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Fix taxon constraint violations #3455

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merged 4 commits into from
Dec 24, 2024
Merged

Fix taxon constraint violations #3455

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ed03865
Fix TC violations on crustacean nerves.
gouttegd Dec 23, 2024
2a1c6eb
Refresh imports.
gouttegd Dec 23, 2024
c993a17
Re-serialise edit file.
gouttegd Dec 23, 2024
ded52d2
Mark synonyms as abbreviations where appropriate.
gouttegd Dec 23, 2024
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45 changes: 42 additions & 3 deletions src/ontology/imports/merged_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -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/2024-12-17/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-12-17")
<http://purl.obolibrary.org/obo/uberon/releases/2024-12-23/imports/merged_import.owl>
Annotation(owl:versionInfo "2024-12-23")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Expand Down Expand Up @@ -10138,6 +10138,9 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6605>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6656>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6657>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6681>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6682>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6683>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6692>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6830>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6843>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6960>))
Expand All @@ -10149,6 +10152,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7147>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_716545>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7203>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_72037>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_72041>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7214>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7215>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7227>))
Expand Down Expand Up @@ -12515,7 +12519,6 @@ 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>))
Expand Down Expand Up @@ -147264,6 +147267,30 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_6681> "
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_6681> <http://purl.obolibrary.org/obo/NCBITaxon_2172821>)
DisjointClasses(<http://purl.obolibrary.org/obo/NCBITaxon_6681> <http://purl.obolibrary.org/obo/NCBITaxon_72037>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_6682> (Eucarida)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_6682> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_6682> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_6682> "NCBITaxon:6682")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_6682> "Eucarida")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_6682> <http://purl.obolibrary.org/obo/NCBITaxon_72041>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_6683> (Decapoda)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_6683> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_6683> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_6683> "NCBITaxon:6683")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_6683> "Decapoda")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_6683> <http://purl.obolibrary.org/obo/NCBITaxon_6682>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_6692> (Pleocyemata)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_6692> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_6692> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_6692> "NCBITaxon:6692")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_6692> "Pleocyemata")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_6692> <http://purl.obolibrary.org/obo/NCBITaxon_6683>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_6830> (Copepoda)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_6830> "GC_ID:1")
Expand Down Expand Up @@ -147369,6 +147396,14 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_72037> "Hexanauplia")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_72037> <http://purl.obolibrary.org/obo/NCBITaxon_2172821>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_72041> (Eumalacostraca)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_72041> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_72041> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_72041> "NCBITaxon:72041")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_72041> "Eumalacostraca")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_72041> <http://purl.obolibrary.org/obo/NCBITaxon_6681>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_7214> (Drosophilidae)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_7214> "GC_ID:1")
Expand Down Expand Up @@ -157431,6 +157466,9 @@ DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162>
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6657>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6657>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6681>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_72037>))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6681>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6681>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6682>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6682>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6683>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6683>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6692>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6692>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6830>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6830>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6843>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6843>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_6960>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_6960>)))
Expand All @@ -157444,6 +157482,7 @@ DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162>
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_716545>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_716545>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_7203>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_7203>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_72037>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_72037>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_72041>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_72041>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_7214>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_7214>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_7215>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_7215>)))
DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_7227>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_7227>)))
Expand Down
1 change: 1 addition & 0 deletions src/ontology/imports/ncbitaxon_terms.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,7 @@ NCBITaxon:65997
NCBITaxon:6656
NCBITaxon:6657
NCBITaxon:6681
NCBITaxon:6692
NCBITaxon:6830
NCBITaxon:6843
NCBITaxon:70846
Expand Down
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