Merge pull request #3336 from obophenotype/fix-taxon-constraints

Fix the check for taxon constraint violations

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.5
+# ODK Version: v1.5.2
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                efb88af827f2af6cc513d695dc0dd59380e3e34c4ecf16d3648ebcfbba0aa64f
+CONFIG_HASH=                9531f9cc87d9bbbcf0d424b5845e95234e9cd34df6d28bdbb856a4ba7b5557ad
 
 
 # ----------------------------------------
@@ -47,7 +47,7 @@ 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 id-format 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.5
+ODK_VERSION_MAKEFILE =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -370,7 +370,7 @@ ALLSEED = $(PRESEED)  $(TMPDIR)/all_pattern_terms.txt \
 $(IMPORTSEED): $(ALLSEED) | $(TMPDIR)
 	if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi
 
-ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 
+ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 OMO:0002000 
 
 # ----------------------------------------
 # Import modules

src/ontology/imports/merged_import.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/uberon/releases/2024-08-06/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-08-06")
+<http://purl.obolibrary.org/obo/uberon/releases/2024-08-13/imports/merged_import.owl>
+Annotation(owl:versionInfo "2024-08-13")
 
 Declaration(Class(<http://birdgenenames.org/cgnc/GeneReport?id=10067>))
 Declaration(Class(<http://birdgenenames.org/cgnc/GeneReport?id=14621>))
@@ -12466,6 +12466,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000425>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000700>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0006012>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0002000>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003000>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003002>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003003>))
@@ -12546,7 +12547,6 @@ Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/date>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
-Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
 Declaration(AnnotationProperty(<http://usefulinc.com/ns/doap#GitRepository>))
 Declaration(AnnotationProperty(<http://usefulinc.com/ns/doap#bug-database>))
 Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#SubsetProperty>))
@@ -12711,13 +12711,55 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OMO_0003011> "lat
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/RO_0002161> "tooth SubClassOf 'never in taxon' value 'Aves'")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002161> "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(<http://purl.obolibrary.org/obo/IAO_0000425> <http://purl.obolibrary.org/obo/RO_0002161> "Class: ?X DisjointWith: RO_0002162 some ?Y ")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/OMO_0002000> <http://purl.obolibrary.org/obo/RO_0002161> "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
+PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
+CONSTRUCT {
+  in_taxon: a owl:ObjectProperty .
+  ?x owl:disjointWith [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom ?taxon
+  ] .
+  ?x rdfs:subClassOf [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom [
+      a owl:Class ;
+      owl:complementOf ?taxon
+    ]
+  ] .
+}
+WHERE {
+  ?x never_in_taxon: ?taxon .
+}")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002161> "never in taxon")
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0002161> <https://github.com/obophenotype/uberon/wiki/Taxon-constraints>)
 
 # Annotation Property: <http://purl.obolibrary.org/obo/RO_0002171> (mutually spatially disjoint with)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002171> "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000425> <http://purl.obolibrary.org/obo/RO_0002171> "Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/OMO_0002000> <http://purl.obolibrary.org/obo/RO_0002171> "PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
+PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171>
+CONSTRUCT {
+  part_of: a owl:ObjectProperty .
+  [
+    a owl:Restriction ;
+    owl:onProperty part_of: ;
+    owl:someValuesFrom ?x ;
+    owl:disjointWith [
+      a owl:Restriction ;
+      owl:onProperty part_of: ;
+      owl:someValuesFrom ?y
+    ]
+  ]
+}
+WHERE {
+  ?x mutually_spatially_disjoint_with: ?y .
+}")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002171> "mutually spatially disjoint with"@en)
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0002171> <http://purl.obolibrary.org/obo/RO_0002163>)
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0002171> "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI)
@@ -12738,6 +12780,30 @@ AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0002174> <ht
 # Annotation Property: <http://purl.obolibrary.org/obo/RO_0002175> (present in taxon)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002175> "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(<http://purl.obolibrary.org/obo/OMO_0002000> <http://purl.obolibrary.org/obo/RO_0002175> "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
+PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
+CONSTRUCT {
+  in_taxon: a owl:ObjectProperty .
+  ?witness rdfs:label ?label .
+  ?witness rdfs:subClassOf ?x .
+  ?witness rdfs:subClassOf [
+    a owl:Restriction ;
+    owl:onProperty in_taxon: ;
+    owl:someValuesFrom ?taxon
+  ] .
+}
+WHERE {
+  ?x present_in_taxon: ?taxon .
+  BIND(IRI(CONCAT(
+    \"http://purl.obolibrary.org/obo/RO_0002175#\",
+    MD5(STR(?x)),
+    \"-\",
+    MD5(STR(?taxon))
+  )) as ?witness)
+  BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)
+}")
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/RO_0002175> "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 <http://purl.obolibrary.org/obo/RO_0002175> "present in taxon"@en)
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0002175> <https://github.com/obophenotype/uberon/wiki/Taxon-constraints>)
@@ -46784,10 +46850,9 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_2000062> <http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>)
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/CL_2000062> "http://www.ncbi.nlm.nih.gov/books/NBK53245/")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_2000062> "placental villus capillary endothelial cell")
-EquivalentClasses(<http://purl.obolibrary.org/obo/CL_2000062> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_0002144> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0010005>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/CL_2000062> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_0002144> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001987>)))
 SubClassOf(<http://purl.obolibrary.org/obo/CL_2000062> <http://purl.obolibrary.org/obo/CL_0002144>)
 SubClassOf(<http://purl.obolibrary.org/obo/CL_2000062> <http://purl.obolibrary.org/obo/CL_0009092>)
-SubClassOf(<http://purl.obolibrary.org/obo/CL_2000062> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0010005>))
 
 # Class: <http://purl.obolibrary.org/obo/CL_2000063> (ovarian fibroblast)
 

src/ontology/uberon-edit.obo

@@ -110900,7 +110900,6 @@ xref: XAO:0000326
 is_a: UBERON:0001048 {source="XAO"} ! primordium
 is_a: UBERON:0003104 ! mesenchyme
 relationship: develops_from UBERON:0004872 {source="XAO"} ! splanchnic layer of lateral plate mesoderm
-relationship: part_of UBERON:0005602 {source="EHDAA2-modified"} ! dorsal mesogastrium
 property_value: external_ontology_notes "check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme" xsd:string {external_ontology="EMAPA"}
 
 [Term]
@@ -143152,7 +143151,6 @@ is_a: UBERON:0010913 ! vertebral element
 intersection_of: UBERON:0010913 ! vertebral element
 intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue
 relationship: develops_from UBERON:0011095 ! vertebra pre-cartilage condensation
-relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra
 relationship: present_in_taxon NCBITaxon:7764 {notes="vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist", source="PMC3157150"} ! Eptatretus burgeri
 property_value: external_ontology_notes "This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups" xsd:string {external_ontology="EHDAA2"}
 
@@ -143166,7 +143164,7 @@ xref: VHOG:0000582
 intersection_of: UBERON:0010913 ! vertebral element
 intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation
 relationship: develops_from UBERON:0003089 {source="EHDAA2-abduced"} ! sclerotome
-relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra
+relationship: has_potential_to_develop_into UBERON:0011094 ! vertebra cartilage element
 
 [Term]
 id: UBERON:0011096

src/ontology/uberon-odk.yaml

@@ -29,6 +29,10 @@ release_artefacts:
   - custom-common-anatomy
 edit_format: obo
 import_group:
+  annotation_properties:
+    - rdfs:label
+    - IAO:0000115
+    - OMO:0002000
   use_base_merging: TRUE
   slme_individuals: exclude
   exclude_iri_patterns: