diff --git a/.gitignore b/.gitignore index f8cfb6a0..54347507 100644 --- a/.gitignore +++ b/.gitignore @@ -323,3 +323,4 @@ src/ontology/reports/xrefs.tsv src/ontology/imports/*.json /src/metadata src/mappings/*.owl +.claude/ diff --git a/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntity.yaml b/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntity.yaml index 42abf912..02425335 100644 --- a/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntity.yaml @@ -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 @@ -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 diff --git a/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntityWithRole.yaml b/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntityWithRole.yaml index 7c048b50..3ffe2905 100644 --- a/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntityWithRole.yaml +++ b/src/patterns/dosdp-dev/abnormalLevelOfChemicalEntityWithRole.yaml @@ -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 @@ -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