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Add or map 'mass' related terms from VT #146

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merged 16 commits into from
Dec 7, 2023
Merged

Add or map 'mass' related terms from VT #146

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e95bc6c
Add mass related terms from VT
rays22 Sep 23, 2022
4292c82
Update SSSOM mapping file
rays22 Sep 23, 2022
690af81
Update dosdp patterns file
rays22 Sep 23, 2022
33d36df
Merge branch 'master' into issue85mass
rays22 Sep 27, 2022
0128a75
Update dosdp patterns file
rays22 Sep 27, 2022
bf1cf3a
Merge branch 'master' into issue85mass
matentzn Nov 26, 2022
bdb2377
Update dosdp patterns file
matentzn Nov 26, 2022
d4ec130
Update files to latest versions
rays22 Dec 6, 2023
917a05f
A short title (less than 50 character; no period )
rays22 Dec 6, 2023
384685e
Merge branch 'master' into issue85mass
rays22 Dec 6, 2023
4885d33
Refresh definitions
rays22 Dec 6, 2023
de56ddc
Update dosdp patterns file
rays22 Dec 6, 2023
50e32c5
Resolve conflicts with master branch
rays22 Dec 7, 2023
119fce7
Merge master
rays22 Dec 7, 2023
854d48d
Add back new terms
rays22 Dec 7, 2023
801fbc6
Update dosdp patterns file
rays22 Dec 7, 2023
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2 changes: 2 additions & 0 deletions src/patterns/data/default/entity_attribute.tsv
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Expand Up @@ -4385,3 +4385,5 @@ OBA:2045451 attribute of response to allergen in serum UBERON:0001977 blood ser
OBA:2045452 attribute of response to thyroid hormone in plasma UBERON:0001969 blood plasma OBA:2045454 attribute of response to thyroid hormone https://orcid.org/0000-0001-8314-2140
OBA:2030004 total skin mass UBERON:0002097 skin of body PATO:0000125 mass mass of the entire skin https://orcid.org/0000-0003-2699-3066
OBA:2050351 breast density UBERON:0000310 breast PATO:0001019 mass density breast tissue density PMID:37345113 https://orcid.org/0000-0001-6757-4744
OBA:VT1000472 subcutaneous adipose mass UBERON:0002190 subcutaneous adipose tissue PATO:0000125 mass https://orcid.org/0000-0001-8314-2140
OBA:VT0010482 body fat mass UBERON:0001013 adipose tissue PATO:0000125 mass 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 @@ -5452,3 +5452,4 @@ OBA:2045447 oxygen concentration in capillary blood CHEBI:25805 oxygen atom PAT
OBA:2045448 attribute of response to heparin in plasma CHEBI:28304 heparin PATO:0000077 response to UBERON:0001969 blood plasma https://orcid.org/0000-0001-8314-2140
OBA:2045449 plasma thyroxine level CHEBI:30660 thyroxine PATO:0000070 amount UBERON:0001969 blood plasma https://orcid.org/0000-0001-8314-2140
OBA:2045450 blood hemoglobin attribute CHEBI:35143 hemoglobin PATO:0000001 quality UBERON:0000178 blood blood haemoglobin attribute https://orcid.org/0000-0001-8314-2140
OBA:VT0010690 pericardial fat pad mass UBERON:0003916 fat pad PATO:0000125 mass UBERON:0035814 pericardial fat https://orcid.org/0000-0001-8314-2140
29 changes: 29 additions & 0 deletions src/patterns/definitions.owl
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Expand Up @@ -14657,6 +14657,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010476>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010477>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010480>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010481>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010482>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010484>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010487>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010489>))
Expand Down Expand Up @@ -14725,6 +14726,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010676>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010677>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010679>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010684>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010690>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010693>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010694>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0010695>))
Expand Down Expand Up @@ -14860,6 +14862,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000434>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000435>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000436>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000444>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000472>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000479>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000574>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT1000575>))
Expand Down Expand Up @@ -119498,6 +119501,14 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0010481> "blood immunoglobulin M amount"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0010481> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/GO_0071754> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_VT0010482> (body fat mass)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0010482> "The mass of a adipose tissue."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_VT0010482> "https://orcid.org/0000-0001-8314-2140"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT0010482> "mass of adipose tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0010482> "body fat mass"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0010482> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001013>)))

# Class: <http://purl.obolibrary.org/obo/OBA_VT0010484> (nervous system serotonin amount)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0010484> "The amount of a serotonin when measured in nervous system."^^xsd:string)
Expand Down Expand Up @@ -119974,6 +119985,14 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0010684> "peritoneum morphology"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0010684> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000051> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0002358>)))

# Class: <http://purl.obolibrary.org/obo/OBA_VT0010690> (pericardial fat pad mass)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0010690> "The mass of a fat pad when measured in pericardial fat."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_VT0010690> "https://orcid.org/0000-0001-8314-2140"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT0010690> "pericardial fat fat pad mass"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT0010690> "pericardial fat pad mass"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT0010690> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0003916> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0035814>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_VT0010693> (longissimus muscle morphology)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "obo:oba/patterns/entity_attribute_part_of"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0010693> "The morphology of a longissimus muscle."^^xsd:string)
Expand Down Expand Up @@ -120921,6 +120940,14 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT1000444> "adipose androstenone amount"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT1000444> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CHEBI_37894> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001013>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_VT1000472> (subcutaneous adipose mass)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT1000472> "The mass of a subcutaneous adipose tissue."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_VT1000472> "https://orcid.org/0000-0001-8314-2140"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_VT1000472> "mass of subcutaneous adipose tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_VT1000472> "subcutaneous adipose mass"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_VT1000472> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002190>)))

# Class: <http://purl.obolibrary.org/obo/OBA_VT1000479> (muscle lipid amount)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT1000479> "The amount of a lipid when measured in muscle organ."^^xsd:string)
Expand Down Expand Up @@ -123638,6 +123665,7 @@ SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> Ob
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000995>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000995>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000996>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000996>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000998>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000998>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001013>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001013>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001043>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001043>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001052>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001052>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001062>))))
Expand Down Expand Up @@ -123686,6 +123714,7 @@ SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> Ob
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002114>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002114>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002115>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002115>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002116>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002116>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002190>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002190>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002247>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002247>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002366>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002366>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002367>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000125> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002367>))))
Expand Down