Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added new 'density' term #294

Merged
merged 9 commits into from
Dec 7, 2023
Merged

Added new 'density' term #294

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
b953d39
Added new 'density' term
ar-ibrahim Oct 5, 2023
e61bf1e
Update dosdp patterns file
ar-ibrahim Oct 5, 2023
a3a345d
Update src/patterns/data/default/entity_attribute.tsv
ar-ibrahim Dec 7, 2023
f0131b0
Merge branch 'master' into add_NTR_density
ar-ibrahim Dec 7, 2023
69b1b4c
Merge branch 'add_NTR_density' of https://github.com/obophenotype/bio…
ar-ibrahim Dec 7, 2023
7115f3a
Update dosdp patterns file
ar-ibrahim Dec 7, 2023
689c0ec
Update entity attribute file. Restore previous terms.
rays22 Sep 27, 2023
64d8e69
Updated entity_attribute.tsv
ar-ibrahim Dec 7, 2023
6eea753
Update dosdp patterns file
ar-ibrahim Dec 7, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions src/patterns/data/default/entity_attribute.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4384,3 +4384,4 @@ OBA:2045439 body surface area UBERON:0035159 entire surface of organism PATO:000
OBA:2045451 attribute of response to allergen in serum UBERON:0001977 blood serum OBA:2045453 attribute of response to allergen https://orcid.org/0000-0001-8314-2140
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
rays22 marked this conversation as resolved.
Show resolved Hide resolved
OBA:2050351 breast density UBERON:0000310 breast PATO:0001019 mass density breast tissue density PMID:37345113 https://orcid.org/0000-0001-6757-4744
26 changes: 24 additions & 2 deletions src/patterns/definitions.owl
View file
Open in desktop
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/oba/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/oba/releases/2023-12-05/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-12-05"^^xsd:string)
<http://purl.obolibrary.org/obo/oba/releases/2023-12-07/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-12-07"^^xsd:string)

Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
Expand Down Expand Up @@ -1494,6 +1494,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005147>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005148>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005178>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005180>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005184>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005271>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005277>))
Declaration(Class(<http://purl.obolibrary.org/obo/MONDO_0005301>))
Expand Down Expand Up @@ -12509,7 +12510,9 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050346>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050347>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050348>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050349>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050351>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050352>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050353>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060000>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060001>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060002>))
Expand Down Expand Up @@ -104458,6 +104461,16 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2050349> "level of interleukin-12 subunit beta in blood"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050349> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000001369> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_2050351> (breast density)

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_2050351> "The mass density of a breast."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2050351> "https://orcid.org/0000-0001-6757-4744"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/OBA_2050351> "PMID:37345113"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2050351> "breast tissue density"^^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_2050351> "mass density of breast"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2050351> "breast density"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050351> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001019> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000310>)))

# Class: <http://purl.obolibrary.org/obo/OBA_2050352> (trait in response to hypoglycemic agent)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2050352> "A trait that affects the response to a stimulus with hypoglycemic agent."^^xsd:string)
Expand All @@ -104466,6 +104479,14 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2050352> "trait in response to hypoglycemic agent"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050352> 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_35526>)))))))

# Class: <http://purl.obolibrary.org/obo/OBA_2050353> (age of onset of pancreatic ductal adenocarcinoma)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2050353> "The age at which pancreatic ductal adenocarcinoma manifestations first appear."^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2050353> "age at onset of pancreatic ductal adenocarcinoma"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2050353> "age pancreatic ductal adenocarcinoma symptoms begin"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2050353> "age of onset of pancreatic ductal adenocarcinoma"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2050353> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/HP_0003674> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/MONDO_0005184>)))

# Class: <http://purl.obolibrary.org/obo/OBA_2060000> (aggressive behavior towards inanimate objects rate)

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_2060000> "The rate of a aggressive behavior towards inanimate objects."^^xsd:string)
Expand Down Expand Up @@ -124491,6 +124512,7 @@ SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000992> Ob
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000992> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001968>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000992> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001968>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000992> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001977>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000992> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001977>))))
SubClassOf(ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001005> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/GO_0030431>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001005> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/GO_0030431>))))
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_0000310>))) 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_0000310>))))
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_0001037>))) 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_0001037>))))
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_0001130>))) 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_0001130>))))
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_0001435>))) 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_0001435>))))
Expand Down