Merge pull request #356 from obophenotype/issue355

Add heel bone density term
obophenotype · Feb 13, 2025 · a42c3fb · a42c3fb
2 parents 45816b3 + b8bc198
commit a42c3fb
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Showing 3 changed files with 35 additions and 11 deletions.
diff --git a/src/patterns/data/default/entity_attribute.tsv b/src/patterns/data/default/entity_attribute.tsv
@@ -117,7 +117,7 @@ OBA:1000105	tissue composition	UBERON:0000479	tissue	PATO:0000025	composition
 OBA:1000106	skeletal tissue composition	UBERON:0004755	skeletal tissue	PATO:0000025	composition			
 OBA:1000107	testis position	UBERON:0000473	testis	PATO:0000140	position			
 OBA:1000109	anatomical pigmentation	UBERON:0000061	anatomical structure	PATO:0002247	degree of pigmentation			
-OBA:1000110	bone density	UBERON:0002481	bone tissue	PATO:0001019	mass density			
+OBA:1000110	bone tissue density	UBERON:0002481	bone tissue	PATO:0001019	mass density			https://orcid.org/0000-0001-8314-2140
 OBA:1000111	adrenal gland size	UBERON:0002369	adrenal gland	PATO:0000117	size			
 OBA:1000112	tooth size	UBERON:0001091	calcareous tooth	PATO:0000117	size			
 OBA:1000113	incisor size	UBERON:0001098	incisor tooth	PATO:0000117	size			
@@ -571,7 +571,6 @@ OBA:VT0004954	thymus mass	UBERON:0002370	thymus	PATO:0000125	mass
 OBA:VT0004972	regulatory T cell quantity	CL:0000815	regulatory T cell	PATO:0001555	has number of			
 OBA:VT0004976	B-1 B cell quantity	CL:0000819	B-1 B cell	PATO:0001555	has number of			
 OBA:VT0005006	osteoblast physiology trait	CL:0000062	osteoblast	PATO:0001509	functionality			
-OBA:VT0005007	bone mineral mass	UBERON:0001474	bone element	PATO:0001019	mass density			
 OBA:VT0005045	thymus cortex area	UBERON:0002123	cortex of thymus	PATO:0001323	area			
 OBA:VT0005069	NK cell physiology trait	CL:0000623	natural killer cell	PATO:0001509	functionality			
 OBA:VT0005078	cytotoxic T cell physiology trait	CL:0000910	cytotoxic T cell	PATO:0001509	functionality			
@@ -4387,3 +4386,5 @@ OBA:VT1000472	subcutaneous adipose mass	UBERON:0002190	subcutaneous adipose tiss
 OBA:VT0010482	body fat mass	UBERON:0001013	adipose tissue	PATO:0000125	mass			https://orcid.org/0000-0001-8314-2140
 OBA:2050418	voice quality trait	UBERON:0034681	vocal organ	PATO:0001519	sound quality		PMID:37294764	https://orcid.org/0000-0001-6757-4744
 OBA:2045460	body extent	UBERON:0000468	multicellular organism	PATO:0001708	1-D extent			https://orcid.org/0000-0001-6757-4744
+OBA:2045558	heel bone density	UBERON:0001450	calcaneus	PATO:0001019	mass density			https://orcid.org/0000-0001-8314-2140
+OBA:2045559	bone density	UBERON:0001474	bone element	PATO:0001019	mass density			https://orcid.org/0000-0001-8314-2140
diff --git a/src/patterns/data/default/entity_attribute_location.tsv b/src/patterns/data/default/entity_attribute_location.tsv
@@ -8052,3 +8052,4 @@ OBA:2052957		PR:Q96J42		PATO:0000070	amount	UBERON:0000178	blood				PMID:3841286
 OBA:2052958		PR:O75356		PATO:0000070	amount	UBERON:0000178	blood				PMID:38412862	https://orcid.org/0000-0001-6757-4744
 OBA:2052959		PR:P51531		PATO:0000070	amount	UBERON:0000178	blood				PMID:38412862	https://orcid.org/0000-0001-6757-4744
 OBA:2052960		PR:P00441		PATO:0000070	amount	UBERON:0000178	blood				PMID:38412862	https://orcid.org/0000-0001-6757-4744
+OBA:VT0005007	bone mineral amount	CHEBI:46662	mineral	PATO:0000070	amount	UBERON:0001474	bone element	bone mineral mass				https://orcid.org/0000-0001-8314-2140
diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2025-01-28/patterns/definitions.owl>
-Annotation(owl:versionInfo "2025-01-28")
+<http://purl.obolibrary.org/obo/oba/releases/2025-02-12/patterns/definitions.owl>
+Annotation(owl:versionInfo "2025-02-12")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
@@ -12261,6 +12261,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045554>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045555>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045556>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045557>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045558>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2045559>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050003>))
@@ -59398,11 +59400,12 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_1000109> "anatomical pigmentation")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_1000109> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0002247> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000061>)))
 
-# Class: <http://purl.obolibrary.org/obo/OBA_1000110> (bone density)
+# Class: <http://purl.obolibrary.org/obo/OBA_1000110> (bone tissue density)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_1000110> "The mass density of a bone tissue.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_1000110> "https://orcid.org/0000-0001-8314-2140")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_1000110> "mass density of bone tissue")
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_1000110> "bone density")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_1000110> "bone tissue density")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_1000110> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002481>)))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_1000111> (adrenal gland size)
@@ -109468,6 +109471,22 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045557> "response to environmental contaminant characteristics")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045557> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001236> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0050896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CHEBI_24431> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/CHEBI_78298>)))))))
 
+# Class: <http://purl.obolibrary.org/obo/OBA_2045558> (heel bone density)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2045558> "The mass density of a calcaneus.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2045558> "https://orcid.org/0000-0001-8314-2140")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045558> "mass density of calcaneus")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045558> "heel bone density")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045558> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001450>)))
+
+# Class: <http://purl.obolibrary.org/obo/OBA_2045559> (bone density)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2045559> "The mass density of a bone element.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2045559> "https://orcid.org/0000-0001-8314-2140")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2045559> "mass density of bone element")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2045559> "bone density")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2045559> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001474>)))
+
 # Class: <http://purl.obolibrary.org/obo/OBA_2050001> (ascending aorta diameter)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2050001> "The diameter of a ascending aorta.")
@@ -171061,12 +171080,14 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0005006> "osteoblast physiology trait")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0005006> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001509> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/CL_0000062>)))
 
-# Class: <http://purl.obolibrary.org/obo/OBA_VT0005007> (bone mineral mass)
+# Class: <http://purl.obolibrary.org/obo/OBA_VT0005007> (bone mineral amount)
 
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0005007> "The mass density of a bone element.")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT0005007> "mass density of bone element")
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0005007> "bone mineral mass")
-EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0005007> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001474>)))
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0005007> "The amount of a mineral when measured in bone element.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_VT0005007> "https://orcid.org/0000-0001-8314-2140")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT0005007> "bone element mineral amount")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT0005007> "bone mineral mass")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0005007> "bone mineral amount")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0005007> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CHEBI_46662> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001474>)))))
 
 # Class: <http://purl.obolibrary.org/obo/OBA_VT0005008> (osteoblast development trait)
 
@@ -180833,6 +180854,7 @@ SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> Ob
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001437>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001437>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001438>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001438>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001447>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001447>))))
+SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001450>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001450>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001474>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001474>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001686>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001686>))))
 SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002293>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002293>))))