From 96d18da80a4925ab816a79353af492ae083ce75f Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Mon, 14 Apr 2025 16:03:14 +0100 Subject: [PATCH] Update the EQ in abnormalLevelOfChemicalEntity This commit intends to restrict the scope of the abnormalLevelOfChemicalEntity pattern to apply to chemical qualities only in anatomical entities. To achieve this, the logical definition will be updated. If applied, this commit will fix #981. --- .../abnormalLevelOfChemicalEntity.yaml | 35 +++++++++++-------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntity.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntity.yaml index 42abf912..cfd1c8ae 100644 --- a/src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntity.yaml +++ b/src/patterns/dosdp-patterns/abnormalLevelOfChemicalEntity.yaml @@ -1,29 +1,34 @@ pattern_name: abnormalLevelOfChemicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalLevelOfChemicalEntity.yaml -description: "An abnormal amount of a chemical or protein. For example, MP_0011230 'abnormal folic acid level or HP:0012146 Abnormality of von Willebrand factor.'" +description: "An abnormal amount of a chemical or protein that is part of an + organism. For example, MP_0011230 'abnormal folic acid level or + HP:0012146 Abnormality of von Willebrand factor.'" contributors: - - https://orcid.org/0000-0003-4606-0597 - - https://orcid.org/0000-0002-9900-7880 - - https://orcid.org/0000-0002-3528-5267 - - https://orcid.org/0000-0001-5208-3432 - - https://orcid.org/0000-0003-4148-4606 - - https://orcid.org/0000-0001-7941-2961 - - https://orcid.org/0000-0002-7356-1779 - - https://orcid.org/0000-0001-9076-6015 + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-9900-7880 # Yvonne M. Bradford + - https://orcid.org/0000-0002-3528-5267 # Sofia Robb + - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky + - https://orcid.org/0000-0003-4148-4606 # Midori A. Harris + - https://orcid.org/0000-0001-7941-2961 # Leigh Carmody + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0001-9076-6015 # Christian A. Grove + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik classes: amount: PATO:0000070 abnormal: PATO:0000460 chemical entity: CHEBI:24431 + anatomical_entity: UBERON:0001062 relations: - inheres_in: RO:0000052 + characteristic_of: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051 + part_of: BFO:0000050 annotationProperties: - exact_synonym: oio:hasExactSynonym + exact_synonym: oio:hasExactSynonym vars: chemical_entity: "'chemical entity'" @@ -31,7 +36,7 @@ vars: name: text: "abnormal %s level" vars: - - chemical_entity + - chemical_entity def: @@ -40,7 +45,9 @@ 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 ('characteristic_of' some (%s + and ('part_of' some 'anatomical_entity'))) + and ('has_modifier' some 'abnormal')" vars: - chemical_entity -