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Add heel bone density term #356

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Feb 13, 2025
Merged

Add heel bone density term #356

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1c83293
Add heel bone density term
rays22 Feb 12, 2025
3b4333b
Update dosdp patterns file
rays22 Feb 12, 2025
53e6945
Fix labels to better reflect meaning of terms
rays22 Feb 12, 2025
b8bc198
Update dosdp patterns file
rays22 Feb 12, 2025
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5 changes: 3 additions & 2 deletions src/patterns/data/default/entity_attribute.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
1 change: 1 addition & 0 deletions src/patterns/data/default/entity_attribute_location.tsv
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Expand Up @@ -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
40 changes: 31 additions & 9 deletions src/patterns/definitions.owl
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Expand Up @@ -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>))
Expand Down Expand Up @@ -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>))
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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.")
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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>))))
Expand Down