From d8ce6fb8d0b1cba93d56de849397fbb75fd0a41e Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 24 Sep 2024 15:46:40 +0100 Subject: [PATCH 1/3] import --- src/ontology/imports/uberon_terms.txt | 3 ++- src/patterns/definitions.owl | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index e127eb66f..58b07f596 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -53,4 +53,5 @@ UBERON:0004903 UBERON:0004642 UBERON:0006250 UBERON:0014727 -UBERON:0014729 \ No newline at end of file +UBERON:0014729 +UBERON:0013740 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 4e4ccaafc..5fc7c7cd2 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-17") + +Annotation(owl:versionInfo "2024-09-24") Declaration(Class()) Declaration(Class()) From 616718a1d488c4f69ded568a803c943eb0f84ed4 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 24 Sep 2024 15:56:31 +0100 Subject: [PATCH 2/3] merged import --- src/ontology/imports/merged_import.owl | 167 +++++++++++++++++++++---- 1 file changed, 143 insertions(+), 24 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index ff5037546..9318c8bfa 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 "2024-09-17") + +Annotation(owl:versionInfo "2024-09-24") Declaration(Class()) Declaration(Class()) @@ -44,7 +44,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8720,7 +8719,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10117,6 +10116,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13090,6 +13090,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -116916,7 +116922,7 @@ AnnotationAssertion( "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].") AnnotationAssertion(rdfs:label "protein") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -118499,6 +118505,7 @@ SubClassOf( (prominin) AnnotationAssertion(Annotation( "InterPro:IPR008795") Annotation( "PMID:11467842") "A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain.") +AnnotationAssertion( "PANTHER:PTHR22730") AnnotationAssertion( "PIRSF:PIRSF017831") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000001785") @@ -122098,20 +122105,20 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein-containing molecular entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000064867") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") -AnnotationAssertion(rdfs:label "protein-containing molecular entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing material entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000050567") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") +AnnotationAssertion(rdfs:label "protein-containing material entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (SCO-spondin (human)) @@ -122352,7 +122359,7 @@ SubClassOf( ObjectSomeValuesFrom( (natural killer cells antigen CD94 (mouse)) -AnnotationAssertion(Annotation( "OMA:O54707") Annotation( "PRO:DNx") "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse.") +AnnotationAssertion(Annotation( "OMA:O54707") Annotation( "PANTHER:PTHR22800:SF15") Annotation( "PRO:DNx") "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse.") AnnotationAssertion( "UniProtKB:O54707") AnnotationAssertion(Annotation( "UniProtKB:O54707") "CD94 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:O54707") "killer cell lectin-like receptor subfamily D member 1 (mouse)") @@ -122453,7 +122460,7 @@ SubClassOf( ObjectSomeValuesFrom( (CD83 antigen (mouse)) -AnnotationAssertion(Annotation( "OMA:O88324") Annotation( "PRO:DNx") "A CD83 molecule that is encoded in the genome of mouse.") +AnnotationAssertion(Annotation( "OMA:O88324") Annotation( "PANTHER:PTHR15193:SF0") Annotation( "PRO:DNx") "A CD83 molecule that is encoded in the genome of mouse.") AnnotationAssertion( "UniProtKB:O88324") AnnotationAssertion(Annotation( "UniProtKB:O88324") "CD83 (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mCD83") @@ -122535,7 +122542,6 @@ SubClassOf( ObjectSomeValuesFrom( (eomesodermin homolog (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:O95936") "An eomesodermin that is encoded in the genome of human.") -AnnotationAssertion(Annotation(rdfs:label "PR:O95936 located_in GO:0005654") "Reactome:R-HSA-452232") AnnotationAssertion( "UniProtKB:O95936") AnnotationAssertion(Annotation( "UniProtKB:O95936") "T-box brain protein 2 (human)") AnnotationAssertion(Annotation( "UniProtKB:O95936") "T-brain-2 (human)") @@ -126347,7 +126353,7 @@ AnnotationAssertion(Annotation( "ADP-ribosyl cyclase 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "ADPRC 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "T10 (human)") -AnnotationAssertion(Annotation( "UniProtKB:P28907") "cADPR hydrolase 1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P28907") "cADPr hydrolase 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "cyclic ADP-ribose hydrolase 1 (human)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hCD38") AnnotationAssertion( "protein") @@ -127768,7 +127774,7 @@ AnnotationAssertion(Annotation( "UniProtKB:P56528") "CD38 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "I-19 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "NIM-R5 antigen (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:P56528") "cADPR hydrolase 1 (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P56528") "cADPr hydrolase 1 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "cyclic ADP-ribose hydrolase 1 (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mCD38") AnnotationAssertion( "protein") @@ -161305,6 +161311,53 @@ SubClassOf(Annotation( "NCB SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) +# Class: (median eminence of neurohypophysis) + +AnnotationAssertion(Annotation( "BIRNLEX:925") "Elevation on the ventral surface of the brain located at the zone of attachment between the hypothalamic floor and the hypophysis (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg. 446).") +AnnotationAssertion(Annotation( "BIRNLEX:925") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "ME") +AnnotationAssertion( "AAO:0010539") +AnnotationAssertion( "BAMS:ME") +AnnotationAssertion( "BIRNLEX:925") +AnnotationAssertion( "BM:ME") +AnnotationAssertion( "BTO:0001954") +AnnotationAssertion( "DHBA:13338") +AnnotationAssertion( "DMBA:15689") +AnnotationAssertion( "EHDAA2:0001080") +AnnotationAssertion( "EHDAA:7540") +AnnotationAssertion( "EMAPA:17521") +AnnotationAssertion( "FMA:74634") +AnnotationAssertion( "GAID:463") +AnnotationAssertion( "HBA:12916") +AnnotationAssertion( "MA:0000859") +AnnotationAssertion( "MBA:10671") +AnnotationAssertion( "MESH:D008473") +AnnotationAssertion( "SCTID:369121004") +AnnotationAssertion(Annotation( "BIRNLEX:925") "UMLS:C0025056") +AnnotationAssertion( "VHOG:0001179") +AnnotationAssertion( "Wikipedia:Median_eminence") +AnnotationAssertion(Annotation( "BIRNLEX:925") "neuronames:402") +AnnotationAssertion(Annotation( "FMA:74634") Annotation( "FMA:TA") Annotation( ) "eminentia mediana hypothalami") +AnnotationAssertion( "median eminence") +AnnotationAssertion( "median eminence of hypothalamus") +AnnotationAssertion( "median eminence of posterior lobe of pituitary gland") +AnnotationAssertion( "median eminence of tuber cinereum") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia medialis (Shantha)") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia mediana") +AnnotationAssertion(Annotation( "Wikipedia:Median_eminence") Annotation( ) "eminentia mediana hypothalami") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia postinfundibularis") +AnnotationAssertion(Annotation( "NeuroNames:402") "medial eminence") +AnnotationAssertion( "UBERON:0002197") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "median eminence of neurohypophysis") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) + # Class: (neurohypophysis) 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.") @@ -219296,6 +219349,72 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (base of crypt of Lieberkuhn) + +AnnotationAssertion(Annotation( "UBERON:md") Annotation( "http://orcid.org/0000-0002-6601-2165") "The basal portion (further from lumen) of an intestinal crypt. Contains multipotent stem cells. Stem cells in the crypts divide to form daughter cells. One daughter cell from each stem cell division is retained as a stem cell. The other becomes committed to differentiate along one of four pathways to become an enterocyte, enteroendocrine cell, goblet cell or Paneth cell.") +AnnotationAssertion( "basal portion of intestinal gland") +AnnotationAssertion( "base of intestinal gland") +AnnotationAssertion( "base part of epithelium of intestinal gland") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013739") +AnnotationAssertion(rdfs:label "base of crypt of Lieberkuhn") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (wall of crypt of Lieberkuhn) + +AnnotationAssertion(Annotation( "UBERON:md") Annotation( "http://orcid.org/0000-0002-6601-2165") "The lateral parts of an intestinal crypt, continuous distally with the base and proximally with the intestinal villus epithelium.") +AnnotationAssertion( "wall of intestinal gland") +AnnotationAssertion( "wall part of epithelium of intestinal gland") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013740") +AnnotationAssertion(rdfs:label "wall of crypt of Lieberkuhn") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (base of crypt of Lieberkuhn of large intestine) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A base of crypt of Lieberkuhn that is part of a large intestine.") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013741") +AnnotationAssertion(rdfs:label "base of crypt of Lieberkuhn of large intestine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (wall of crypt of Lieberkuhn of large intestine) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A wall of crypt of Lieberkuhn that is part of a large intestine.") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013742") +AnnotationAssertion(rdfs:label "wall of crypt of Lieberkuhn of large intestine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (base of crypt of Lieberkuhn of small intestine) + +AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The basal portion (further from lumen) of a intestinal crypt that is located in the small intestine.") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013743") +AnnotationAssertion(rdfs:label "base of crypt of Lieberkuhn of small intestine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (wall of crypt of Lieberkuhn of small intestine) + +AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "The lateral parts of an intestinal crypt that is located in the small intestine, continuous distally with the base and proximally with the intestinal villus epithelium.") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0013744") +AnnotationAssertion(rdfs:label "wall of crypt of Lieberkuhn of small intestine") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (metaphysis of humerus) AnnotationAssertion(Annotation( "OBOL:automatic") "A metaphysis that is part of a metaphysis.") From ea4bcff97fa58278b18beea5cab76d13ea88088a Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 24 Sep 2024 15:57:42 +0100 Subject: [PATCH 3/3] def, refs --- src/ontology/cl-edit.owl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 94d1b506b..b60a7f6d1 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3070,6 +3070,7 @@ Declaration(Class(obo:CL_4047006)) Declaration(Class(obo:CL_4047007)) Declaration(Class(obo:CL_4047011)) Declaration(Class(obo:CL_4047012)) +Declaration(Class(obo:CL_4047021)) Declaration(Class(obo:CL_4047051)) Declaration(Class(obo:CL_4047052)) Declaration(Class(obo:CL_4052001)) @@ -3201,6 +3202,7 @@ Declaration(Class(obo:UBERON_0011949)) Declaration(Class(obo:UBERON_0012398)) Declaration(Class(obo:UBERON_0012399)) Declaration(Class(obo:UBERON_0012419)) +Declaration(Class(obo:UBERON_0013740)) Declaration(Class(obo:UBERON_0014727)) Declaration(Class(obo:UBERON_0014729)) Declaration(Class(obo:UBERON_0027368)) @@ -32454,6 +32456,15 @@ AnnotationAssertion(terms:date obo:CL_4047012 "2024-09-06T08:41:39Z"^^xsd:dateTi AnnotationAssertion(rdfs:label obo:CL_4047012 "angiogenic pericyte"@en) SubClassOf(obo:CL_4047012 obo:CL_0000669) +# Class: obo:CL_4047021 (laminin enterocyte of colon) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14585148") Annotation(oboInOwl:hasDbXref "PMID:35101094") obo:IAO_0000115 obo:CL_4047021 "An enterocyte located in the epithelium of the large intestine. This cell expresses and interacts with specific laminin isoforms, particularly laminin-332 (composed of α3, β3, and γ2 chains) and laminin-511 (composed of α5, β1, and γ1 chains). Laminin enterocytes of the colon are attached to the basement membrane via hemidesmosomes containing α6β4 integrin, which binds to laminins. This cell exhibits differential expression of laminin chains along the crypt-surface axis") +AnnotationAssertion(terms:contributor obo:CL_4047021 ) +AnnotationAssertion(terms:date obo:CL_4047021 "2024-09-24T14:36:31Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4047021 "laminin enterocyte of colon"@en) +EquivalentClasses(obo:CL_4047021 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013740))) +SubClassOf(obo:CL_4047021 obo:CL_1000347) + # Class: obo:CL_4047051 (small intestine BEST4+ enterocyte) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.")