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Added new 'response to' term #299

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merged 10 commits into from
Nov 14, 2023
Merged

Added new 'response to' term #299

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30f2477
Added new 'response to' term
ar-ibrahim Oct 26, 2023
89610f4
Update dosdp patterns file
ar-ibrahim Oct 26, 2023
0bc11ef
Update response_to_chemical_stimulus_trait.tsv
ar-ibrahim Nov 13, 2023
b3cc7d5
Update response_to_chemical_with_role_stimulus.tsv
ar-ibrahim Nov 13, 2023
470f26a
Update definitions.owl
ar-ibrahim Nov 13, 2023
6b8d7d1
Update merged_import.owl
ar-ibrahim Nov 13, 2023
653d5d6
Merge branch 'master' into add_response-to-antidiabetic_term
ar-ibrahim Nov 13, 2023
8482d85
Update dosdp patterns file
ar-ibrahim Nov 13, 2023
322509e
Update definitions.owl
ar-ibrahim Nov 13, 2023
45c7b79
Merge branch 'add_response-to-antidiabetic_term' of https://github.co…
ar-ibrahim Nov 13, 2023
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1 change: 1 addition & 0 deletions src/patterns/data/default/response_to_chemical_stimulus_trait.tsv
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Expand Up @@ -117,3 +117,4 @@ OBA:2050330 CHEBI:135983 teriparatide https://orcid.org/0000-0001-6757-4744
OBA:2050333 CHEBI:31941 oxaliplatin https://orcid.org/0000-0001-6757-4744
OBA:2045298 CHEBI:145810 insulin https://orcid.org/0000-0001-8314-2140
OBA:2045299 CHEBI:17234 glucose https://orcid.org/0000-0001-8314-2140
OBA:2050352 CHEBI:35526 hypoglycemic agent https://orcid.org/0000-0001-6757-4744
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It would be better to use the response_to_chemical_with_role_stimulus pattern template, because the CHEBI:35526 hypoglycemic agent is a subclass of CHEBI:50906 role and I would think that putting it into the response_to_chemical_stimulus_trait template should result in logical errors.
It is interesting that the QC did not catch it. How does owl:Nothing look like when you open oba-edit.obo in Protege?

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I think if you use theresponse_to_chemical_with_role_stimulus pattern, then the response to hypoglycemic agent will be a subclass of trait in response to drug, which it is not at the moment. Using a role entity in the response_to_chemical_stimulus_trait used to generate logical errors. It is strange it does in this case.

14 changes: 12 additions & 2 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/2023-10-17/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-10-17"^^xsd:string)
<http://purl.obolibrary.org/obo/oba/releases/2023-10-26/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-10-26"^^xsd:string)

Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
Expand Down Expand Up @@ -243,6 +243,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35475>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35476>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35498>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35523>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35526>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35530>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35581>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_35610>))
Expand Down Expand Up @@ -12438,6 +12439,7 @@ 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_2050352>))
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 @@ -103837,6 +103839,14 @@ 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_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)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2050352> "https://orcid.org/0000-0001-6757-4744"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2050352> "response to hypoglycemic agent trait"^^xsd:string)
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> <http://purl.obolibrary.org/obo/CHEBI_35526>)))))

# 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