Fix biological attribute child violation errors

If applied, this commit will fix #312.
obophenotype · May 21, 2024 · 39a7d06 · 39a7d06
1 parent b2654f1
commit 39a7d06
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
@@ -102203,7 +102203,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynon
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/OBA_2045455> "body mass index")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/OBA_2045455> "height-adjusted BMI")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045455> "body mass to height ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045455> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0001259>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0001253>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045455> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0001259>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0001253>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2045456> (body mass to body extent ratio)
 
@@ -102215,7 +102215,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/OBA_2045456> "BMI")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/OBA_2045456> "body mass index")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045456> "body mass to body extent ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045456> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0001259>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_2045460>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045456> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0001259>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_2045460>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2045457> (waist to height ratio)
 
@@ -102226,7 +102226,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045457> "waist height ratio")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045457> "waist-height ratio")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045457> "waist to height ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045457> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_1001085>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0001253>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045457> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_1001085>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0001253>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2045458> (visceral to subcutaneous adipose tissue ratio)
 
@@ -102235,15 +102235,15 @@ AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibra
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/attribute_ratio") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045458> "the ratio of visceral adipose tissue quantity to subcutaneous adipose tissue amount")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045458> "visceral:subcutaneous adipose tissue ratio")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045458> "visceral to subcutaneous adipose tissue ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045458> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_2045224>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_0004504>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045458> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_2045224>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_0004504>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2045459> (digit length ratio)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/attribute_ratio") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2045459> "A compound attribute that is the ratio of digit length to digit length.")
 AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2045459> "https://orcid.org/0000-0001-8314-2140")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/attribute_ratio") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045459> "the ratio of digit length to digit length")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045459> "digit length ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045459> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0002544>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0002544>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045459> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0002544>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_VT0002544>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2045460> (body extent)
 
@@ -104660,7 +104660,7 @@ AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibra
 AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2050350> "https://orcid.org/0000-0001-8314-2140")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/attribute_ratio") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2050350> "the ratio of urine sodium amount to urine potassium amount")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2050350> "urinary sodium to potassium ratio")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050350> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0006274>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_2050095>)))
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050350> ObjectIntersectionOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020202> <http://purl.obolibrary.org/obo/OBA_VT0006274>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0020203> <http://purl.obolibrary.org/obo/OBA_2050095>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0001062>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_2050351> (breast density)
 

diff --git a/src/patterns/dosdp-patterns/attribute_ratio.yaml b/src/patterns/dosdp-patterns/attribute_ratio.yaml
@@ -19,6 +19,7 @@ contributors:
 classes:
   ratio: PATO:0001470
   quality: PATO:0000001
+  anatomical_entity: UBERON:0001062
   external_resource: xsd:anyURI
   orcid: xsd:anyURI
 
@@ -90,7 +91,8 @@ xref:
 equivalentTo:
   text: "('ratio'
     and ('has_numerator' some %s)
-    and ('has_denominator' some %s))"
+    and ('has_denominator' some %s))
+    and ('characteristic_of_part_of' some 'anatomical_entity')"
   vars:
     - attribute1
     - attribute2