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Restrict chemical entity patterns to anatomical entities (#981) #1023

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Restrict chemical entity patterns to anatomical entities (#981) #1023

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d5baa97
Restrict chemical entity patterns to anatomical entities (#981)
matentzn Apr 5, 2026
eab9ef6
Add .claude/ to gitignore
matentzn Apr 5, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -323,3 +323,4 @@ src/ontology/reports/xrefs.tsv
src/ontology/imports/*.json
/src/metadata
src/mappings/*.owl
.claude/
4 changes: 3 additions & 1 deletion src/patterns/dosdp-dev/abnormalLevelOfChemicalEntity.yaml
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Expand Up @@ -16,11 +16,13 @@ classes:
amount: PATO:0000070
abnormal: PATO:0000460
chemical entity: CHEBI:24431
anatomical entity: UBERON:0001062

relations:
inheres_in: RO:0000052
has_modifier: RO:0002573
has_part: BFO:0000051
part_of: BFO:0000050

annotationProperties:
exact_synonym: oio:hasExactSynonym
Expand All @@ -40,7 +42,7 @@ def:
- chemical_entity

equivalentTo:
text: "'has_part' some ('amount' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
text: "'has_part' some ('amount' and ('inheres_in' some (%s and ('part_of' some 'anatomical entity'))) and ('has_modifier' some 'abnormal'))"
vars:
- chemical_entity

4 changes: 3 additions & 1 deletion src/patterns/dosdp-dev/abnormalLevelOfChemicalEntityWithRole.yaml
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Expand Up @@ -11,12 +11,14 @@ classes:
abnormal: PATO:0000460
chemical entity: CHEBI:24431
role: CHEBI:50906
anatomical entity: UBERON:0001062

relations:
inheres_in: RO:0000052
has_modifier: RO:0002573
has_part: BFO:0000051
has_role: RO:0000087
part_of: BFO:0000050

annotationProperties:
exact_synonym: oio:hasExactSynonym
Expand All @@ -35,6 +37,6 @@ def:
- role

equivalentTo:
text: "'has_part' some ('amount' and ('inheres_in' some ('chemical entity' and ('has_role' some %s))) and ('has_modifier' some 'abnormal'))"
text: "'has_part' some ('amount' and ('inheres_in' some ('chemical entity' and ('has_role' some %s) and ('part_of' some 'anatomical entity'))) and ('has_modifier' some 'abnormal'))"
vars:
- role