annotation( "FMA:TA") Annotation( ) "crus dextrum (Diaphragma)") -AnnotationAssertion(Annotation( "FMA:58286") Annotation( "FMA:TA") Annotation( ) "crus dextrum diaphragmatis") -AnnotationAssertion(Annotation( "FMA:58286") "external sphincter of esophagus") -AnnotationAssertion(Annotation( "FMA:58286") "right crus of diaphragm") -AnnotationAssertion(Annotation( "FMA:58286") "right crus of lumbar part of diaphragm") -AnnotationAssertion( "uberon") -AnnotationAssertion( "UBERON:0014766") -AnnotationAssertion(rdfs:label "right crus of diaphragm") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (left crus of diaphragm) - -AnnotationAssertion(Annotation( "OBOL:automatic") "A crus of diaphragm that is in_the_left_side_of a diaphragm.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) -AnnotationAssertion( "FMA:58287") -AnnotationAssertion( "SCTID:244937004") -AnnotationAssertion(Annotation( "FMA:58287") Annotation( "FMA:TA") Annotation( ) "crus sinistrum (Diaphragma)") -AnnotationAssertion(Annotation( "FMA:58287") Annotation( "FMA:TA") Annotation( ) "crus sinistrum diaphragmatis") -AnnotationAssertion(Annotation( "FMA:58287") "left crus of diaphragm") -AnnotationAssertion(Annotation( "FMA:58287") "left crus of lumbar part of diaphragm") -AnnotationAssertion( "uberon") -AnnotationAssertion( "UBERON:0014767") -AnnotationAssertion(rdfs:label "left crus of diaphragm") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (palpebral vein) @@ -216774,19 +217216,22 @@ AnnotationAssertion(Annotation( "UBERON:0014769") AnnotationAssertion(rdfs:label "palpebral vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (palpebral artery) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An artery that supplies blood to an eyelid.") -AnnotationAssertion( "In humans, the eyelids are supplied with blood by two arches on each upper and lower lid. The arches are formed by anastamoses of the lateral palpebral arteries and medial palpebral arteries, branching off from the lacrimal artery and ophthalmic artery, respectively. In amphibians, the eyelids may be supplied by branches of the lateral pretrosal arteries.[cjm]") AnnotationAssertion( "SCTID:148571007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0014770") AnnotationAssertion(rdfs:label "palpebral artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prosomere) @@ -216800,6 +217245,8 @@ AnnotationAssertion( "UBERON:0014775") AnnotationAssertion(rdfs:label "prosomere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain neuromere) @@ -216817,6 +217264,8 @@ AnnotationAssertion(Annotation( "UBERON:0014776") AnnotationAssertion(rdfs:label "midbrain neuromere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal neuromere) @@ -216830,6 +217279,8 @@ AnnotationAssertion(Annotation( "UBERON:0014777") AnnotationAssertion(rdfs:label "spinal neuromere") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cloacal muscle) @@ -216838,6 +217289,9 @@ AnnotationAssertion( "UBERON:0014783") AnnotationAssertion(rdfs:label "cloacal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lingual septum) @@ -216854,6 +217308,8 @@ AnnotationAssertion(Annotation( "UBERON:0014790") AnnotationAssertion(rdfs:label "lingual septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of forelimb stylopod) @@ -216867,6 +217323,8 @@ AnnotationAssertion(Annotation( "UBERON:0014791") AnnotationAssertion(rdfs:label "musculature of forelimb stylopod") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pelvic complex) @@ -216881,6 +217339,8 @@ AnnotationAssertion( "UBERON:0014792") AnnotationAssertion(rdfs:label "musculature of pelvic complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (musculature of pectoral complex) @@ -216897,6 +217357,8 @@ AnnotationAssertion( "UBERON:0014793") AnnotationAssertion(rdfs:label "musculature of pectoral complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pectoral appendage muscle) @@ -216905,6 +217367,7 @@ AnnotationAssertion( "UBERON:0014794") AnnotationAssertion(rdfs:label "pectoral appendage muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (pelvic appendage muscle) @@ -216914,6 +217377,7 @@ AnnotationAssertion( "UBERON:0014795") AnnotationAssertion(rdfs:label "pelvic appendage muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "prolog") ObjectSomeValuesFrom( )) # Class: (brainstem white matter) @@ -216932,6 +217396,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brainstem white matter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle organ, vertebrate) @@ -216962,8 +217428,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle organ, vertebrate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (primordial vasculature) @@ -216975,12 +217446,13 @@ AnnotationAssertion( "UBERON:0014903") AnnotationAssertion(rdfs:label "primordial vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intersomitic vessel) AnnotationAssertion(Annotation( "MGI:anna") "One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites.") -AnnotationAssertion(Annotation( "ZFA:0001285, ZFIN:ZDB-PUB-030908-4") "Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4].") AnnotationAssertion( "EFO:0003664") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37389") AnnotationAssertion( "TAO:0001285") @@ -217016,14 +217488,15 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "perivascular space") AnnotationAssertion( "https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex marginal layer) AnnotationAssertion(Annotation( "MP:0000792") Annotation( "http://orcid.org/0000-0002-6601-2165") "Developing superficial cortical layer located just under the pia matter, develops from the marginal layer of the neural tube and becomes cortical layer I.") -AnnotationAssertion( "in humans develops into cortical layer I") -AnnotationAssertion(Annotation( "EMAPA") "EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2") AnnotationAssertion(Annotation( "BRAINSPAN:BRAINSPAN") Annotation( "MP:0000792") Annotation( ) "MZ") AnnotationAssertion(Annotation( "PBA:294021774") "marginal zone") AnnotationAssertion( "EMAPA:17546") @@ -217042,7 +217515,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (layer of developing cerebral cortex) -AnnotationAssertion( "these layers primarily refer to the mammalian future neocortex") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0014950") AnnotationAssertion(rdfs:label "layer of developing cerebral cortex") @@ -217058,7 +217530,7 @@ AnnotationAssertion( "UBERON:0015004") AnnotationAssertion(rdfs:label "tibia endochondral element") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical vertebra endochondral element) @@ -217071,6 +217543,9 @@ AnnotationAssertion( "cervical vertebra endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic vertebra endochondral element) @@ -217082,6 +217557,10 @@ AnnotationAssertion( "thoracic vertebra endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibula endochondral element) @@ -217092,13 +217571,12 @@ AnnotationAssertion( "UBERON:0015013") AnnotationAssertion(rdfs:label "fibula endochondral element") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (rib endochondral element) AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern") "A rib bone or its cartilage or pre-cartilage precursor.") -AnnotationAssertion( "Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern") "rib skeletal element") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern") "rib element") AnnotationAssertion( "uberon") @@ -217117,6 +217595,7 @@ AnnotationAssertion( "forelimb endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb endochondral element) @@ -217128,6 +217607,7 @@ AnnotationAssertion( "hindlimb endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (phalanx endochondral element) @@ -217139,7 +217619,7 @@ AnnotationAssertion( "UBERON:0015023") AnnotationAssertion(rdfs:label "phalanx endochondral element") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -217153,6 +217633,9 @@ AnnotationAssertion( "manual digit phalanx endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -217166,6 +217649,9 @@ AnnotationAssertion( "pedal digit phalanx endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -217179,6 +217665,9 @@ AnnotationAssertion( "pedal digit metatarsal endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit metacarpus endochondral element) @@ -217191,6 +217680,9 @@ AnnotationAssertion( "manual digit metacarpus endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (carpus endochondral element) @@ -217203,6 +217695,8 @@ AnnotationAssertion( "carpus endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tarsus endochondral element) @@ -217215,6 +217709,8 @@ AnnotationAssertion( "tarsus endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (femur endochondral element) @@ -217226,9 +217722,8 @@ AnnotationAssertion( "UBERON:0015052") AnnotationAssertion(rdfs:label "femur endochondral element") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (humerus endochondral element) @@ -217239,8 +217734,7 @@ AnnotationAssertion( "UBERON:0015053") AnnotationAssertion(rdfs:label "humerus endochondral element") EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac endochondral element) @@ -217252,6 +217746,8 @@ AnnotationAssertion( "UBERON:0015054") AnnotationAssertion(rdfs:label "iliac endochondral element") EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -217264,6 +217760,8 @@ AnnotationAssertion( "UBERON:0015056") AnnotationAssertion(rdfs:label "ischial endochondral element") EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -217301,6 +217799,7 @@ AnnotationAssertion( "UBERON:0015060") AnnotationAssertion(rdfs:label "sphenoid endochondral element") EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -217314,26 +217813,29 @@ AnnotationAssertion( "limb endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (autopod endochondral element) AnnotationAssertion(Annotation( "OBOL:automatic") "An endochondral element that is part of a autopod region.") -AnnotationAssertion( ) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015063") AnnotationAssertion(rdfs:label "autopod endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "cjm") ObjectSomeValuesFrom( )) # Class: (autopod cartilage) AnnotationAssertion(Annotation( "OBOL:automatic") "An autopod endochondral element that is composed primarily of cartilage tissue.") -AnnotationAssertion( ) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015064") AnnotationAssertion(rdfs:label "autopod cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal carpal endochondral element) @@ -217344,7 +217846,8 @@ AnnotationAssertion(Annotation( "UBERON:0015078") AnnotationAssertion(rdfs:label "proximal carpal endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (proximal carpal cartilage) @@ -217353,7 +217856,9 @@ AnnotationAssertion( "UBERON:0015079") AnnotationAssertion(rdfs:label "proximal carpal cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal carpal bone pre-cartilage condensation) @@ -217363,7 +217868,8 @@ AnnotationAssertion( "UBERON:0015080") AnnotationAssertion(rdfs:label "proximal carpal bone pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (proximal tarsal endochondral element) @@ -217373,7 +217879,8 @@ AnnotationAssertion(Annotation( "UBERON:0015081") AnnotationAssertion(rdfs:label "proximal tarsal endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) # Class: (proximal tarsal cartilage) @@ -217382,7 +217889,9 @@ AnnotationAssertion( "UBERON:0015082") AnnotationAssertion(rdfs:label "proximal tarsal cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal tarsal bone pre-cartilage condensation) @@ -217392,6 +217901,8 @@ AnnotationAssertion( "UBERON:0015083") AnnotationAssertion(rdfs:label "proximal tarsal bone pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (subepicardial layer of epicardium) @@ -217402,21 +217913,25 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0015128") AnnotationAssertion(rdfs:label "subepicardial layer of epicardium") -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (epicardial fat) AnnotationAssertion(Annotation( "DOI:10.5935/abc.20130138") "Visceral intrapericardial fat contiguous with the myocardial surface.") AnnotationAssertion( "FMA:9871") -AnnotationAssertion( "SCTID:42267001") AnnotationAssertion( "epicardial adipose tissue") AnnotationAssertion( "pericardial adipose tissue") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015129") AnnotationAssertion(rdfs:label "epicardial fat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (connective tissue of prostate gland) @@ -217428,7 +217943,10 @@ AnnotationAssertion( "UBERON:0015130") AnnotationAssertion(rdfs:label "connective tissue of prostate gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autopod hair) @@ -217440,6 +217958,8 @@ AnnotationAssertion( "UBERON:0015144") AnnotationAssertion(rdfs:label "autopod hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pes hair) @@ -217452,6 +217972,8 @@ AnnotationAssertion( "UBERON:0015145") AnnotationAssertion(rdfs:label "pes hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus hair) @@ -217463,6 +217985,8 @@ AnnotationAssertion( "UBERON:0015146") AnnotationAssertion(rdfs:label "manus hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pinna hair) @@ -217473,6 +217997,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pinna hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail hair) @@ -217483,6 +218009,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tail hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal hair) @@ -217495,24 +218023,24 @@ AnnotationAssertion(Annotation( "UBERON:0015150") AnnotationAssertion(rdfs:label "dorsal hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland of ocular region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/614") "A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.") -AnnotationAssertion( "the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]") -AnnotationAssertion( "the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]") AnnotationAssertion( "ocular gland") AnnotationAssertion( "uberon") AnnotationAssertion( "orbital gland") AnnotationAssertion( "UBERON:0015152") AnnotationAssertion(rdfs:label "gland of ocular region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "inferred") ObjectSomeValuesFrom( )) # Class: (lateral gland of orbital region) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A gland that is located in or around the ocular region, nearer the outer canthi.") -AnnotationAssertion( "The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104") AnnotationAssertion( "lateral ocular gland") AnnotationAssertion( "lateral orbital gland") AnnotationAssertion( "uberon") @@ -217533,19 +218061,20 @@ AnnotationAssertion( "UBERON:0015155") AnnotationAssertion(rdfs:label "conjunctival space") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multi-unit eye) AnnotationAssertion(Annotation( "PMID:21062451") Annotation( "http://orcid.org/0000-0002-6601-2165") "An eye consisting of multiple light-sensing organs.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "present on tentacular crown") Annotation( "PMID:21062451") ) -AnnotationAssertion(Annotation( "present on mantle edge in arcacean Bivalvia") Annotation( "PMID:21062451") ) -AnnotationAssertion(Annotation( "The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species") Annotation( "PMID:21062451") ) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015165") AnnotationAssertion(rdfs:label "multi-unit eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endometrial blood vessel) @@ -217558,6 +218087,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endometrial blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somite border) @@ -217576,6 +218108,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "somite border") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somite boundary epithelium) @@ -217587,6 +218122,8 @@ AnnotationAssertion( "UBERON:0015179") AnnotationAssertion(rdfs:label "somite boundary epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck of tooth) @@ -217605,12 +218142,14 @@ AnnotationAssertion(Annotation( "UBERON:0015181") AnnotationAssertion(rdfs:label "neck of tooth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-connected functional system) AnnotationAssertion(Annotation( "AEO:0000093") Annotation( "AEO:JB") Annotation( "FBC:DOS") Annotation( "FBbt:00007278") "An anatomical group whose component structures share a common function.") AnnotationAssertion( "AEO:0000093") -AnnotationAssertion(Annotation( ) "FBbt:00007278") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015203") AnnotationAssertion(rdfs:label "non-connected functional system") @@ -217624,17 +218163,20 @@ AnnotationAssertion( "UBERON:0015204") AnnotationAssertion(rdfs:label "glandular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral structure) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any structure that is placed on one side of the left-right axis of a bilaterian.") -AnnotationAssertion( "This class is primarily to implement taxon constraints. It may be removed in the future.") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015212") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lateral structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (arcuate ligament) @@ -217646,12 +218188,14 @@ AnnotationAssertion( "UBERON:0015214") AnnotationAssertion(rdfs:label "arcuate ligament") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (circulatory organ) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.") AnnotationAssertion( "heart") -AnnotationAssertion( "SPD:0000130") AnnotationAssertion( "cardiac pump") AnnotationAssertion( "heart or heart like organ") AnnotationAssertion( "circulatory vessel") @@ -217667,18 +218211,18 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (nucleus of dorsal thalamus) AnnotationAssertion(Annotation( "OBOL:automatic") "A nucleus of brain that is part of a dorsal thalamus.") -AnnotationAssertion(Annotation( "Hagfish possess a habenular complex and separate nuclei in the dorsal thalamus") Annotation( "Butler, 1996, p. 303") ) AnnotationAssertion( "dorsal thalamic nucleus") AnnotationAssertion( "nucleus of thalamus proper") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015233") AnnotationAssertion(rdfs:label "nucleus of dorsal thalamus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pineal complex) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals.") -AnnotationAssertion( ) AnnotationAssertion( "TAO:0001359") AnnotationAssertion( "ZFA:0001359") AnnotationAssertion( "uberon") @@ -217697,6 +218241,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "digit skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas left lobe) @@ -217707,6 +218253,9 @@ AnnotationAssertion( "UBERON:0015280") AnnotationAssertion(rdfs:label "pancreas left lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pancreas right lobe) @@ -217717,6 +218266,9 @@ AnnotationAssertion( "UBERON:0015281") AnnotationAssertion(rdfs:label "pancreas right lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system basement membrane) @@ -217727,6 +218279,7 @@ AnnotationAssertion( "UBERON:0015329") AnnotationAssertion(rdfs:label "respiratory system basement membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) # Class: (heart plus pericardium) @@ -217751,6 +218304,9 @@ AnnotationAssertion( "UBERON:0015418") AnnotationAssertion(rdfs:label "urethra mesenchymal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteral valve) @@ -217763,6 +218319,9 @@ AnnotationAssertion( "UBERON:0015420") AnnotationAssertion(rdfs:label "ureteral valve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcutaneous lymph node) @@ -217773,6 +218332,9 @@ AnnotationAssertion( "UBERON:0015453") AnnotationAssertion(rdfs:label "subcutaneous lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (axilla skin) @@ -217787,6 +218349,8 @@ AnnotationAssertion( "UBERON:0015474") AnnotationAssertion(rdfs:label "axilla skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nose skin) @@ -217801,6 +218365,8 @@ AnnotationAssertion( "UBERON:0015476") AnnotationAssertion(rdfs:label "nose skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proper hepatic artery) @@ -217835,6 +218401,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left hepatic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -217853,6 +218421,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right hepatic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -217866,6 +218436,9 @@ AnnotationAssertion( "UBERON:0015485") AnnotationAssertion(rdfs:label "choledocho-duodenal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontal gyrus) @@ -217876,6 +218449,8 @@ AnnotationAssertion( "UBERON:0015593") AnnotationAssertion(rdfs:label "frontal gyrus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anal canal epithelium) @@ -217890,7 +218465,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anal canal epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue layer of ejaculatory duct) @@ -217902,6 +218479,9 @@ AnnotationAssertion( "UBERON:0015717") AnnotationAssertion(rdfs:label "smooth muscle tissue layer of ejaculatory duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heterogeneous tissue) @@ -217923,7 +218503,10 @@ AnnotationAssertion( "UBERON:0015766") AnnotationAssertion(rdfs:label "epithelium of duct of salivary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle layer in fatty layer of subcutaneous tissue) @@ -217935,11 +218518,12 @@ AnnotationAssertion( "UBERON:0015783") AnnotationAssertion(rdfs:label "smooth muscle layer in fatty layer of subcutaneous tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory segment of nasal mucosa) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The portion of the nasal mucosa that is part of the respiratory system.") -AnnotationAssertion(Annotation( "Wikipedia:Nasal_cavity") "lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose.") AnnotationAssertion( "FMA:77198") AnnotationAssertion(Annotation( "FMA:77198") Annotation( "FMA:TA") Annotation( ) "pars respiratoria tunicae mucosae nasi") AnnotationAssertion(Annotation( "FMA:77198") "respiratory zone of nasal mucosa") @@ -217947,17 +218531,21 @@ AnnotationAssertion( "UBERON:0015786") AnnotationAssertion(rdfs:label "respiratory segment of nasal mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (upper respiratory conduit) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any anatomical conduit which is part of the upper respiratory tract.") -AnnotationAssertion(Annotation( "FMA:265132") "Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132].") AnnotationAssertion( "FMA:265132") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "FMA:265132") "respiratory conduit") AnnotationAssertion( "UBERON:0015787") AnnotationAssertion(rdfs:label "upper respiratory conduit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory apparatus chamber) @@ -217966,12 +218554,12 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0015788") AnnotationAssertion(rdfs:label "olfactory apparatus chamber") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cranial or facial muscle) -AnnotationAssertion( "see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper") AnnotationAssertion( "EMAPA:25133") AnnotationAssertion( "MA:0000579") AnnotationAssertion(Annotation( "MA:0000579") "cranial/facial muscle") @@ -217995,6 +218583,8 @@ AnnotationAssertion(Annotation( "UBERON:0015790") AnnotationAssertion(rdfs:label "autopod skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digit connective tissue) @@ -218005,6 +218595,8 @@ AnnotationAssertion( "UBERON:0015791") AnnotationAssertion(rdfs:label "digit connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (left lung lobar bronchus epithelium) @@ -218016,6 +218608,9 @@ AnnotationAssertion( "UBERON:0015794") AnnotationAssertion(rdfs:label "left lung lobar bronchus epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right lung lobar bronchus epitheium) @@ -218026,6 +218621,9 @@ AnnotationAssertion( "UBERON:0015795") AnnotationAssertion(rdfs:label "right lung lobar bronchus epitheium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver blood vessel) @@ -218037,6 +218635,9 @@ AnnotationAssertion(Annotation( "UBERON:0015796") AnnotationAssertion(rdfs:label "liver blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ear epithelium) @@ -218047,6 +218648,8 @@ AnnotationAssertion( "UBERON:0015807") AnnotationAssertion(rdfs:label "ear epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye epithelium) @@ -218057,6 +218660,9 @@ AnnotationAssertion( "UBERON:0015808") AnnotationAssertion(rdfs:label "eye epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (middle ear epithelium) @@ -218067,6 +218673,8 @@ AnnotationAssertion( "UBERON:0015813") AnnotationAssertion(rdfs:label "middle ear epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer ear epithelium) @@ -218077,6 +218685,8 @@ AnnotationAssertion( "UBERON:0015814") AnnotationAssertion(rdfs:label "outer ear epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (foregut epithelium) @@ -218087,6 +218697,8 @@ AnnotationAssertion( "UBERON:0015833") AnnotationAssertion(rdfs:label "foregut epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duodenum lamina propria) @@ -218103,7 +218715,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duodenum lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (visceral abdominal lymph node) @@ -218123,11 +218735,12 @@ AnnotationAssertion( "UBERON:0015870") AnnotationAssertion(rdfs:label "lymph node of head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial lymph node) AnnotationAssertion(Annotation( "Wikipedia:Facial_lymph_nodes") Annotation( "http://www.bartleby.com/107/177.html") "Any of the lymph nodes that are part of a face.") -AnnotationAssertion( "In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein.") AnnotationAssertion( "FMA:61222") AnnotationAssertion( "SCTID:279139005") AnnotationAssertion( "Wikipedia:Facial_lymph_nodes") @@ -218136,6 +218749,8 @@ AnnotationAssertion( "UBERON:0015871") AnnotationAssertion(rdfs:label "facial lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (superficial lymph node) @@ -218146,6 +218761,8 @@ AnnotationAssertion( "UBERON:0015917") AnnotationAssertion(rdfs:label "superficial lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deep lymph node) @@ -218155,6 +218772,8 @@ AnnotationAssertion( "UBERON:0015918") AnnotationAssertion(rdfs:label "deep lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node of lower limb) @@ -218165,6 +218784,8 @@ AnnotationAssertion( "UBERON:0016398") AnnotationAssertion(rdfs:label "lymph node of lower limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node of upper limb) @@ -218175,6 +218796,8 @@ AnnotationAssertion( "UBERON:0016399") AnnotationAssertion(rdfs:label "lymph node of upper limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary capillary) @@ -218188,6 +218811,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary capillary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (male breast) @@ -218201,6 +218826,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "male breast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medullary cavity of long bone) @@ -218211,6 +218838,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "medullary cavity of long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (compact bone of long bone) @@ -218221,6 +218850,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "compact bone of long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (compact bone of diaphysis) @@ -218231,13 +218863,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "compact bone of diaphysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chest wall) AnnotationAssertion(Annotation( "FMA:50060") "Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall.") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37233") AnnotationAssertion( "FMA:50060") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D035441") AnnotationAssertion( "NCIT:C62484") AnnotationAssertion( "SCTID:181608004") AnnotationAssertion( "uberon") @@ -218245,6 +218879,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chest wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair of head) @@ -218257,6 +218893,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair of head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair of trunk) @@ -218268,6 +218906,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair of trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophageal hiatus) @@ -218281,6 +218921,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "esophageal hiatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver stroma) @@ -218294,11 +218937,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "liver stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (capsule of liver) AnnotationAssertion(Annotation( "Wikipedia:Fibrous_capsule_of_Glisson") "A collagenous capsule covering the external surface of the liver.") -AnnotationAssertion( "It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells.") AnnotationAssertion( "FMA:15813") AnnotationAssertion( "SCTID:362185005") AnnotationAssertion( "Wikipedia:Fibrous_capsule_of_Glisson") @@ -218316,6 +218961,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchial lymph node) @@ -218328,11 +218977,13 @@ AnnotationAssertion( "UBERON:0016481") AnnotationAssertion(rdfs:label "bronchial lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (auditory system) AnnotationAssertion(Annotation( "NLXANAT:090817") "Is the sensory system for the sense of hearing.") -AnnotationAssertion(Annotation( "FMA") "Auditory system is general anatomical term in FMA") AnnotationAssertion( "EMAPA:36002") AnnotationAssertion( "FMA:7192") AnnotationAssertion( "MA:0002443") @@ -218345,14 +218996,13 @@ AnnotationAssertion( "UBERON:0016490") AnnotationAssertion(rdfs:label "auditory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebral centrum element) AnnotationAssertion(Annotation( "VSAO:0000183") Annotation( "VSAO:curator") Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( "https://github.com/obophenotype/uberon/issues/207") Annotation( "https://github.com/obophenotype/uberon/issues/80") "Skeletal element that functionally replaces the notochord[VSAP,modified].") -AnnotationAssertion(Annotation( "2012-08-14") Annotation( "VSAO:0000183") Annotation( "VSAO") Annotation( "VSAO:curator") "Skeletal element that surrounds the notochord.[VSAO]") -AnnotationAssertion(Annotation( "MP:0000141,ISBN:0-683-40008-8,PMID:10572046") "the main cylindrical portion of the vertebra ventral to the vertebral canal") -AnnotationAssertion( "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.") AnnotationAssertion(Annotation( "VSAO:0000183") "centrum") AnnotationAssertion( "VSAO:0000183") AnnotationAssertion( "centrum of vertebra") @@ -218374,6 +219024,8 @@ AnnotationAssertion( "UBERON:0016502") AnnotationAssertion(rdfs:label "stomach fundus lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cavity of right ventricle) @@ -218386,6 +219038,8 @@ AnnotationAssertion( "UBERON:0016509") AnnotationAssertion(rdfs:label "cavity of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of male urethra) @@ -218398,6 +219052,8 @@ AnnotationAssertion( "UBERON:0016510") AnnotationAssertion(rdfs:label "epithelium of male urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of fundus of stomach) @@ -218409,6 +219065,8 @@ AnnotationAssertion( "UBERON:0016511") AnnotationAssertion(rdfs:label "lamina propria of fundus of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of duodenum) @@ -218421,6 +219079,8 @@ AnnotationAssertion( "UBERON:0016512") AnnotationAssertion(rdfs:label "lumen of duodenum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cavity of left atrium) @@ -218433,6 +219093,8 @@ AnnotationAssertion( "UBERON:0016513") AnnotationAssertion(rdfs:label "cavity of left atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cavity of left ventricle) @@ -218444,6 +219106,8 @@ AnnotationAssertion( "UBERON:0016514") AnnotationAssertion(rdfs:label "cavity of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscular layer of prostatic urethra) @@ -218457,6 +219121,9 @@ AnnotationAssertion( "UBERON:0016515") AnnotationAssertion(rdfs:label "muscular layer of prostatic urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lamina propria of prostatic urethra) @@ -218469,6 +219136,8 @@ AnnotationAssertion( "UBERON:0016516") AnnotationAssertion(rdfs:label "lamina propria of prostatic urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of jejunum) @@ -218481,6 +219150,8 @@ AnnotationAssertion( "UBERON:0016517") AnnotationAssertion(rdfs:label "lumen of jejunum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of female urethra) @@ -218493,6 +219164,8 @@ AnnotationAssertion( "UBERON:0016520") AnnotationAssertion(rdfs:label "epithelium of female urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cavity of right atrium) @@ -218504,6 +219177,8 @@ AnnotationAssertion( "UBERON:0016522") AnnotationAssertion(rdfs:label "cavity of right atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (frontal lobe) @@ -218544,7 +219219,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (lobe of cerebral hemisphere) AnnotationAssertion(Annotation( "FMA:61823") "Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified].") -AnnotationAssertion( ) AnnotationAssertion( "UBERON:0000322") AnnotationAssertion( "BIRNLEX:922") AnnotationAssertion( "BTO:0000445") @@ -218565,6 +219239,7 @@ AnnotationAssertion( "We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts.") AnnotationAssertion(rdfs:label "lobe of cerebral hemisphere") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of cerebral lobe) @@ -218574,6 +219249,8 @@ AnnotationAssertion( "UBERON:0016527") AnnotationAssertion(rdfs:label "white matter of cerebral lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of frontal lobe) @@ -218586,6 +219263,8 @@ AnnotationAssertion( "UBERON:0016528") AnnotationAssertion(rdfs:label "white matter of frontal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortex of cerebral lobe) @@ -218599,6 +219278,9 @@ AnnotationAssertion( "UBERON:0016529") AnnotationAssertion(rdfs:label "cortex of cerebral lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parietal cortex) @@ -218608,7 +219290,6 @@ AnnotationAssertion( "EMAPA:35667") AnnotationAssertion( "FMA:242203") AnnotationAssertion( "MA:0000916") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D010296") AnnotationAssertion( "NLX:79282") AnnotationAssertion( "SCTID:369217001") AnnotationAssertion( "neuronames:2473") @@ -218621,6 +219302,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "parietal cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of parietal lobe) @@ -218631,6 +219314,8 @@ AnnotationAssertion( "UBERON:0016531") AnnotationAssertion(rdfs:label "white matter of parietal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of temporal lobe) @@ -218641,6 +219326,8 @@ AnnotationAssertion( "UBERON:0016534") AnnotationAssertion(rdfs:label "white matter of temporal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of limbic lobe) @@ -218650,6 +219337,8 @@ AnnotationAssertion( "UBERON:0016536") AnnotationAssertion(rdfs:label "white matter of limbic lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (temporal cortex) @@ -218659,7 +219348,6 @@ AnnotationAssertion( "DMBA:16044") AnnotationAssertion( "FMA:242201") AnnotationAssertion( "MA:0000941") -AnnotationAssertion(Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D013702") AnnotationAssertion( "NLX:94939") AnnotationAssertion( "SCTID:362343001") AnnotationAssertion(Annotation( "FMA:242201") "cortex of temporal lobe") @@ -218670,6 +219358,8 @@ AnnotationAssertion(Annotation( "UBERON:0016538") AnnotationAssertion(rdfs:label "temporal cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limbic cortex) @@ -218681,6 +219371,8 @@ AnnotationAssertion(Annotation( "UBERON:0016542") AnnotationAssertion(rdfs:label "limbic cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal ectoderm) @@ -218692,6 +219384,10 @@ AnnotationAssertion( "UBERON:0016545") AnnotationAssertion(rdfs:label "pharyngeal ectoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central nervous system gray matter layer) @@ -218706,6 +219402,8 @@ AnnotationAssertion( "UBERON:0016548") AnnotationAssertion(rdfs:label "central nervous system gray matter layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central nervous system white matter layer) @@ -218718,13 +219416,15 @@ AnnotationAssertion( "UBERON:0016549") AnnotationAssertion(rdfs:label "central nervous system white matter layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord column) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0016550") AnnotationAssertion(rdfs:label "spinal cord column") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (phlegm) @@ -218736,6 +219436,8 @@ AnnotationAssertion( "UBERON:0016552") AnnotationAssertion(rdfs:label "phlegm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory system mucus) @@ -218744,6 +219446,8 @@ AnnotationAssertion( "UBERON:0016553") AnnotationAssertion(rdfs:label "respiratory system mucus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of midbrain) @@ -218758,6 +219462,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white matter of midbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral blood vessel) @@ -218766,7 +219472,8 @@ AnnotationAssertion( "UBERON:0016565") AnnotationAssertion(rdfs:label "cerebral blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pit) @@ -218788,6 +219495,9 @@ AnnotationAssertion( "UBERON:0016570") AnnotationAssertion(rdfs:label "lamina of gray matter of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (auditory hillocks, pharyngeal arch 1 derived) @@ -218796,6 +219506,9 @@ AnnotationAssertion( "UBERON:0016611") AnnotationAssertion(rdfs:label "auditory hillocks, pharyngeal arch 1 derived") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (auditory hillocks, pharyngeal arch 2 derived) @@ -218804,6 +219517,9 @@ AnnotationAssertion( "UBERON:0016612") AnnotationAssertion(rdfs:label "auditory hillocks, pharyngeal arch 2 derived") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal part of optic cup) @@ -218814,7 +219530,10 @@ AnnotationAssertion( "UBERON:0016854") AnnotationAssertion(rdfs:label "dorsal part of optic cup") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future central nervous system) @@ -218826,8 +219545,10 @@ AnnotationAssertion( "UBERON:0016879") AnnotationAssertion(rdfs:label "future central nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future nervous system) @@ -218840,20 +219561,21 @@ AnnotationAssertion( "future nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (shoulder joint) AnnotationAssertion(Annotation( "http://www.innerbody.com/image/skel17.html") "The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D012785") AnnotationAssertion( "SCTID:361835002") AnnotationAssertion( "joint of shoulder region") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0016884") AnnotationAssertion(rdfs:label "shoulder joint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of terminal part of digestive tract) @@ -218865,6 +219587,8 @@ AnnotationAssertion( "UBERON:0016885") AnnotationAssertion(rdfs:label "epithelium of terminal part of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle tissue of terminal part of digestive tract) @@ -218875,6 +219599,8 @@ AnnotationAssertion( "UBERON:0016886") AnnotationAssertion(rdfs:label "muscle tissue of terminal part of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire extraembryonic component) @@ -218910,6 +219636,8 @@ AnnotationAssertion( "UBERON:0016896") AnnotationAssertion(rdfs:label "periosteum of long bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (metaphysis of fibula) @@ -218921,6 +219649,9 @@ AnnotationAssertion( "UBERON:0016928") AnnotationAssertion(rdfs:label "metaphysis of fibula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin bony tubercle) @@ -218931,6 +219662,10 @@ AnnotationAssertion(Annotation( "UBERON:0017163") AnnotationAssertion(rdfs:label "skin bony tubercle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intertarsal sesamoid) @@ -218940,16 +219675,22 @@ AnnotationAssertion( "UBERON:0017261") AnnotationAssertion(rdfs:label "intertarsal sesamoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vomerine dentition) AnnotationAssertion(Annotation( "OBOL:automatic") "A set of teeth in which each tooth that attaches to a vomer.") -AnnotationAssertion( "AAO:0000635") AnnotationAssertion( "uberon") AnnotationAssertion( "vomerine teeth") AnnotationAssertion( "UBERON:0017615") AnnotationAssertion(rdfs:label "vomerine dentition") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paired venous dural sinus) @@ -218959,6 +219700,10 @@ AnnotationAssertion( "UBERON:0017635") AnnotationAssertion(rdfs:label "paired venous dural sinus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal body wall) @@ -218967,6 +219712,8 @@ AnnotationAssertion( "UBERON:0017649") AnnotationAssertion(rdfs:label "dorsal body wall") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (developing mesenchymal structure) @@ -218976,6 +219723,8 @@ AnnotationAssertion( "UBERON:0017650") AnnotationAssertion(rdfs:label "developing mesenchymal structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (salivary gland primordium) @@ -218984,8 +219733,9 @@ AnnotationAssertion( "UBERON:0017651") AnnotationAssertion(rdfs:label "salivary gland primordium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominal viscera) @@ -219000,6 +219750,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "abdominal viscera") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (proximal mesopodial endochondral element) @@ -219009,7 +219761,9 @@ AnnotationAssertion( "UBERON:0017750") AnnotationAssertion(rdfs:label "proximal mesopodial endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proximal mesopodial cartilage element) @@ -219018,6 +219772,8 @@ AnnotationAssertion( "UBERON:0017751") AnnotationAssertion(rdfs:label "proximal mesopodial cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (muscle layer of rectum) @@ -219032,6 +219788,8 @@ AnnotationAssertion( "UBERON:0018111") AnnotationAssertion(rdfs:label "muscle layer of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rectum smooth muscle tissue) @@ -219043,6 +219801,10 @@ AnnotationAssertion( "UBERON:0018112") AnnotationAssertion(rdfs:label "rectum smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left kidney interstitium) @@ -219054,6 +219816,8 @@ AnnotationAssertion( "UBERON:0018113") AnnotationAssertion(rdfs:label "left kidney interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right kidney interstitium) @@ -219065,6 +219829,8 @@ AnnotationAssertion( "UBERON:0018114") AnnotationAssertion(rdfs:label "right kidney interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left renal pelvis) @@ -219077,6 +219843,9 @@ AnnotationAssertion( "UBERON:0018115") AnnotationAssertion(rdfs:label "left renal pelvis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right renal pelvis) @@ -219089,6 +219858,9 @@ AnnotationAssertion( "UBERON:0018116") AnnotationAssertion(rdfs:label "right renal pelvis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left renal cortex interstitium) @@ -219098,6 +219870,8 @@ AnnotationAssertion( "UBERON:0018117") AnnotationAssertion(rdfs:label "left renal cortex interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (right renal cortex interstitium) @@ -219107,6 +219881,8 @@ AnnotationAssertion( "UBERON:0018118") AnnotationAssertion(rdfs:label "right renal cortex interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (left renal medulla interstitium) @@ -219116,6 +219892,8 @@ AnnotationAssertion( "UBERON:0018119") AnnotationAssertion(rdfs:label "left renal medulla interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (right renal medulla interstitium) @@ -219125,6 +219903,8 @@ AnnotationAssertion( "UBERON:0018120") AnnotationAssertion(rdfs:label "right renal medulla interstitium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (fibrocollagenous connective tissue) @@ -219133,6 +219913,8 @@ AnnotationAssertion( "UBERON:0018135") AnnotationAssertion(rdfs:label "fibrocollagenous connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (caudal vertebra endochondral element) @@ -219147,11 +219929,13 @@ AnnotationAssertion( "caudal vertebra endochondral element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transverse process of cervical vertebra) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A transverse process that is part of a cervical vertebra.") -AnnotationAssertion( "May be homologous with the cervical ribs of some vertebrates") AnnotationAssertion( "FMA:23894") AnnotationAssertion( "FMA:9913") AnnotationAssertion( "SCTID:280730000") @@ -219159,20 +219943,23 @@ AnnotationAssertion( "UBERON:0018143") AnnotationAssertion(rdfs:label "transverse process of cervical vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical rib) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A rib that is attached to a cervical vertebra.") AnnotationAssertion( "Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad]") AnnotationAssertion(Annotation( "should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116") ) -AnnotationAssertion( "May be homologous with the transverse processes of cervical vertebra") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37825") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "MESH:D057070") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0018144") AnnotationAssertion(rdfs:label "cervical rib") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of lower lip) @@ -219184,6 +219971,8 @@ AnnotationAssertion( "UBERON:0018150") AnnotationAssertion(rdfs:label "skin of lower lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of upper lip) @@ -219195,6 +219984,9 @@ AnnotationAssertion( "UBERON:0018151") AnnotationAssertion(rdfs:label "skin of upper lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ligament of middle ear) @@ -219203,6 +219995,8 @@ AnnotationAssertion( "UBERON:0018154") AnnotationAssertion(rdfs:label "ligament of middle ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary part of lymphatic system) @@ -219215,6 +220009,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary part of lymphatic system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary lymphatic vessel) @@ -219229,6 +220028,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -219243,6 +220045,7 @@ AnnotationAssertion( "axillary sweat gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "ISBN:0123813611") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stroma of pancreas) @@ -219255,16 +220058,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stroma of pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (capsule of pancreas) AnnotationAssertion(Annotation( "ISBN:0123813611") "A capsule that divides the parenchyma of the pancreas into lobes and lobules.") -AnnotationAssertion( "typically thin but can thicken with age") AnnotationAssertion( "pancreatic capsule") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0018235") AnnotationAssertion(rdfs:label "capsule of pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rhombomere boundary) @@ -219274,7 +220080,10 @@ AnnotationAssertion( "UBERON:0018239") AnnotationAssertion(rdfs:label "rhombomere boundary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thymic artery) @@ -219291,6 +220100,8 @@ AnnotationAssertion( "The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP]") AnnotationAssertion(rdfs:label "thymic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (thyroid vein) @@ -219302,6 +220113,8 @@ AnnotationAssertion( "UBERON:0018246") AnnotationAssertion(rdfs:label "thyroid vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical thymic artery) @@ -219310,23 +220123,25 @@ AnnotationAssertion( "UBERON:0018247") AnnotationAssertion(rdfs:label "cervical thymic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meningeal vein) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "One of the veins draining a meninix.") -AnnotationAssertion( "In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.") AnnotationAssertion( "FMA:50839") AnnotationAssertion( "SCTID:84842006") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0018251") AnnotationAssertion(rdfs:label "meningeal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (internal pudendal vein) AnnotationAssertion(Annotation( "Wikipedia:Internal_pudendal_veins") "Accompanying vein of internal pudendal artery.") AnnotationAssertion( ) -AnnotationAssertion( "In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins") AnnotationAssertion( "FMA:18917") AnnotationAssertion( "SCTID:14885008") AnnotationAssertion( "Wikipedia:Internal_pudendal_veins") @@ -219347,7 +220162,6 @@ AnnotationAssertion( ) AnnotationAssertion( "EHDAA2:0001842") AnnotationAssertion( "EMAPA:35578") -AnnotationAssertion( "MA:0000165") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0018254") AnnotationAssertion( ) @@ -219370,6 +220184,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "jejunal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal vein) @@ -219382,7 +220199,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lacrimal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosa of digestive tract) @@ -219391,11 +220210,12 @@ AnnotationAssertion( "UBERON:0018257") AnnotationAssertion(rdfs:label "submucosa of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of muscle tissue) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Any organ component layer that consists of muscle tissue.") -AnnotationAssertion(Annotation( "NCIT") "NCITA class may refer to smooth muscle only") AnnotationAssertion( "FMA:45634") AnnotationAssertion( "NCIT:C75444") AnnotationAssertion( "UMLS:C0225358") @@ -219403,11 +220223,12 @@ AnnotationAssertion( "UBERON:0018260") AnnotationAssertion(rdfs:label "layer of muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscular coat of digestive tract) AnnotationAssertion(Annotation( "OBOL:automatic") "A muscular coat that is part of a digestive tract.") -AnnotationAssertion( "responsible for gut movement, such as peristalsis") AnnotationAssertion( "tunica muscularis of digestive tract") AnnotationAssertion( "uberon") AnnotationAssertion( "muscular layer of digestive tract") @@ -219416,6 +220237,8 @@ AnnotationAssertion( "UBERON:0018261") AnnotationAssertion(rdfs:label "muscular coat of digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adrenal tissue) @@ -219428,6 +220251,10 @@ AnnotationAssertion( "UBERON:0018303") AnnotationAssertion(rdfs:label "adrenal tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (foramen for glossopharyngeal nerve) @@ -219436,7 +220263,9 @@ AnnotationAssertion( "UBERON:0018321") AnnotationAssertion(rdfs:label "foramen for glossopharyngeal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ilioischiadic foramen) @@ -219445,9 +220274,12 @@ AnnotationAssertion( "UBERON:0018326") AnnotationAssertion(rdfs:label "ilioischiadic foramen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (facial nerve canal) @@ -219461,12 +220293,13 @@ AnnotationAssertion(Annotation( "UBERON:0018413") AnnotationAssertion(rdfs:label "facial nerve canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ethmoid foramen) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An bone foramen in the ethmoid bone.") -AnnotationAssertion( "There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]") AnnotationAssertion( "Wikipedia:Ethmoidal_foramina") AnnotationAssertion( "ethmoidal foramen") AnnotationAssertion(Annotation( ) "foramina ethmoidalia") @@ -219477,6 +220310,9 @@ AnnotationAssertion( "Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina") AnnotationAssertion(rdfs:label "ethmoid foramen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lumen of intestine) @@ -219493,6 +220329,8 @@ AnnotationAssertion(Annotation( "UBERON:0018543") AnnotationAssertion(rdfs:label "lumen of intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trigeminal nerve muscle) @@ -219504,6 +220342,8 @@ AnnotationAssertion( "UBERON:0018544") AnnotationAssertion(rdfs:label "trigeminal nerve muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac muscle tissue of ventricle) @@ -219516,6 +220356,7 @@ AnnotationAssertion(Annotation( "UBERON:0018649") AnnotationAssertion(rdfs:label "cardiac muscle tissue of ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck of bone element) @@ -219527,7 +220368,8 @@ AnnotationAssertion( "UBERON:0018664") AnnotationAssertion(rdfs:label "neck of bone element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/Hidden-GCIs") ) +SubClassOf( ) +SubClassOf( ) # Class: (neck of scapula) @@ -219540,6 +220382,8 @@ AnnotationAssertion( "UBERON:0018667") AnnotationAssertion(rdfs:label "neck of scapula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck of fibula) @@ -219553,6 +220397,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neck of fibula") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (heart vasculature) @@ -219564,6 +220412,9 @@ AnnotationAssertion( "UBERON:0018674") AnnotationAssertion(rdfs:label "heart vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (thoracic splanchnic nerve) @@ -219574,6 +220425,9 @@ AnnotationAssertion( "UBERON:0018679") AnnotationAssertion(rdfs:label "thoracic splanchnic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (nursing stage) @@ -219583,6 +220437,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0018685") AnnotationAssertion(rdfs:label "nursing stage") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -219594,8 +220449,10 @@ AnnotationAssertion( "UBERON:0018692") AnnotationAssertion(rdfs:label "dorsal side of post-anal tail") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bladder organ) @@ -219606,7 +220463,7 @@ AnnotationAssertion( "UBERON:0018707") AnnotationAssertion(rdfs:label "bladder organ") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -219618,6 +220475,8 @@ AnnotationAssertion( "UBERON:0019042") AnnotationAssertion(rdfs:label "reproductive system mucosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (intramuscular adipose tissue) @@ -219628,6 +220487,8 @@ AnnotationAssertion(Annotation( "UBERON:0019143") AnnotationAssertion(rdfs:label "intramuscular adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carotid artery endothelium) @@ -219638,6 +220499,8 @@ AnnotationAssertion( "UBERON:0019189") AnnotationAssertion(rdfs:label "carotid artery endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucous gland of lung) @@ -219651,6 +220514,11 @@ AnnotationAssertion( "UBERON:0019190") AnnotationAssertion(rdfs:label "mucous gland of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac artery endothelium) @@ -219659,6 +220527,8 @@ AnnotationAssertion( "UBERON:0019196") AnnotationAssertion(rdfs:label "iliac artery endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin epithelium) @@ -219668,6 +220538,8 @@ AnnotationAssertion( "UBERON:0019204") AnnotationAssertion(rdfs:label "skin epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tongue papilla epithelium) @@ -219677,6 +220549,9 @@ AnnotationAssertion( "UBERON:0019206") AnnotationAssertion(rdfs:label "tongue papilla epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chorioretinal region) @@ -219691,6 +220566,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chorioretinal region") SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -219706,6 +220583,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white matter of hindbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of forebrain) @@ -219718,6 +220597,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "white matter of forebrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of myelencephalon) @@ -219728,6 +220609,8 @@ AnnotationAssertion( "UBERON:0019262") AnnotationAssertion(rdfs:label "white matter of myelencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter of hindbrain) @@ -219740,6 +220623,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gray matter of hindbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter of forebrain) @@ -219751,6 +220636,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gray matter of forebrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter of midbrain) @@ -219762,6 +220649,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gray matter of midbrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gray matter of diencephalon) @@ -219770,6 +220659,8 @@ AnnotationAssertion( "UBERON:0019269") AnnotationAssertion(rdfs:label "gray matter of diencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of metencephalon) @@ -219779,6 +220670,8 @@ AnnotationAssertion( "UBERON:0019291") AnnotationAssertion(rdfs:label "white matter of metencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of pons) @@ -219787,6 +220680,9 @@ AnnotationAssertion( "UBERON:0019292") AnnotationAssertion(rdfs:label "white matter of pons") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (white matter of pontine tegmentum) @@ -219803,6 +220699,8 @@ AnnotationAssertion( "UBERON:0019293") AnnotationAssertion(rdfs:label "white matter of pontine tegmentum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sensory organ epithelium) @@ -219812,6 +220710,8 @@ AnnotationAssertion( "UBERON:0019304") AnnotationAssertion(rdfs:label "sensory organ epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nose epithelium) @@ -219821,6 +220721,9 @@ AnnotationAssertion( "UBERON:0019306") AnnotationAssertion(rdfs:label "nose epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of external nose) @@ -219832,6 +220735,8 @@ AnnotationAssertion( "epithelium of external nose") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glossopharyngeal nerve root) @@ -219843,7 +220748,9 @@ AnnotationAssertion( "UBERON:0019310") AnnotationAssertion(rdfs:label "glossopharyngeal nerve root") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (root of olfactory nerve) @@ -219854,6 +220761,8 @@ AnnotationAssertion( "UBERON:0019311") AnnotationAssertion(rdfs:label "root of olfactory nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (exocrine gland of integumental system) @@ -219864,6 +220773,8 @@ AnnotationAssertion( "UBERON:0019319") AnnotationAssertion(rdfs:label "exocrine gland of integumental system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (accessory XI nerve nucleus) @@ -219886,8 +220797,7 @@ AnnotationAssertion( "See also: Wikipedia:Spinal_accessory_nucleus") AnnotationAssertion(rdfs:label "accessory XI nerve nucleus") SubClassOf(Annotation( "FMA") ) -SubClassOf(Annotation( "MA") ) -SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (auricular blood vessel) @@ -219898,6 +220808,8 @@ AnnotationAssertion( "UBERON:0020550") AnnotationAssertion(rdfs:label "auricular blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral nerve fasciculus) @@ -219911,6 +220823,8 @@ AnnotationAssertion( "UBERON:0022248") AnnotationAssertion(rdfs:label "cerebral nerve fasciculus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (strand of hair on external ear) @@ -219922,6 +220836,8 @@ AnnotationAssertion( "UBERON:0022279") AnnotationAssertion(rdfs:label "strand of hair on external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of crypt of Lieberkuhn of small intestine) @@ -219932,6 +220848,9 @@ AnnotationAssertion(Annotation( "UBERON:0022280") AnnotationAssertion(rdfs:label "epithelium of crypt of Lieberkuhn of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelium of crypt of Lieberkuhn of large intestine) @@ -219942,16 +220861,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelium of crypt of Lieberkuhn of large intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal gland bud) AnnotationAssertion(Annotation( "MGI:anna") "The single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland).") -AnnotationAssertion( "in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe") AnnotationAssertion( "EMAPA:35464") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0022284") AnnotationAssertion(rdfs:label "lacrimal gland bud") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface of eyeball) @@ -219962,6 +220884,8 @@ AnnotationAssertion(Annotation( "UBERON:0022288") AnnotationAssertion(rdfs:label "surface of eyeball") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (splenic arteriole) @@ -219971,6 +220895,9 @@ AnnotationAssertion( "UBERON:0022292") AnnotationAssertion(rdfs:label "splenic arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (reproductive gland secretion) @@ -219984,6 +220911,8 @@ AnnotationAssertion( "UBERON:0022293") AnnotationAssertion(rdfs:label "reproductive gland secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nervous system cell part layer) @@ -219997,17 +220926,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nervous system cell part layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (primary motor cortex layer 5) -AnnotationAssertion( "Note that in some lamination schemes, more particularly so in primates, this layer is referred to as layer IV thus resulting in some confusion when compared to the present scheme where the lamina dissecans is referred to layer IV[DOI:10.1155/2008/381243]") AnnotationAssertion( "NLX:144263") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "NLX:144263") "primary motor cortex lamina V") AnnotationAssertion(Annotation( "NLX:144263") "primary motor cortex layer V") AnnotationAssertion( "UBERON:0022315") AnnotationAssertion(rdfs:label "primary motor cortex layer 5") -SubClassOf(Annotation( "nlx") ) +SubClassOf( ) SubClassOf(Annotation( "nlx") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "nlx") ObjectSomeValuesFrom( )) @@ -220021,9 +220952,12 @@ AnnotationAssertion(Annotation( "UBERON:0022317") AnnotationAssertion(rdfs:label "olfactory cortex layer 1") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "nlx") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory cortex layer 2) @@ -220034,7 +220968,10 @@ AnnotationAssertion(Annotation( "UBERON:0022318") AnnotationAssertion(rdfs:label "olfactory cortex layer 2") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "nlx") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (dorsal cochlear nucleus pyramidal cell layer) @@ -220044,6 +220981,10 @@ AnnotationAssertion( "UBERON:0022320") AnnotationAssertion(rdfs:label "dorsal cochlear nucleus pyramidal cell layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral serous membrane) @@ -220054,6 +220995,10 @@ AnnotationAssertion( "UBERON:0022350") AnnotationAssertion(rdfs:label "visceral serous membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parietal serous membrane) @@ -220066,6 +221011,10 @@ AnnotationAssertion( "UBERON:0022351") AnnotationAssertion(rdfs:label "parietal serous membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basal layer of endometrium) @@ -220080,6 +221029,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "basal layer of endometrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer layer of endometrium) @@ -220094,6 +221045,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outer layer of endometrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesentery of ileum) @@ -220105,6 +221058,8 @@ AnnotationAssertion( "UBERON:0022357") AnnotationAssertion(rdfs:label "mesentery of ileum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placenta blood vessel) @@ -220117,6 +221072,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "placenta blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (male mammary gland duct) @@ -220125,6 +221083,8 @@ AnnotationAssertion( "UBERON:0022360") AnnotationAssertion(rdfs:label "male mammary gland duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung field) @@ -220135,7 +221095,10 @@ AnnotationAssertion( "UBERON:0022361") AnnotationAssertion(rdfs:label "lung field") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural system) @@ -220158,6 +221121,8 @@ AnnotationAssertion( "UBERON:0024045") AnnotationAssertion(rdfs:label "white matter of the cerebellar cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chemoarchitectural part of brain) @@ -220168,7 +221133,6 @@ AnnotationAssertion( "UBERON:0024090") AnnotationAssertion(rdfs:label "chemoarchitectural part of brain") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (thalamic fiber tract) @@ -220178,6 +221142,8 @@ AnnotationAssertion( "UBERON:0025261") AnnotationAssertion(rdfs:label "thalamic fiber tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (motor system) @@ -220199,6 +221165,8 @@ AnnotationAssertion( "UBERON:0025533") AnnotationAssertion(rdfs:label "proprioceptive system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chemoarchitectural part of striatum) @@ -220208,6 +221176,8 @@ AnnotationAssertion( "UBERON:0025736") AnnotationAssertion(rdfs:label "chemoarchitectural part of striatum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (matrix compartment) @@ -220241,6 +221211,8 @@ AnnotationAssertion( "UBERON:0029001") AnnotationAssertion(rdfs:label "matrix compartment of caudate nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (matrix compartment of putamen) @@ -220250,6 +221222,8 @@ AnnotationAssertion( "UBERON:0029002") AnnotationAssertion(rdfs:label "matrix compartment of putamen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striosomal part of caudate nucleus) @@ -220259,6 +221233,8 @@ AnnotationAssertion( "UBERON:0029004") AnnotationAssertion(rdfs:label "striosomal part of caudate nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striosomal part of putamen) @@ -220268,6 +221244,8 @@ AnnotationAssertion( "UBERON:0029005") AnnotationAssertion(rdfs:label "striosomal part of putamen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (developing neuroepithelium) @@ -220306,7 +221284,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cerebellum marginal layer) -AnnotationAssertion( "In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047]") AnnotationAssertion( "DHBA:12695") AnnotationAssertion( "EHDAA2:0001152") AnnotationAssertion( "EMAPA:17789") @@ -220316,6 +221293,8 @@ AnnotationAssertion(Annotation( "UBERON:0034708") AnnotationAssertion(rdfs:label "cerebellum marginal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindbrain marginal layer) @@ -220327,6 +221306,9 @@ AnnotationAssertion(Annotation( "UBERON:0034709") AnnotationAssertion(rdfs:label "hindbrain marginal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord ventricular layer) @@ -220337,7 +221319,9 @@ AnnotationAssertion( "UBERON:0034710") AnnotationAssertion(rdfs:label "spinal cord ventricular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortical preplate) @@ -220361,6 +221345,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cranial neuron projection bundle") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -220374,7 +221359,9 @@ AnnotationAssertion( "This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893]") AnnotationAssertion(rdfs:label "epiphyseal tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pineal tract) @@ -220387,7 +221374,9 @@ AnnotationAssertion( "This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893]") AnnotationAssertion(rdfs:label "pineal tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -220398,6 +221387,8 @@ AnnotationAssertion( "UBERON:0034717") AnnotationAssertion(rdfs:label "integumental taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lip taste bud) @@ -220407,6 +221398,9 @@ AnnotationAssertion( "UBERON:0034719") AnnotationAssertion(rdfs:label "lip taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head taste bud) @@ -220415,6 +221409,9 @@ AnnotationAssertion( "UBERON:0034720") AnnotationAssertion(rdfs:label "head taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pharyngeal taste bud) @@ -220424,6 +221421,8 @@ AnnotationAssertion( "UBERON:0034721") AnnotationAssertion(rdfs:label "pharyngeal taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mouth roof taste bud) @@ -220434,6 +221433,8 @@ AnnotationAssertion( "UBERON:0034722") AnnotationAssertion(rdfs:label "mouth roof taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophageal taste bud) @@ -220443,6 +221444,10 @@ AnnotationAssertion( "UBERON:0034724") AnnotationAssertion(rdfs:label "esophageal taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trunk taste bud) @@ -220451,6 +221456,10 @@ AnnotationAssertion( "UBERON:0034726") AnnotationAssertion(rdfs:label "trunk taste bud") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autonomic nerve) @@ -220465,7 +221474,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0034728") AnnotationAssertion(rdfs:label "autonomic nerve") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -220480,11 +221489,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sympathetic nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory tract linking bulb to ipsilateral dorsal telencephalon) -AnnotationAssertion(Annotation( "ZFA:0000229") "Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain.") AnnotationAssertion( "TAO:0000229") AnnotationAssertion( "ZFA:0000229") AnnotationAssertion( "uberon") @@ -220493,6 +221503,8 @@ AnnotationAssertion(Annotation( "UBERON:0034730") AnnotationAssertion(rdfs:label "olfactory tract linking bulb to ipsilateral dorsal telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (morphological feature) @@ -220527,6 +221539,8 @@ AnnotationAssertion( "UBERON:0034873") AnnotationAssertion(rdfs:label "bodily gas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (air in respiratory system) @@ -220538,6 +221552,8 @@ AnnotationAssertion( "UBERON:0034874") AnnotationAssertion(rdfs:label "air in respiratory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future pituitary gland) @@ -220548,8 +221564,10 @@ AnnotationAssertion( "UBERON:0034875") AnnotationAssertion(rdfs:label "future pituitary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future neurohypophysis) @@ -220562,8 +221580,10 @@ AnnotationAssertion(Annotation( "UBERON:0034876") AnnotationAssertion(rdfs:label "future neurohypophysis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prechordal mesoderm) @@ -220573,6 +221593,9 @@ AnnotationAssertion( "UBERON:0034878") AnnotationAssertion(rdfs:label "prechordal mesoderm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cervical sympathetic nerve trunk) @@ -220587,11 +221610,12 @@ AnnotationAssertion( "UBERON:0034901") AnnotationAssertion(rdfs:label "cervical sympathetic nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left atrium endocardium) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "Endocardium that is part of the left atrium.") -AnnotationAssertion(Annotation( "FMA:7286") "Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein.") AnnotationAssertion( "FMA:7286") AnnotationAssertion( "SCTID:190064008") AnnotationAssertion( "VHOG:0001226") @@ -220602,6 +221626,8 @@ AnnotationAssertion(Annotation( "UBERON:0034903") AnnotationAssertion(rdfs:label "left atrium endocardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gland lumen) @@ -220610,6 +221636,8 @@ AnnotationAssertion( "UBERON:0034905") AnnotationAssertion(rdfs:label "gland lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pineal parenchyma) @@ -220620,6 +221648,8 @@ AnnotationAssertion( "UBERON:0034907") AnnotationAssertion(rdfs:label "pineal parenchyma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (scapular muscle) @@ -220628,6 +221658,8 @@ AnnotationAssertion( "UBERON:0034908") AnnotationAssertion(rdfs:label "scapular muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multi organ part structure) @@ -220666,7 +221698,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "CARO:0020000") -AnnotationAssertion(Annotation( ) "FBbt:00007276") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0034923") AnnotationAssertion( ) @@ -220697,7 +221728,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "FBbt:00100152") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0034926") AnnotationAssertion( ) @@ -220713,7 +221743,9 @@ AnnotationAssertion( "UBERON:0034928") AnnotationAssertion(rdfs:label "dorsal surface of penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (external soft tissue zone) @@ -220721,6 +221753,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0034929") AnnotationAssertion(rdfs:label "external soft tissue zone") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -220739,6 +221772,8 @@ AnnotationAssertion(Annotation( "UBERON:0034932") AnnotationAssertion(rdfs:label "epithelium of biliary system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (layer of smooth muscle tissue) @@ -220747,6 +221782,8 @@ AnnotationAssertion( "UBERON:0034933") AnnotationAssertion(rdfs:label "layer of smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venous sinus cavity) @@ -220758,6 +221795,8 @@ AnnotationAssertion( "UBERON:0034940") AnnotationAssertion(rdfs:label "venous sinus cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (zone of organ) @@ -220778,6 +221817,8 @@ AnnotationAssertion( "UBERON:0034945") AnnotationAssertion(rdfs:label "excreted gas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (gas excreted from digestive tract) @@ -220791,6 +221832,8 @@ AnnotationAssertion( "In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum") AnnotationAssertion(rdfs:label "gas excreted from digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gas in respiratory system) @@ -220801,6 +221844,8 @@ AnnotationAssertion( "UBERON:0034947") AnnotationAssertion(rdfs:label "gas in respiratory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic lymph sac) @@ -220811,8 +221856,8 @@ AnnotationAssertion( "primary lymph sac") AnnotationAssertion( "UBERON:0034953") AnnotationAssertion(rdfs:label "embryonic lymph sac") +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "VHOG") ObjectSomeValuesFrom( )) # Class: (epithelial layer of duct) @@ -220825,7 +221870,8 @@ AnnotationAssertion( "UBERON:0034969") AnnotationAssertion(rdfs:label "epithelial layer of duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paraganglion (generic)) @@ -220839,7 +221885,7 @@ AnnotationAssertion(Annotation( "UBERON:0034978") AnnotationAssertion(rdfs:label "paraganglion (generic)") SubClassOf(Annotation( "cjm") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf(Annotation( "Wikipedia") ObjectSomeValuesFrom( )) # Class: (hindbrain cortical intermediate zone) @@ -220851,6 +221897,8 @@ AnnotationAssertion( "UBERON:0034994") AnnotationAssertion(rdfs:label "hindbrain cortical intermediate zone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jaw mesenchyme) @@ -220861,6 +221909,8 @@ AnnotationAssertion( "UBERON:0034995") AnnotationAssertion(rdfs:label "jaw mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (outer renal medulla loop of Henle) @@ -220870,6 +221920,8 @@ AnnotationAssertion( "UBERON:0034996") AnnotationAssertion(rdfs:label "outer renal medulla loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal medulla loop of Henle) @@ -220880,6 +221932,8 @@ AnnotationAssertion( "UBERON:0034997") AnnotationAssertion(rdfs:label "renal medulla loop of Henle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (preputial swelling) @@ -220887,7 +221941,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0035004") AnnotationAssertion(rdfs:label "preputial swelling") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (preputial swelling of male) @@ -220898,6 +221952,7 @@ AnnotationAssertion(Annotation( "UBERON:0035005") AnnotationAssertion(rdfs:label "preputial swelling of male") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (preputial swelling of female) @@ -220908,6 +221963,7 @@ AnnotationAssertion(Annotation( "UBERON:0035006") AnnotationAssertion(rdfs:label "preputial swelling of female") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) # Class: (functional part of brain) @@ -220931,6 +221987,9 @@ AnnotationAssertion(Annotation( "UBERON:0035020") AnnotationAssertion(rdfs:label "left vagus X nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right vagus X nerve trunk) @@ -220944,6 +222003,9 @@ AnnotationAssertion(Annotation( "UBERON:0035021") AnnotationAssertion(rdfs:label "right vagus X nerve trunk") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eyelid epithelium) @@ -220954,6 +222016,8 @@ AnnotationAssertion( "UBERON:0035034") AnnotationAssertion(rdfs:label "eyelid epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (naris epithelium) @@ -220964,6 +222028,8 @@ AnnotationAssertion( "UBERON:0035036") AnnotationAssertion(rdfs:label "naris epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jaw epithelium) @@ -220973,6 +222039,8 @@ AnnotationAssertion( "UBERON:0035037") AnnotationAssertion(rdfs:label "jaw epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (rectal artery) @@ -220982,6 +222050,8 @@ AnnotationAssertion( "UBERON:0035039") AnnotationAssertion(rdfs:label "rectal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (olfactory cortex layer 3) @@ -220991,7 +222061,10 @@ AnnotationAssertion( "UBERON:0035044") AnnotationAssertion(rdfs:label "olfactory cortex layer 3") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "nlx") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "NIFSTD") ObjectSomeValuesFrom( )) # Class: (excretory duct of salivary gland) @@ -221002,10 +222075,11 @@ AnnotationAssertion( "UBERON:0035049") AnnotationAssertion(rdfs:label "excretory duct of salivary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (excretory duct) -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006341") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0035050") AnnotationAssertion(rdfs:label "excretory duct") @@ -221018,6 +222092,8 @@ AnnotationAssertion( "UBERON:0035053") AnnotationAssertion(rdfs:label "interlobular duct of salivary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (duct of eccrine sweat gland) @@ -221028,6 +222104,9 @@ AnnotationAssertion( "UBERON:0035073") AnnotationAssertion(rdfs:label "duct of eccrine sweat gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duct of apocrine sweat gland) @@ -221037,15 +222116,9 @@ AnnotationAssertion( "UBERON:0035074") AnnotationAssertion(rdfs:label "duct of apocrine sweat gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (thymus subunit) - -AnnotationAssertion( "FMA:71193") -AnnotationAssertion( "uberon") -AnnotationAssertion( "lobe or lobule of thymus") -AnnotationAssertion( "UBERON:0035075") -AnnotationAssertion(rdfs:label "thymus subunit") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transverse process-bearing vertebra) @@ -221056,6 +222129,8 @@ AnnotationAssertion(Annotation( "UBERON:0035083") AnnotationAssertion(rdfs:label "transverse process-bearing vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (extrinsic post-anal tail muscle) @@ -221064,6 +222139,8 @@ AnnotationAssertion( "UBERON:0035091") AnnotationAssertion(rdfs:label "extrinsic post-anal tail muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transverse process of caudal vertebra) @@ -221072,6 +222149,8 @@ AnnotationAssertion( "UBERON:0035102") AnnotationAssertion(rdfs:label "transverse process of caudal vertebra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (plantar nerve) @@ -221087,7 +222166,8 @@ AnnotationAssertion( "Divided into medial and plantar based on the location of the foot supplied") AnnotationAssertion(rdfs:label "plantar nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (material entity in digestive tract) @@ -221100,6 +222180,8 @@ AnnotationAssertion( "UBERON:0035118") AnnotationAssertion(rdfs:label "material entity in digestive tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manus cartilage element) @@ -221109,6 +222191,9 @@ AnnotationAssertion( "UBERON:0035128") AnnotationAssertion(rdfs:label "manus cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA-modified") ObjectSomeValuesFrom( )) # Class: (pes cartilage element) @@ -221119,6 +222204,9 @@ AnnotationAssertion( "UBERON:0035129") AnnotationAssertion(rdfs:label "pes cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EMAPA-modified") ObjectSomeValuesFrom( )) # Class: (auditory ossicle endochondral element) @@ -221135,6 +222223,7 @@ AnnotationAssertion( ) "ossicular chain element") AnnotationAssertion( "UBERON:0035130") AnnotationAssertion(rdfs:label "auditory ossicle endochondral element") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:11523816") ObjectSomeValuesFrom( )) @@ -221149,6 +222238,8 @@ AnnotationAssertion( "UBERON:0035131") AnnotationAssertion(rdfs:label "auditory ossicle cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (auditory ossicle pre-cartilage element) @@ -221158,6 +222249,8 @@ AnnotationAssertion( "UBERON:0035132") AnnotationAssertion(rdfs:label "auditory ossicle pre-cartilage element") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (entire surface of organism) @@ -221171,6 +222264,8 @@ AnnotationAssertion( "UBERON:0035159") AnnotationAssertion(rdfs:label "entire surface of organism") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior surface of prostate) @@ -221186,6 +222281,8 @@ AnnotationAssertion( "UBERON:0035165") AnnotationAssertion(rdfs:label "posterior surface of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) # Class: (right ear) @@ -221199,6 +222296,9 @@ AnnotationAssertion( "UBERON:0035174") AnnotationAssertion(rdfs:label "right ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (superficial lymphatic vessel) @@ -221212,6 +222312,8 @@ AnnotationAssertion( "UBERON:0035198") AnnotationAssertion(rdfs:label "superficial lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (branch of internal carotid artery) @@ -221225,6 +222327,8 @@ AnnotationAssertion( "UBERON:0035237") AnnotationAssertion(rdfs:label "branch of internal carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck of gallbladder) @@ -221240,6 +222344,9 @@ AnnotationAssertion( "UBERON:0035267") AnnotationAssertion(rdfs:label "neck of gallbladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left ear) @@ -221252,6 +222359,9 @@ AnnotationAssertion( "UBERON:0035295") AnnotationAssertion(rdfs:label "left ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostatic capsule) @@ -221266,6 +222376,10 @@ AnnotationAssertion( "UBERON:0035316") AnnotationAssertion(rdfs:label "prostatic capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right common iliac artery) @@ -221280,6 +222394,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right common iliac artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral wall of nasopharynx) @@ -221292,6 +222409,11 @@ AnnotationAssertion( "UBERON:0035383") AnnotationAssertion(rdfs:label "lateral wall of nasopharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (branch of external carotid artery) @@ -221305,6 +222427,8 @@ AnnotationAssertion( "UBERON:0035398") AnnotationAssertion(rdfs:label "branch of external carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior wall of nasopharynx) @@ -221317,6 +222441,10 @@ AnnotationAssertion( "UBERON:0035401") AnnotationAssertion(rdfs:label "posterior wall of nasopharynx") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hypophysial artery) @@ -221325,6 +222453,8 @@ AnnotationAssertion( "UBERON:0035403") AnnotationAssertion(rdfs:label "hypophysial artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (postcapillary venule) @@ -221351,6 +222481,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0035431") AnnotationAssertion(rdfs:label "mediastinal pleura") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -221369,6 +222500,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right suprarenal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior surface of kidney) @@ -221383,6 +222517,9 @@ AnnotationAssertion( "UBERON:0035471") AnnotationAssertion(rdfs:label "posterior surface of kidney") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface of prostate) @@ -221397,6 +222534,8 @@ AnnotationAssertion( "UBERON:0035480") AnnotationAssertion(rdfs:label "surface of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left suprarenal vein) @@ -221412,6 +222551,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left suprarenal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior surface of prostate) @@ -221428,6 +222570,8 @@ AnnotationAssertion( "UBERON:0035523") AnnotationAssertion(rdfs:label "anterior surface of prostate") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left common iliac artery) @@ -221442,6 +222586,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left common iliac artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (esophageal artery) @@ -221458,8 +222605,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "esophageal artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (deep lymphatic vessel) @@ -221474,6 +222623,8 @@ AnnotationAssertion( "UBERON:0035545") AnnotationAssertion(rdfs:label "deep lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (uveal vein) @@ -221484,6 +222635,8 @@ AnnotationAssertion( "UBERON:0035546") AnnotationAssertion(rdfs:label "uveal vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colic artery) @@ -221493,6 +222646,8 @@ AnnotationAssertion( "colic artery") AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of integument) @@ -221511,6 +222666,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasculature of integument") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (superficial vein) @@ -221528,6 +222685,8 @@ AnnotationAssertion(Annotation( "UBERON:0035550") AnnotationAssertion(rdfs:label "superficial vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deep vasculature) @@ -221537,6 +222696,8 @@ AnnotationAssertion( "UBERON:0035551") AnnotationAssertion(rdfs:label "deep vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (deep vein) @@ -221552,6 +222713,8 @@ AnnotationAssertion(Annotation( "UBERON:0035552") AnnotationAssertion(rdfs:label "deep vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left cardiac chamber) @@ -221562,6 +222725,9 @@ AnnotationAssertion( "UBERON:0035553") AnnotationAssertion(rdfs:label "left cardiac chamber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right cardiac chamber) @@ -221572,6 +222738,9 @@ AnnotationAssertion( "UBERON:0035554") AnnotationAssertion(rdfs:label "right cardiac chamber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral line sense organ) @@ -221580,6 +222749,8 @@ AnnotationAssertion( "UBERON:0035555") AnnotationAssertion(rdfs:label "lateral line sense organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (profundal placode) @@ -221607,11 +222778,15 @@ AnnotationAssertion( "UBERON:0035606") AnnotationAssertion(rdfs:label "cartilage of external acoustic meatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dura mater lymph vessel) AnnotationAssertion(Annotation( "DOI:10.1038/nature14432") Annotation( "DOI:10.1111/joa.12381") "Any lymph vessel that is located in the dura mater of the brain.") -AnnotationAssertion( "while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura") AnnotationAssertion( "dural lymph vessel") AnnotationAssertion( "uberon") AnnotationAssertion( "dural lymph vasculature") @@ -221619,7 +222794,10 @@ AnnotationAssertion( "Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphatics in the cerebral dura mater, but this is disputed by Bucchieri et al (DOI:10.1111/joa.12381)") AnnotationAssertion(rdfs:label "dura mater lymph vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair canal) @@ -221628,7 +222806,12 @@ AnnotationAssertion( "UBERON:0035610") AnnotationAssertion(rdfs:label "hair canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ocular adnexa) @@ -221663,6 +222846,8 @@ AnnotationAssertion( "UBERON:0035642") AnnotationAssertion(rdfs:label "laryngeal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve innervating pinna) @@ -221674,6 +222859,8 @@ AnnotationAssertion( "UBERON:0035648") AnnotationAssertion(rdfs:label "nerve innervating pinna") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (nerve of penis) @@ -221686,6 +222873,8 @@ AnnotationAssertion( "UBERON:0035649") AnnotationAssertion(rdfs:label "nerve of penis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nerve of clitoris) @@ -221699,6 +222888,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nerve of clitoris") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glans) @@ -221708,6 +222899,8 @@ AnnotationAssertion( "glans") EquivalentClasses( ObjectUnionOf( )) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -221722,7 +222915,9 @@ AnnotationAssertion( "UBERON:0035763") AnnotationAssertion(rdfs:label "cavity of cardiac chamber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary lymph node) @@ -221733,6 +222928,8 @@ AnnotationAssertion( "UBERON:0035764") AnnotationAssertion(rdfs:label "pulmonary lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intrapulmonary bronchus) @@ -221743,6 +222940,8 @@ AnnotationAssertion( "UBERON:0035767") AnnotationAssertion(rdfs:label "intrapulmonary bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminal clot) @@ -221752,6 +222951,8 @@ AnnotationAssertion( "UBERON:0035784") AnnotationAssertion(rdfs:label "seminal clot") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (future mouth) @@ -221780,6 +222981,8 @@ AnnotationAssertion( "UBERON:0035805") AnnotationAssertion(rdfs:label "muscle layer of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serous cavity) @@ -221789,6 +222992,8 @@ AnnotationAssertion( "UBERON:0035809") AnnotationAssertion(rdfs:label "serous cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pericardial fat) @@ -221799,6 +223004,8 @@ AnnotationAssertion( "UBERON:0035814") AnnotationAssertion(rdfs:label "pericardial fat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paracardial fat) @@ -221808,6 +223015,8 @@ AnnotationAssertion( "UBERON:0035815") AnnotationAssertion(rdfs:label "paracardial fat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral fat) @@ -221816,6 +223025,8 @@ AnnotationAssertion( "UBERON:0035818") AnnotationAssertion(rdfs:label "visceral fat") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abdominopelvic cavity) @@ -221827,6 +223038,9 @@ AnnotationAssertion( "UBERON:0035819") AnnotationAssertion(rdfs:label "abdominopelvic cavity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peritoneal sac) @@ -221837,6 +223051,7 @@ AnnotationAssertion( "EMAPA:16137") "peritoneal component") AnnotationAssertion( "UBERON:0035820") AnnotationAssertion(rdfs:label "peritoneal sac") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -221854,6 +223069,7 @@ AnnotationAssertion( "left adrenal gland cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left adrenal gland medulla) @@ -221867,6 +223083,7 @@ AnnotationAssertion( "left adrenal gland medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right adrenal gland cortex) @@ -221880,6 +223097,7 @@ AnnotationAssertion( "right adrenal gland cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right adrenal gland medulla) @@ -221893,21 +223111,7 @@ AnnotationAssertion( "right adrenal gland medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) - -# Class: (costal diaphragm) - -AnnotationAssertion(Annotation( "PMID:23586979") "The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon.") -AnnotationAssertion( "FMA:58277") -AnnotationAssertion( "SCTID:368048007") -AnnotationAssertion(Annotation( "FMA:58277") "costal part of diaphragm") -AnnotationAssertion(Annotation( "FMA:TA") Annotation( ) "pars costalis diaphragmatis") -AnnotationAssertion( "uberon") -AnnotationAssertion( "UBERON:0035831") -AnnotationAssertion(rdfs:label "costal diaphragm") -SubClassOf( ) -SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:23586979") ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sulcus of parietal lobe) @@ -221920,6 +223124,8 @@ AnnotationAssertion(Annotation( "UBERON:0035927") AnnotationAssertion(rdfs:label "sulcus of parietal lobe") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epididymal lumen) @@ -221932,7 +223138,9 @@ AnnotationAssertion( "UBERON:0035956") AnnotationAssertion(rdfs:label "epididymal lumen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of blood vessel) @@ -221945,6 +223153,9 @@ AnnotationAssertion(Annotation( "UBERON:0035965") AnnotationAssertion(rdfs:label "wall of blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory primordium epithelium) @@ -221954,6 +223165,12 @@ AnnotationAssertion( "UBERON:0036072") AnnotationAssertion(rdfs:label "respiratory primordium epithelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (respiratory primordium mesenchyme) @@ -221964,6 +223181,9 @@ AnnotationAssertion( "UBERON:0036073") AnnotationAssertion(rdfs:label "respiratory primordium mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) # Class: (cardiopharyngeal field) @@ -221972,9 +223192,10 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0036146") AnnotationAssertion(rdfs:label "cardiopharyngeal field") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin appendage follicle) @@ -221986,6 +223207,12 @@ AnnotationAssertion( "UBERON:0036150") AnnotationAssertion(rdfs:label "skin appendage follicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroelastic connective tissue) @@ -221994,6 +223221,8 @@ AnnotationAssertion( "UBERON:0036186") AnnotationAssertion(rdfs:label "fibroelastic connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (rectosigmoid junction) @@ -222005,7 +223234,9 @@ AnnotationAssertion(Annotation( "UBERON:0036214") AnnotationAssertion(rdfs:label "rectosigmoid junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical surface region) @@ -222025,12 +223256,13 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (coelomic fluid) AnnotationAssertion(Annotation( "PMID:10874572") Annotation( "https://github.com/obophenotype/uberon/issues/1326") "A bodily fluid that is located in the coelom.") -AnnotationAssertion( "he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]") AnnotationAssertion( "BTO:0001708") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0036217") AnnotationAssertion(rdfs:label "coelomic fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (corticobulbar and corticospinal tracts) @@ -222050,6 +223282,8 @@ AnnotationAssertion( "UBERON:0036225") AnnotationAssertion(rdfs:label "respiratory system gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (post-embryonic notochord) @@ -222064,17 +223298,20 @@ AnnotationAssertion( "UBERON:0036242") AnnotationAssertion(rdfs:label "post-embryonic notochord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vaginal fluid) AnnotationAssertion(Annotation( "http://www.bumc.bu.edu/sexualmedicine/physicianinformation/female-genital-anatomy/") "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands.") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0003084") AnnotationAssertion( "uberon") AnnotationAssertion( "vaginal discharge") AnnotationAssertion( "vaginal secretion") AnnotationAssertion( "UBERON:0036243") AnnotationAssertion(rdfs:label "vaginal fluid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretion of serous membrane) @@ -222086,7 +223323,9 @@ AnnotationAssertion( "UBERON:0036244") AnnotationAssertion(rdfs:label "secretion of serous membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (parenchyma of mammary gland) @@ -222098,6 +223337,9 @@ AnnotationAssertion( "UBERON:0036245") AnnotationAssertion(rdfs:label "parenchyma of mammary gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (joint of auditory ossicle) @@ -222110,7 +223352,9 @@ AnnotationAssertion( "UBERON:0036248") AnnotationAssertion(rdfs:label "joint of auditory ossicle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (orifice of skull) @@ -222121,6 +223365,8 @@ AnnotationAssertion( "UBERON:0036253") AnnotationAssertion(rdfs:label "orifice of skull") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (uterine ligament) @@ -222131,6 +223377,9 @@ AnnotationAssertion( "UBERON:0036262") AnnotationAssertion(rdfs:label "uterine ligament") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (zygomaticotemporal nerve) @@ -222146,7 +223395,7 @@ AnnotationAssertion(Annotation( "Wikipedia:Zygomaticotemporal_nerve") "zygomaticotemporal branch") AnnotationAssertion( "UBERON:0036264") AnnotationAssertion(rdfs:label "zygomaticotemporal nerve") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (vulval vein) @@ -222156,6 +223405,8 @@ AnnotationAssertion( "UBERON:0036267") AnnotationAssertion(rdfs:label "vulval vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pelvic vein) @@ -222164,6 +223415,8 @@ AnnotationAssertion( "UBERON:0036268") AnnotationAssertion(rdfs:label "pelvic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (penis blood vessel) @@ -222175,6 +223428,8 @@ AnnotationAssertion(Annotation( "UBERON:0036269") AnnotationAssertion(rdfs:label "penis blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (wall of left ventricle) @@ -222207,7 +223462,9 @@ AnnotationAssertion( "UBERON:0036288") AnnotationAssertion(rdfs:label "anterior wall of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior wall of right ventricle) @@ -222217,6 +223474,8 @@ AnnotationAssertion( "UBERON:0036289") AnnotationAssertion(rdfs:label "anterior wall of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocardium of anterior wall of left ventricle) @@ -222225,6 +223484,8 @@ AnnotationAssertion( "UBERON:0036290") AnnotationAssertion(rdfs:label "myocardium of anterior wall of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocardium of anterior wall of right ventricle) @@ -222233,6 +223494,8 @@ AnnotationAssertion( "UBERON:0036291") AnnotationAssertion(rdfs:label "myocardium of anterior wall of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lip) @@ -222243,6 +223506,8 @@ AnnotationAssertion( "UBERON:0036294") AnnotationAssertion(rdfs:label "mucosa of lip") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (renal pelvis/ureter) @@ -222266,7 +223531,9 @@ AnnotationAssertion( "UBERON:0036301") AnnotationAssertion(rdfs:label "vasculature of spleen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of central nervous system plus retina) @@ -222284,6 +223551,7 @@ AnnotationAssertion( "vasculature of central nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anatomical border) @@ -222306,6 +223574,7 @@ AnnotationAssertion( "wall of coronary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of appendix) @@ -222317,7 +223586,7 @@ AnnotationAssertion( "UBERON:0036337") AnnotationAssertion(rdfs:label "wall of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -222329,7 +223598,8 @@ AnnotationAssertion( "UBERON:0036343") AnnotationAssertion(rdfs:label "wall of gallbladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of brachiocephalic artery) @@ -222362,9 +223632,9 @@ AnnotationAssertion( "UBERON:0036362") AnnotationAssertion(rdfs:label "wall of anal canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of right ureter) @@ -222412,6 +223682,8 @@ AnnotationAssertion( "wall of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of urethra) @@ -222423,6 +223695,7 @@ AnnotationAssertion( "wall of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of vagina) @@ -222434,6 +223707,8 @@ AnnotationAssertion( "wall of vagina") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of synovial tendon sheath) @@ -222444,6 +223719,7 @@ AnnotationAssertion( "wall of synovial tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of lateral ventricle) @@ -222453,7 +223729,7 @@ AnnotationAssertion( "UBERON:0036654") AnnotationAssertion(rdfs:label "wall of lateral ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of fourth ventricle) @@ -222463,7 +223739,7 @@ AnnotationAssertion( "UBERON:0036657") AnnotationAssertion(rdfs:label "wall of fourth ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of central canal of spinal cord) @@ -222474,6 +223750,8 @@ AnnotationAssertion( "UBERON:0036658") AnnotationAssertion(rdfs:label "wall of central canal of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -222484,6 +223762,8 @@ AnnotationAssertion( "UBERON:0036661") AnnotationAssertion(rdfs:label "wall of ventricular system of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -222496,6 +223776,7 @@ AnnotationAssertion( "wall of eyeball") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of orbit) @@ -222506,7 +223787,9 @@ AnnotationAssertion( "UBERON:0037089") AnnotationAssertion(rdfs:label "wall of orbit") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of common carotid artery) @@ -222530,6 +223813,7 @@ AnnotationAssertion( "wall of heart") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) @@ -222543,6 +223827,7 @@ AnnotationAssertion( "wall of membranous labyrinth") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of lacrimal duct) @@ -222554,6 +223839,7 @@ AnnotationAssertion( "wall of lacrimal duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (wall of male urethra) @@ -222586,6 +223872,8 @@ AnnotationAssertion( "UBERON:0037458") AnnotationAssertion(rdfs:label "hair of neck") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hair of limb) @@ -222595,6 +223883,8 @@ AnnotationAssertion( "UBERON:0037459") AnnotationAssertion(rdfs:label "hair of limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subarachnoid space of brain) @@ -222604,6 +223894,7 @@ AnnotationAssertion( "subarachnoid space of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subarachnoid space of spinal cord) @@ -222613,6 +223904,7 @@ AnnotationAssertion( "subarachnoid space of spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cystic artery) @@ -222625,7 +223917,10 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") Annotation( "Wikipedia") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sigmoid vein) @@ -222634,6 +223929,8 @@ AnnotationAssertion( "UBERON:0039228") AnnotationAssertion(rdfs:label "sigmoid vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (pancreatic artery) @@ -222643,6 +223940,8 @@ AnnotationAssertion( "UBERON:0039261") AnnotationAssertion(rdfs:label "pancreatic artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethral artery) @@ -222653,6 +223952,8 @@ AnnotationAssertion( "UBERON:0039355") AnnotationAssertion(rdfs:label "urethral artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethral vein) @@ -222662,6 +223963,8 @@ AnnotationAssertion( "UBERON:0039377") AnnotationAssertion(rdfs:label "urethral vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (right ovarian vein) @@ -222673,6 +223976,7 @@ AnnotationAssertion( "right ovarian vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (left ovarian vein) @@ -222684,6 +223988,7 @@ AnnotationAssertion( "left ovarian vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "FMA") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (collection of hair on external ear) @@ -222694,6 +223999,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "collection of hair on external ear") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of face) @@ -222714,6 +224021,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skin of face") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spleen pulp) @@ -222733,6 +224042,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen pulp") SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) # Class: (parenchyma of spleen) @@ -222744,6 +224054,9 @@ AnnotationAssertion( "UBERON:1000024") AnnotationAssertion(rdfs:label "parenchyma of spleen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive tract junction) @@ -222754,6 +224067,8 @@ AnnotationAssertion( "UBERON:1100000") AnnotationAssertion(rdfs:label "digestive tract junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral line ganglion) @@ -222769,25 +224084,25 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lateral line ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior lateral line nerve) AnnotationAssertion(Annotation( "ZFIN:curator") "Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0000175") AnnotationAssertion(Annotation( "TAO:0000175") "caudal lateral line nerve") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2000175") AnnotationAssertion(rdfs:label "posterior lateral line nerve") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral line primordium) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0000228") AnnotationAssertion(Annotation( "TAO:0000228") Annotation( ) "lateral line primordia") AnnotationAssertion(Annotation( "TAO:0000228") "llp") @@ -222799,30 +224114,28 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (olfactory tract linking bulb to ipsilateral ventral telencephalon) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0000238") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2000238") AnnotationAssertion(rdfs:label "olfactory tract linking bulb to ipsilateral ventral telencephalon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior lateral line nerve) AnnotationAssertion(Annotation( "ZFIN:curator") "Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0000425") AnnotationAssertion(Annotation( "TAO:0000425") "rostral lateral line nerve") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2000425") AnnotationAssertion(rdfs:label "anterior lateral line nerve") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior lateral line neuromast) AnnotationAssertion(Annotation( "ZFIN:curator") "Neuromast that is part of the posterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.).") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0000940") AnnotationAssertion(Annotation( "TAO:0000940") "neuromast posterior") AnnotationAssertion(Annotation( "TAO:0000940") Annotation( ) "neuromasts posterior") @@ -222843,13 +224156,12 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:2001053") AnnotationAssertion(rdfs:label "future internal carotid artery") -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (axial vasculature) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001073") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001073") @@ -222858,7 +224170,6 @@ SubClassOf( (posterior lateral line placode) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001156") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001156") @@ -222870,12 +224181,12 @@ DisjointClasses(Annotation( # Class: (posterior lateral line primordium) AnnotationAssertion(Annotation( "ZFIN:curator") "A migrating group of cells originating from the posterior lateral line placode. The primordium deposits seven to nine neuromasts and interneuromasts between them during its posterior migration to the tail. Gompel et al, 2001.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001157") AnnotationAssertion(Annotation( "TAO:0001157") Annotation( ) "posterior lateral line primordia") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001157") AnnotationAssertion(rdfs:label "posterior lateral line primordium") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -222892,11 +224203,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regenerating fin/limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (posterior lateral line ganglion) AnnotationAssertion(Annotation( "ZFIN:curator") "The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001314") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001314") @@ -222908,7 +224220,6 @@ DisjointClasses(Annotation( # Class: (anterior lateral line placode) AnnotationAssertion(Annotation( "ZFA:0001316") Annotation( "ZFA:curator") "Dorsolateral placode that gives rise to the anterior lateral line.") -AnnotationAssertion(Annotation( "XAO:EJS") "Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS].") AnnotationAssertion( "EFO:0003461") AnnotationAssertion( "TAO:0001316") AnnotationAssertion( "XAO:0004221") @@ -222920,6 +224231,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anterior lateral line placode") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regeneration epithelium of fin/limb) @@ -222938,6 +224251,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regeneration epithelium of fin/limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior lateral line ganglion) @@ -222952,26 +224267,28 @@ AnnotationAssertion( "anterior lateral line ganglion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (primitive olfactory epithelium) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001431") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001431") AnnotationAssertion(rdfs:label "primitive olfactory epithelium") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (postcranial axial cartilage) AnnotationAssertion(Annotation( "ZFIN:curator") "Cartilage which is part of the axial skeleton.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001457") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001457") AnnotationAssertion(rdfs:label "postcranial axial cartilage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anterior lateral line system) @@ -222995,12 +224312,13 @@ AnnotationAssertion( "UBERON:2001470") AnnotationAssertion(rdfs:label "anterior lateral line") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (posterior lateral line system) AnnotationAssertion(Annotation( "ZFIN:curator") "The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001471") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2001471") @@ -223010,7 +224328,6 @@ SubClassOf( (anterior lateral line neuromast) AnnotationAssertion(Annotation( "ZFIN:curator") "Neuromast that is part of the anterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.).") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0001472") AnnotationAssertion(Annotation( "TAO:0001472") "neuromast anterior") AnnotationAssertion( "uberon") @@ -223022,7 +224339,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (anterior lateral line primordium) AnnotationAssertion(Annotation( "ZFIN:curator") "A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0005117") AnnotationAssertion(Annotation( "TAO:0005117") Annotation( ) "anterior lateral line primordia") AnnotationAssertion( "uberon") @@ -223033,7 +224349,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (protoneuromast) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0005227") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "TAO:0005227") "immature neuromast") @@ -223048,7 +224363,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "Wikipedia:Capillary#Types") Annotation( "Wikipedia:Fenestra_(histology)") "Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse.") AnnotationAssertion( "the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences") -AnnotationAssertion( "Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA].") AnnotationAssertion(Annotation( "ZFA:0005260") "fenestrated blood vessel endothelium") AnnotationAssertion( "FMA:63196") AnnotationAssertion( "NCIT:C32595") @@ -223066,7 +224380,6 @@ SubClassOf(Annotation( "ZFA # Class: (preplacodal ectoderm) AnnotationAssertion(Annotation( "ZFIN:curator") "Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/tao.owl") "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "ZFA:0007013") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:2007013") @@ -223076,62 +224389,67 @@ SubClassOf( (external integument structure) AnnotationAssertion(Annotation( "AAO:EJS") "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3000961") AnnotationAssertion(rdfs:comment "Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305") AnnotationAssertion(rdfs:label "external integument structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (head external integument structure) AnnotationAssertion(Annotation( "AAO:EJS") "Dermal, epidermal, glandular and pigment structures of the external head integument.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3000972") AnnotationAssertion(rdfs:label "head external integument structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (body external integument structure) AnnotationAssertion(Annotation( "AAO:EJS") "Dermal, epidermal, glandular and pigment structures of the body integument.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3000977") AnnotationAssertion(rdfs:label "body external integument structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (limb external integument structure) AnnotationAssertion(Annotation( "AAO:EJS") "Dermal, epidermal, glandular and pigment structures of the limb integument.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3000981") AnnotationAssertion(rdfs:label "limb external integument structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tail external integument structure) AnnotationAssertion(Annotation( "AAO:EJS") "Dermal, epidermal, glandular and pigment structures of the tail integument.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3000982") AnnotationAssertion(rdfs:label "tail external integument structure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vasculature of respiratory integument) AnnotationAssertion(Annotation( "AAO:EJS") "Blood vessels in respiratory skin.") AnnotationAssertion( "Modified from the original AAO source") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3010200") AnnotationAssertion(rdfs:label "vasculature of respiratory integument") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lateral line nucleus) -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/aao.owl") "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:3010706") AnnotationAssertion(rdfs:label "lateral line nucleus") @@ -223148,11 +224466,12 @@ AnnotationAssertion( "UBERON:4000013") AnnotationAssertion(rdfs:label "mineralized skeletal tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mineralized extracellular matrix) AnnotationAssertion(Annotation( "PSPUB:0000170") "Extracellular matrix that is mineralized.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/vsao.owl") "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:4000020") AnnotationAssertion(rdfs:label "mineralized extracellular matrix") @@ -223162,11 +224481,12 @@ SubClassOf( (mineralized bone tissue) AnnotationAssertion(Annotation( "PSPUB:0000170") "Bone tissue mineralized with hydroxyapatite.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/vsao.owl") "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:4000115") AnnotationAssertion(rdfs:label "mineralized bone tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -223174,11 +224494,14 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (cellular bone tissue) AnnotationAssertion(Annotation( "PSPUB:0000170") "Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes.") -AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/vsao.owl") "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:4000118") AnnotationAssertion(rdfs:label "cellular bone tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal element projection) @@ -223188,6 +224511,7 @@ AnnotationAssertion( "skeletal element projection") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neck of humerus) @@ -223201,8 +224525,9 @@ AnnotationAssertion(Annotation( "UBERON:4200172") AnnotationAssertion(rdfs:label "neck of humerus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (surface of bone) @@ -223213,6 +224538,8 @@ AnnotationAssertion( "UBERON:4200230") AnnotationAssertion(rdfs:label "surface of bone") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forelimb bud mesenchyme) @@ -223222,6 +224549,9 @@ AnnotationAssertion( "UBERON:4300226") AnnotationAssertion(rdfs:label "forelimb bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hindlimb bud mesenchyme) @@ -223231,11 +224561,13 @@ AnnotationAssertion( "UBERON:4300227") AnnotationAssertion(rdfs:label "hindlimb bud mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit plus metapodial segment) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.") -AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/458") "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "pedal digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "pedal digit ( phalanges plus metapodial) plus soft tissue") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "pedal digit digitopodial subdivision") @@ -223244,13 +224576,14 @@ AnnotationAssertion( "UBERON:5001466") AnnotationAssertion(rdfs:label "pedal digit plus metapodial segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit plus metapodial segment) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.") -AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/458") "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "manual digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "manual digit ( phalanges plus metapodial) plus soft tissue") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "manual digit digitopodial subdivision") @@ -223259,13 +224592,14 @@ AnnotationAssertion( "UBERON:5002389") AnnotationAssertion(rdfs:label "manual digit plus metapodial segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digit plus metapodial segment) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.") -AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/458") "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "digit ( phalanges plus metapodial) plus soft tissue") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "digit digitopodial subdivision") @@ -223274,73 +224608,75 @@ AnnotationAssertion( "UBERON:5002544") AnnotationAssertion(rdfs:label "digit plus metapodial segment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pedal digit digitopodial skeleton) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element.") -AnnotationAssertion( "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "pedal digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "pedal digit skeleton") AnnotationAssertion( "UBERON:5101466") AnnotationAssertion(rdfs:label "pedal digit digitopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (manual digit digitopodial skeleton) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element.") -AnnotationAssertion( "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "manual digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "manual digit skeleton") AnnotationAssertion( "UBERON:5102389") AnnotationAssertion(rdfs:label "manual digit digitopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (individual digit of digitopodial skeleton) AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.") -AnnotationAssertion( "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") Annotation( ) "digit") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "digit skeleton") AnnotationAssertion( "UBERON:5102544") AnnotationAssertion(rdfs:label "individual digit of digitopodial skeleton") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arthropod tagma) AnnotationAssertion(Annotation( "doi:10.1016/B978-0-12-385026-3.00024-3") "One of the main divisions of the whole organism of arthropods formed from groups of segments.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "FBbt:00000002") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6000002") AnnotationAssertion(rdfs:comment "Strictly speaking the term \"tagma\" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods.") AnnotationAssertion(rdfs:label "arthropod tagma") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (panarthropod head) -AnnotationAssertion(Annotation( ) "FBbt:00000004") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6000004") AnnotationAssertion(rdfs:label "panarthropod head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic tagma) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052).") -AnnotationAssertion(Annotation( ) "FBbt:00000137") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6000137") AnnotationAssertion(rdfs:label "embryonic tagma") @@ -223351,7 +224687,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (insect larval tagma) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727).") -AnnotationAssertion(Annotation( ) "FBbt:00001728") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6001728") AnnotationAssertion(rdfs:label "insect larval tagma") @@ -223362,26 +224697,29 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (insect larval head) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any head that is part of some larva.") -AnnotationAssertion(Annotation( ) "FBbt:00001730") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6001730") AnnotationAssertion(rdfs:label "insect larval head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (insect larval sense organ) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any sense organ that is part of some larva.") -AnnotationAssertion(Annotation( ) "FBbt:00002639") AnnotationAssertion( "larval sense organ") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6002639") AnnotationAssertion(rdfs:label "insect larval sense organ") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (insect adult tagma) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004).") -AnnotationAssertion(Annotation( ) "FBbt:00003005") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6003005") AnnotationAssertion(rdfs:label "insect adult tagma") @@ -223392,17 +224730,17 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (insect adult head) AnnotationAssertion(Annotation( "FBC:SPR") "Head of the adult organism.") -AnnotationAssertion(Annotation( ) "FBbt:00003007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6003007") AnnotationAssertion(rdfs:label "insect adult head") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (insect embryonic/larval sensillum) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727).") -AnnotationAssertion(Annotation( ) "FBbt:00007240") AnnotationAssertion( "larval sensillum") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6007240") @@ -223410,12 +224748,10 @@ AnnotationAssertion(rdfs:label " EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (insect embryonic/larval head sensillum) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730).") -AnnotationAssertion(Annotation( ) "FBbt:00007242") AnnotationAssertion( "larval head sensillum") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6007242") @@ -223424,12 +224760,10 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (insect embryonic/larval head sense organ) AnnotationAssertion(Annotation( "FBC:auto_generated_definition") "Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730).") -AnnotationAssertion(Annotation( ) "FBbt:00007280") AnnotationAssertion( "larval head sense organ") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:6007280") @@ -223447,6 +224781,10 @@ AnnotationAssertion( "UBERON:7500062") AnnotationAssertion(rdfs:label "tibial tuberosity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sphenovomerine suture) @@ -223457,6 +224795,9 @@ AnnotationAssertion( "UBERON:7500107") AnnotationAssertion(rdfs:label "sphenovomerine suture") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left side of back) @@ -223467,6 +224808,8 @@ AnnotationAssertion( "left side of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right side of back) @@ -223477,6 +224820,8 @@ AnnotationAssertion( "right side of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Purkinje fiber network) @@ -223487,6 +224832,7 @@ AnnotationAssertion( "UBERON:8000009") AnnotationAssertion(rdfs:label "Purkinje fiber network") SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ) +SubClassOf( ) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/issues/1785") Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9791-0064") ObjectSomeValuesFrom( )) @@ -223504,51 +224850,60 @@ AnnotationAssertion( "UBERON:8300000") AnnotationAssertion(rdfs:label "skin of scalp") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right forelimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A forelimb that is on the right side of a pectoral complex.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "FMA:7185") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8300001") AnnotationAssertion(rdfs:label "right forelimb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left forelimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A forelimb that is on the left side of a pectoral complex.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "FMA:7186") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8300002") AnnotationAssertion(rdfs:label "left forelimb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right hindlimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A hindlimb that is on the right side of a pelvic complex.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "FMA:7187") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8300003") AnnotationAssertion(rdfs:label "right hindlimb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left hindlimb) AnnotationAssertion(Annotation( "UBERONREF:0000003") "A hindlimb that is on the left side of a pelvic complex.") -AnnotationAssertion( "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "FMA:7188") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8300004") AnnotationAssertion(rdfs:label "left hindlimb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hepatic acinus zone 1) @@ -223560,7 +224915,6 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:8400001") AnnotationAssertion(rdfs:label "hepatic acinus zone 1") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223577,7 +224931,6 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:8400002") AnnotationAssertion(rdfs:label "hepatic acinus zone 3") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223592,7 +224945,6 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:8400003") AnnotationAssertion(rdfs:label "hepatic acinus zone 2") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223610,6 +224962,7 @@ AnnotationAssertion( "UBERON:8400005") AnnotationAssertion(rdfs:label "metabolic zone of liver") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver lobule periportal region) @@ -223622,7 +224975,6 @@ AnnotationAssertion( "PMID:28126520") "hepatic acinus zone 1") AnnotationAssertion( "UBERON:8400006") AnnotationAssertion(rdfs:label "liver lobule periportal region") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223638,7 +224990,6 @@ AnnotationAssertion( "PMID:28126520") "hepatic acinus zone 3") AnnotationAssertion( "UBERON:8400007") AnnotationAssertion(rdfs:label "liver lobule centrilobular region") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223654,7 +225005,6 @@ AnnotationAssertion( "PMID:28126520") "hepatic acinus zone 2") AnnotationAssertion( "UBERON:8400008") AnnotationAssertion(rdfs:label "liver lobule midzonal region") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:28126520") ObjectSomeValuesFrom( )) @@ -223671,6 +225021,9 @@ AnnotationAssertion( "UBERON:8400021") AnnotationAssertion(rdfs:label "liver serosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (liver subserosa) @@ -223685,6 +225038,9 @@ AnnotationAssertion( "UBERON:8400023") AnnotationAssertion(rdfs:label "liver subserosa") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcapsular region of liver) @@ -223697,6 +225053,8 @@ AnnotationAssertion( "UBERON:8400024") AnnotationAssertion(rdfs:label "subcapsular region of liver") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (duodeno-jejunal junction) @@ -223715,8 +225073,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duodeno-jejunal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (small intestine venule) @@ -223728,6 +225088,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "small intestine venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (small intestine lymphatic vessel) @@ -223739,17 +225101,20 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "small intestine lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ductal plate) AnnotationAssertion(Annotation( "PMID:28515578") Annotation( "http://orcid.org/0000-0002-7073-9172") "In human, ductal plate is a double-layered cylindrical structure of bile duct epithelium that surrounds the portal ramifications by the eighth gestational week. After approximately the 12th gestational week, remodelling of ductal plate begins, and maturity is attained by the end of gestation or early postnatal period.") AnnotationAssertion( ) -AnnotationAssertion( "Temporal stages still need to be fully researched across species.") AnnotationAssertion( ) AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8410003") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ductal plate") +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -223769,6 +225134,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "small intestine arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venule of anorectum) @@ -223779,6 +225146,8 @@ AnnotationAssertion( "UBERON:8410008") AnnotationAssertion(rdfs:label "venule of anorectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole of anorectum) @@ -223789,6 +225158,8 @@ AnnotationAssertion( "UBERON:8410009") AnnotationAssertion(rdfs:label "arteriole of anorectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole of colon) @@ -223798,6 +225169,8 @@ AnnotationAssertion( "UBERON:8410015") AnnotationAssertion(rdfs:label "arteriole of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (descending sigmoid junction) @@ -223810,7 +225183,10 @@ AnnotationAssertion( "UBERON:8410016") AnnotationAssertion(rdfs:label "descending sigmoid junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (left colic vein) @@ -223823,6 +225199,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "left colic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (right colic vein) @@ -223835,6 +225214,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "right colic vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jejuno-ileal junction) @@ -223845,7 +225227,10 @@ AnnotationAssertion( "UBERON:8410019") AnnotationAssertion(rdfs:label "jejuno-ileal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venule of appendix) @@ -223857,6 +225242,8 @@ AnnotationAssertion( "UBERON:8410020") AnnotationAssertion(rdfs:label "venule of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal junction) @@ -223867,6 +225254,8 @@ AnnotationAssertion( "UBERON:8410024") AnnotationAssertion(rdfs:label "intestinal junction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole of appendix) @@ -223880,6 +225269,8 @@ AnnotationAssertion( "UBERON:8410028") AnnotationAssertion(rdfs:label "arteriole of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic vessel of appendix) @@ -223891,6 +225282,8 @@ AnnotationAssertion( "UBERON:8410030") AnnotationAssertion(rdfs:label "lymphatic vessel of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trabecular sinus of lymph node) @@ -223903,6 +225296,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trabecular sinus of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node vein) @@ -223916,6 +225312,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node artery) @@ -223928,6 +225326,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (medullary arteriole of lymph node) @@ -223940,6 +225340,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "medullary arteriole of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (medullary venule of lymph node) @@ -223953,6 +225355,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "medullary venule of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (high endothelial venule) @@ -223977,6 +225381,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "high endothelial venule of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (high endothelial venule of appendix) @@ -223989,6 +225395,8 @@ AnnotationAssertion( "UBERON:8410039") AnnotationAssertion(rdfs:label "high endothelial venule of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (high endothelial venule of small intestine Peyer's patch) @@ -224000,6 +225408,8 @@ AnnotationAssertion( "UBERON:8410040") AnnotationAssertion(rdfs:label "high endothelial venule of small intestine Peyer's patch") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venule of lymph node) @@ -224012,6 +225422,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venule of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arteriole of lymph node) @@ -224024,6 +225436,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arteriole of lymph node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bronchus submucosal gland) @@ -224039,6 +225453,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bronchus submucosal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein of appendix) @@ -224050,6 +225466,8 @@ AnnotationAssertion( "UBERON:8410044") AnnotationAssertion(rdfs:label "vein of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (artery of appendix) @@ -224061,6 +225479,8 @@ AnnotationAssertion( "UBERON:8410045") AnnotationAssertion(rdfs:label "artery of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendix smooth muscle circular layer) @@ -224073,6 +225493,8 @@ AnnotationAssertion( "UBERON:8410046") AnnotationAssertion(rdfs:label "appendix smooth muscle circular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (appendix smooth muscle longitudinal layer) @@ -224085,6 +225507,8 @@ AnnotationAssertion( "UBERON:8410047") AnnotationAssertion(rdfs:label "appendix smooth muscle longitudinal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (venule of colon) @@ -224094,6 +225518,8 @@ AnnotationAssertion( "UBERON:8410048") AnnotationAssertion(rdfs:label "venule of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (serosal nerve fiber of appendix) @@ -224110,20 +225536,26 @@ AnnotationAssertion( "UBERON:8410049") AnnotationAssertion(rdfs:label "serosal nerve fiber of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (anorectum) AnnotationAssertion(Annotation( "DOI:10.1007/978-3-319-26938-2_8") Annotation( "DOI:10.1148/rg.2015150037") Annotation( "PMID:29742860") Annotation( "http://orcid.org/0000-0002-6826-8770") Annotation( "http://orcid.org/0000-0003-3440-1876") "A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus.") AnnotationAssertion( "The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum.") AnnotationAssertion( ) -AnnotationAssertion( "anorectal") AnnotationAssertion( ) AnnotationAssertion( "anorectal canal") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8410050") AnnotationAssertion(rdfs:label "anorectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphatic vessel of colon) @@ -224133,6 +225565,8 @@ AnnotationAssertion( "UBERON:8410051") AnnotationAssertion(rdfs:label "lymphatic vessel of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node germinal center light zone) @@ -224173,6 +225607,8 @@ AnnotationAssertion( "UBERON:8410056") AnnotationAssertion(rdfs:label "capillary of anorectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (capillary of colon) @@ -224183,6 +225619,8 @@ AnnotationAssertion( "UBERON:8410057") AnnotationAssertion(rdfs:label "capillary of colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colon smooth muscle circular layer) @@ -224193,6 +225631,8 @@ AnnotationAssertion( "UBERON:8410060") AnnotationAssertion(rdfs:label "colon smooth muscle circular layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (colon smooth muscle longitudinal layer) @@ -224203,6 +225643,8 @@ AnnotationAssertion( "UBERON:8410061") AnnotationAssertion(rdfs:label "colon smooth muscle longitudinal layer") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymph node follicle marginal zone) @@ -224241,6 +225683,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capillary of small intestine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcapsular sinus ceiling) @@ -224288,6 +225732,10 @@ AnnotationAssertion( "UBERON:8410077") AnnotationAssertion(rdfs:label "airway submucosal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (red bone marrow of sternum) @@ -224298,11 +225746,12 @@ AnnotationAssertion( "UBERON:8410080") AnnotationAssertion(rdfs:label "red bone marrow of sternum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood microvessel) AnnotationAssertion(Annotation( "Wikipedia:Microcirculation") Annotation( "http://orcid.org/0000-0002-7073-9172") "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.") -AnnotationAssertion( "microvascular") AnnotationAssertion( "http://orcid.org/0000-0002-2825-0621") AnnotationAssertion( "microvasculature") AnnotationAssertion( "microvessel") @@ -224322,6 +225771,8 @@ AnnotationAssertion( "UBERON:8420000") AnnotationAssertion(rdfs:label "hair of scalp") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortical layer II/III) @@ -224397,6 +225848,9 @@ AnnotationAssertion( "UBERON:8440011") AnnotationAssertion(rdfs:label "cortical visual area") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (noradrenergic cell groups) @@ -224427,6 +225881,7 @@ AnnotationAssertion( "egg follicle") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/476"^^xsd:anyURI) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (excretory system) @@ -224435,12 +225890,13 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "http://orcid.org/0000-0002-6095-8718") AnnotationAssertion( "2022-05-25T18:21:29Z") -AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "https://github.com/biopragmatics/biomappings") "BTO:0006338") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8450002") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "excretory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental blood) @@ -224450,6 +225906,8 @@ AnnotationAssertion( "UBERON:8470000") AnnotationAssertion(rdfs:label "placental blood") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac vein smooth muscle tissue) @@ -224460,6 +225918,8 @@ AnnotationAssertion( "UBERON:8480000") AnnotationAssertion(rdfs:label "iliac vein smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (capillary of brain) @@ -224470,6 +225930,8 @@ AnnotationAssertion( "UBERON:8480001") AnnotationAssertion(rdfs:label "capillary of brain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (thoracic aorta smooth muscle tissue) @@ -224480,6 +225942,8 @@ AnnotationAssertion( "UBERON:8480002") AnnotationAssertion(rdfs:label "thoracic aorta smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac artery smooth muscle tissue) @@ -224490,6 +225954,8 @@ AnnotationAssertion( "UBERON:8480003") AnnotationAssertion(rdfs:label "iliac artery smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (iliac vein endothelium) @@ -224500,6 +225966,8 @@ AnnotationAssertion( "UBERON:8480004") AnnotationAssertion(rdfs:label "iliac vein endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental artery endothelium) @@ -224510,6 +225978,10 @@ AnnotationAssertion( "UBERON:8480005") AnnotationAssertion(rdfs:label "placental artery endothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenteric lymphatic vessel) @@ -224520,6 +225992,9 @@ AnnotationAssertion( "UBERON:8480006") AnnotationAssertion(rdfs:label "mesenteric lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental artery) @@ -224530,6 +226005,8 @@ AnnotationAssertion( "UBERON:8480007") AnnotationAssertion(rdfs:label "placental artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (placental vein) @@ -224540,6 +226017,8 @@ AnnotationAssertion( "UBERON:8480008") AnnotationAssertion(rdfs:label "placental vein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (skin of clavicle region) @@ -224550,6 +226029,8 @@ AnnotationAssertion( "UBERON:8480025") AnnotationAssertion(rdfs:label "skin of clavicle region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of iliac crest region) @@ -224561,6 +226042,9 @@ AnnotationAssertion( "UBERON:8480026") AnnotationAssertion(rdfs:label "skin of iliac crest region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of external genitalia) @@ -224571,6 +226055,9 @@ AnnotationAssertion( "UBERON:8480029") AnnotationAssertion(rdfs:label "skin of external genitalia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of breast) @@ -224581,6 +226068,8 @@ AnnotationAssertion( "UBERON:8480030") AnnotationAssertion(rdfs:label "skin of breast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subserosa of uterine tube) @@ -224593,6 +226082,10 @@ AnnotationAssertion( "UBERON:8480037") AnnotationAssertion(rdfs:label "subserosa of uterine tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (saphenous vein smooth muscle tissue) @@ -224603,6 +226096,8 @@ AnnotationAssertion( "UBERON:8480068") AnnotationAssertion(rdfs:label "saphenous vein smooth muscle tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin of gonad) @@ -224613,6 +226108,9 @@ AnnotationAssertion( "UBERON:8480074") AnnotationAssertion(rdfs:label "skin of gonad") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lobular bronchiole) @@ -224638,6 +226136,8 @@ AnnotationAssertion( "UBERON:8600001") AnnotationAssertion(rdfs:label "epithelium of lobular bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucosa of lobular bronchiole) @@ -224648,6 +226148,8 @@ AnnotationAssertion( "UBERON:8600002") AnnotationAssertion(rdfs:label "mucosa of lobular bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle tissue of lobular bronchiole) @@ -224658,6 +226160,8 @@ AnnotationAssertion( "UBERON:8600003") AnnotationAssertion(rdfs:label "smooth muscle tissue of lobular bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral muscle tissue) @@ -224696,6 +226200,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bronchial submucosal gland ciliated duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tracheal submucosal gland ciliated duct) @@ -224709,6 +226216,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tracheal submucosal gland ciliated duct") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosal gland acinus) @@ -224721,6 +226231,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "submucosal gland acinus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (submucosal gland ciliated duct) @@ -224748,6 +226260,7 @@ AnnotationAssertion( "PMID:18271171") Annotation( "doi:10.1016/j.mpaic.2008.09.022") rdfs:comment "A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung.") AnnotationAssertion(rdfs:label "bronchopulmonary segment") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -224776,6 +226289,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chorionic plate blood vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental villous stroma) @@ -224789,6 +226304,9 @@ AnnotationAssertion(Annotation( "UBERON:8600023") AnnotationAssertion(rdfs:label "placental villous stroma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary venule) @@ -224799,6 +226317,9 @@ AnnotationAssertion( "UBERON:8600024") AnnotationAssertion(rdfs:label "pulmonary venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -224815,6 +226336,7 @@ AnnotationAssertion( "UBERON:8600034") AnnotationAssertion(rdfs:label "jejunum lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ileum lamina propria) @@ -224829,6 +226351,7 @@ AnnotationAssertion( "UBERON:8600035") AnnotationAssertion(rdfs:label "ileum lamina propria") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (placental disc) @@ -224840,7 +226363,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:8600038") AnnotationAssertion(rdfs:label "placental disc") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (chorionic villous mesenchyme) @@ -224852,6 +226375,10 @@ AnnotationAssertion( "UBERON:8600039") AnnotationAssertion(rdfs:label "chorionic villous mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endometrial lymphatic vessel) @@ -224862,6 +226389,9 @@ AnnotationAssertion( "UBERON:8600042") AnnotationAssertion(rdfs:label "endometrial lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) ############################ @@ -224870,122 +226400,94 @@ EquivalentClasses( ObjectIntersec # Individual: (example to be eventually removed) -AnnotationAssertion( "example to be eventually removed"@en) AnnotationAssertion(rdfs:label "example to be eventually removed"@en) # Individual: (failed exploratory term) -AnnotationAssertion( "failed exploratory term"@en) AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "failed exploratory term"@en) # Individual: (metadata complete) -AnnotationAssertion( "metadata complete"@en) AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) AnnotationAssertion(rdfs:label "metadata complete"@en) # Individual: (organizational term) -AnnotationAssertion( "organizational term"@en) AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) AnnotationAssertion(rdfs:label "organizational term"@en) # Individual: (ready for release) -AnnotationAssertion( "ready for release"@en) AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) AnnotationAssertion(rdfs:label "ready for release"@en) # Individual: (metadata incomplete) -AnnotationAssertion( "metadata incomplete"@en) AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) AnnotationAssertion(rdfs:label "metadata incomplete"@en) # Individual: (uncurated) -AnnotationAssertion( "uncurated"@en) AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) AnnotationAssertion(rdfs:label "uncurated"@en) # Individual: (pending final vetting) -AnnotationAssertion( "pending final vetting"@en) AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) AnnotationAssertion(rdfs:label "pending final vetting"@en) # Individual: (placeholder removed) -AnnotationAssertion( "placeholder removed"@en) AnnotationAssertion(rdfs:label "placeholder removed"@en) # Individual: (terms merged) -AnnotationAssertion( "terms merged"@en) AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) AnnotationAssertion(rdfs:label "terms merged"@en) # Individual: (term imported) -AnnotationAssertion( "term imported"@en) AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) AnnotationAssertion(rdfs:label "term imported"@en) # Individual: (term split) -AnnotationAssertion( "term split"@en) AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) AnnotationAssertion(rdfs:label "term split"@en) # Individual: (universal) -AnnotationAssertion( "universal"@en) AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) AnnotationAssertion(rdfs:label "universal"@en) # Individual: (defined class) -AnnotationAssertion( "defined class"@en) AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "defined class"@en) # Individual: (named class expression) -AnnotationAssertion( "named class expression"@en) AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "named class expression"@en) # Individual: (to be replaced with external ontology term) -AnnotationAssertion( "to be replaced with external ontology term"@en) AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) # Individual: (requires discussion) -AnnotationAssertion( "requires discussion"@en) AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion(rdfs:label "requires discussion"@en) # Individual: (out of scope) AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") -AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") AnnotationAssertion(rdfs:label "out of scope") @@ -224995,28 +226497,12 @@ EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(2 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(1 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "hagfish have median nostril") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) SubClassOf(Annotation( "PMID:25312359") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "midface division only makes sense for gnathostomes") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16417468") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225028,7 +226514,6 @@ SubClassOf(Annotation( "FMA SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:15843440") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "vertebrates") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225046,12 +226531,10 @@ SubClassOf(Annotation( "FMA SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA-abduced-lr") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "definitional") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "only in species that have a stomach") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Vitelline_vein") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225067,15 +226550,7 @@ SubClassOf(ObjectIntersectionOf( SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Mammals") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Mammals") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Aves") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Aves") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "pouches 3 and 4 in human") Annotation( "PMID:16313389") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Vitelline_vein") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "requires review") Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "requires review") Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "may be present in other parts in other species") Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225088,7 +226563,6 @@ SubClassOf(Annotation( "Wik SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "right arch 4 in human") Annotation( "embryology.ch") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia:Vitelline_vein") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipedia") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225112,11 +226586,7 @@ SubClassOf(Annotation( "FMA SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "teleost") Annotation( "NCBIBook:NBK53175") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Euarchontoglires") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "evaginated") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "evaginated") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "https://github.com/obophenotype/uberon/wiki/The-neural-crest") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225136,21 +226606,11 @@ SubClassOf(Annotation( "PMI SubClassOf(Annotation( "PMID:16417468") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "AAO") Annotation( "https://github.com/geneontology/go-ontology/issues/16143") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "human and mouse") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "human and mouse") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "ISBN:9780878932504") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "Wikipathways:WP2062") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "teleosts") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Mammals") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Mammals") Annotation( "EHDAA2") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Mammals") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Aves") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "Aves") Annotation( "ISBN:0073040584-table13.1") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "conservatively place at deuterostome, excluding acoelomates") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225194,7 +226654,6 @@ DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) -DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -225203,35 +226662,23 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -225244,7 +226691,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -225261,7 +226707,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -225269,7 +226714,6 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -225291,60 +226735,50 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/mappings/fbbt-mappings.sssom.tsv b/src/ontology/mappings/fbbt-mappings.sssom.tsv index 7ede72825..708add3c6 100644 --- a/src/ontology/mappings/fbbt-mappings.sssom.tsv +++ b/src/ontology/mappings/fbbt-mappings.sssom.tsv @@ -382,7 +382,6 @@ FBbt:00007019 portion of organism substance semapv:crossSpeciesExactMatch UBERON FBbt:00007020 metatarsus of male prothoracic leg semapv:crossSpeciesExactMatch UBERON:6007020 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl FBbt:00007027 cuboidal/columnar epithelium semapv:crossSpeciesExactMatch UBERON:0000485 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl FBbt:00007045 trunk ectoderm semapv:crossSpeciesExactMatch UBERON:6007045 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl -FBbt:00007046 dorsal ectoderm derivative semapv:crossSpeciesExactMatch UBERON:6007046 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl FBbt:00007060 multi-cell-component structure semapv:crossSpeciesExactMatch UBERON:0005162 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl FBbt:00007070 embryonic/larval posterior inferior protocerebrum semapv:crossSpeciesExactMatch UBERON:6007070 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl FBbt:00007091 subperineurial glial sheath semapv:crossSpeciesCloseMatch UBERON:0000202 semapv:ManualMappingCuration http://purl.obolibrary.org/obo/uberon.owl