diff --git a/src/ontology/Makefile b/src/ontology/Makefile index f980507dec..2b8579b732 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -42,7 +42,7 @@ REPORT_FAIL_ON = ERROR REPORT_LABEL = REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = -SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy +SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format SPARQL_EXPORTS = basic-report ODK_VERSION_MAKEFILE = v1.4.1 diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 0603c65b50..b6a65912b8 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -219068,12 +219068,11 @@ relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:60005380 -name: insect pharynx -def: "Section of the insect foregut anterior to the esophagus." [FBbt:00005380, http://orcid.org/0000-0002-6601-2165] -xref: FBbt:00005380 -is_a: UBERON:0004921 {source="FBbt"} ! subdivision of digestive tract -is_a: UBERON:0006562 {notes="parent may be obsoleted"} ! pharynx -relationship: part_of UBERON:0003929 {source="FBbt"} ! digestive tract epithelium +name: obsolete insect pharynx +comment: Obsoleted because the ID was minted incorrectly. +property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3051" xsd:anyURI +is_obsolete: true +replaced_by: UBERON:6005380 [Term] id: UBERON:6001055 @@ -220225,6 +220224,15 @@ synonym: "margin" BROAD [] is_a: UBERON:6007284 ! insect region of integument relationship: part_of UBERON:0000984 ! imaginal disc-derived wing +[Term] +id: UBERON:6005380 +name: insect pharynx +def: "Section of the insect foregut anterior to the esophagus." [FBbt:00005380, http://orcid.org/0000-0002-6601-2165] +xref: FBbt:00005380 +is_a: UBERON:0004921 {source="FBbt"} ! subdivision of digestive tract +is_a: UBERON:0006562 {note="parent may be obsoleted"} ! pharynx +relationship: part_of UBERON:0003929 {source="FBbt"} ! digestive tract epithelium + [Term] id: UBERON:6005393 name: insect embryonic/larval integumentary system diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index d62c7355d8..bebd93a379 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -108,6 +108,7 @@ robot_report: - obsolete-replaced_by - xrefs-mesh-pattern - label-synonym-polysemy + - id-format custom_sparql_exports: - basic-report owltools_memory: '20G' diff --git a/src/sparql/id-format-violation.sparql b/src/sparql/id-format-violation.sparql new file mode 100644 index 0000000000..2adeb2d7f6 --- /dev/null +++ b/src/sparql/id-format-violation.sparql @@ -0,0 +1,10 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: + +SELECT ?cls WHERE { + ?cls a owl:Class . + FILTER (strstarts(str(?cls), "http://purl.obolibrary.org/obo/UBERON_") && + ! regex(str(?cls), "^http://purl.obolibrary.org/obo/UBERON_[0-9]{7}$")) + FILTER NOT EXISTS { ?cls owl:deprecated ?v } +}