diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml index 32be6a1c..94e16af4 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml @@ -1,12 +1,11 @@ -pattern_name: abnormallyDilatedAnatomicalEntity +pattern_name: abnormallyDilatedImmaterialAnatomicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntity.yaml -description: 'An abnormally dilated anatomical entity, for example, an abnormally dilated cardiac ventricle.' +description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If no space term exists use the abnormallyDilatedAnatomicalEntityLumen pattern.' # examples: # - http://purl.obolibrary.org/obo/HP_0010955 -# - http://purl.obolibrary.org/obo/XPO_0115624 # - http://purl.obolibrary.org/obo/MP_0001123 contributors: @@ -16,7 +15,7 @@ contributors: classes: abnormal: PATO:0000460 - anatomical_entity: UBERON:0001062 + immaterial_anatomical_entity: UBERON:0000466 dilated: PATO:0001571 relations: @@ -28,30 +27,30 @@ annotationProperties: exact_synonym: oio:hasExactSynonym vars: - anatomical_entity: "'anatomical_entity'" + immaterial_anatomical_entity: "'immaterial_anatomical_entity'" name: text: "abnormally dilated %s" vars: - - anatomical_entity + - immaterial_anatomical_entity annotations: - annotationProperty: exact_synonym text: "abnormal %s dilation" vars: - - anatomical_entity + - immaterial_anatomical_entity - annotationProperty: exact_synonym text: "dilated %s" vars: - - anatomical_entity + - immaterial_anatomical_entity def: text: "Abnormal dilation of %s." vars: - - anatomical_entity + - immaterial_anatomical_entity equivalentTo: text: "'has_part' some ('dilated' and ('characteristic_of' some %s) and ('has_modifier' some 'abnormal'))" vars: - - anatomical_entity + - immaterial_anatomical_entity diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml new file mode 100644 index 00000000..b6bb065f --- /dev/null +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml @@ -0,0 +1,56 @@ +pattern_name: abnormallyDilatedAnatomicalEntityLumen + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntityLumen.yaml + +description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not a separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should use the abnormallyDilatedAnatomicalEntity pattern.' + +# examples: +# - http://purl.obolibrary.org/obo/XPO_0115624 +# - http://purl.obolibrary.org/obo/MP_0001123 + +contributors: + - https://orcid.org/0000-0003-4606-0597 + +classes: + abnormal: PATO:0000460 + material_anatomical_entity: UBERON:0000465 + dilated: PATO:0001571 + anatomical space: UBERON:0000464 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + luminal_space_of: RO:0002572 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + material_anatomical_entity: "'material anatomical_entity'" + +name: + text: "abnormally dilated %s" + vars: + - material_anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "abnormal %s dilation" + vars: + - material_anatomical_entity + + - annotationProperty: exact_synonym + text: "dilated %s" + vars: + - material_anatomical_entity + +def: + text: "Abnormal dilation of the lumen of %s." + vars: + - material_anatomical_entity + +equivalentTo: + text: "'has_part' some ('dilated' and ('characteristic_of' some ('anatomical space' and ('luminal space of' some %s))) and ('has_modifier' some 'abnormal'))" + vars: + - material_anatomical_entity