Merge pull request #3052 from obophenotype/3051-fix-insect-pharynx-bo…

…gus-id 3051 Fix 'insect pharynx' bogus ID and add ID format check
obophenotype · Sep 4, 2023 · cc3ebf2 · cc3ebf2
2 parents 9f1575a + 7f6e397
commit cc3ebf2
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Showing 4 changed files with 26 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -0,0 +1,10 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+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 }
+}