From 9a2b0a0266ffd8dd296bcf6312b7f5a180dc468d Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 1 Oct 2025 15:56:38 -0400 Subject: [PATCH 1/5] working on #1002 Creating a new pattern for dilated lumen --- ...mallyDilatedAnatomicalEntityLumen.yaml.txt | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt new file mode 100644 index 00000000..00472f99 --- /dev/null +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt @@ -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 separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should us 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 + anatomical_entity: UBERON:0001062 + 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: + anatomical_entity: "'anatomical_entity'" + +name: + text: "abnormally dilated %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "abnormal %s dilation" + vars: + - anatomical_entity + + - annotationProperty: exact_synonym + text: "dilated %s" + vars: + - anatomical_entity + +def: + text: "Abnormal dilation of the lumen of %s." + vars: + - 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: + - anatomical_entity From dc80b7198b4dd65907c3d6d50afe10cdc9d4486b Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Fri, 3 Oct 2025 12:02:58 -0400 Subject: [PATCH 2/5] working on #1002 abnormallyDilatedAnatomicalEntityLumen Fixed typos in description changed variable to material anatomical entity abnormallyDilatedAnatomicalEntity Added text to description to indicate when each pattern should be used changed title to include Immaterial chanced variable to immaterial anatomical entity --- .../abnormallyDilatedAnatomicalEntity.yaml | 21 +++++++++---------- ...normallyDilatedAnatomicalEntityLumen.yaml} | 16 +++++++------- 2 files changed, 18 insertions(+), 19 deletions(-) rename src/patterns/dosdp-dev/{abnormallyDilatedAnatomicalEntityLumen.yaml.txt => abnormallyDilatedAnatomicalEntityLumen.yaml} (69%) diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml index 32be6a1c..9d13af8e 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 +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyImmaterialDilatedAnatomicalEntity.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 not space term exists use the abnormallyDilatedAnatomicalEntityLumne 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.txt b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml similarity index 69% rename from src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt rename to src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml index 00472f99..728830af 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml.txt +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml @@ -2,7 +2,7 @@ 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 separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should us the abnormallyDilatedAnatomicalEntity pattern.' +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 abnormallyDilatedImmaterialAnatomicalEntity pattern.' # examples: # - http://purl.obolibrary.org/obo/XPO_0115624 @@ -13,7 +13,7 @@ contributors: classes: abnormal: PATO:0000460 - anatomical_entity: UBERON:0001062 + material_anatomical_entity: UBERON:0000465 dilated: PATO:0001571 anatomical space: UBERON:0000464 @@ -27,30 +27,30 @@ annotationProperties: exact_synonym: oio:hasExactSynonym vars: - anatomical_entity: "'anatomical_entity'" + material_anatomical_entity: "'material anatomical_entity'" name: text: "abnormally dilated %s" vars: - - anatomical_entity + - material_anatomical_entity annotations: - annotationProperty: exact_synonym text: "abnormal %s dilation" vars: - - anatomical_entity + - material_anatomical_entity - annotationProperty: exact_synonym text: "dilated %s" vars: - - anatomical_entity + - material_anatomical_entity def: text: "Abnormal dilation of the lumen of %s." vars: - - anatomical_entity + - 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: - - anatomical_entity + - material_anatomical_entity From b12ed46f04d8efa16a0d6582bf2ad338a21efe30 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Fri, 3 Oct 2025 12:09:15 -0400 Subject: [PATCH 3/5] working on #1002 fixed placement of immaterial and changed name of abnormalyDilatedAnatomicalEntity to abnormalyDilatedImmaterialAnatomicalEntity --- ...ty.yaml => abnormallyDilatedImmaterialAnatomicalEntity.yaml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename src/patterns/dosdp-dev/{abnormallyDilatedAnatomicalEntity.yaml => abnormallyDilatedImmaterialAnatomicalEntity.yaml} (97%) diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml similarity index 97% rename from src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml rename to src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml index 9d13af8e..eec290ec 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml @@ -1,6 +1,6 @@ pattern_name: abnormallyDilatedImmaterialAnatomicalEntity -pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyImmaterialDilatedAnatomicalEntity.yaml +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml 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 not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.' From 997f07cc85697833a50954fb9dc47a36ebf2e88b Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Fri, 3 Oct 2025 13:39:52 -0400 Subject: [PATCH 4/5] working on #1002 flipped the name of the existing pattern back to just abnormallyDilatedAnatomicalEntity to avoid breaking downstream dependencies --- ...omicalEntity.yaml => abnormallyDilatedAnatomicalEntity.yaml} | 2 +- .../dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename src/patterns/dosdp-dev/{abnormallyDilatedImmaterialAnatomicalEntity.yaml => abnormallyDilatedAnatomicalEntity.yaml} (97%) diff --git a/src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml similarity index 97% rename from src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml rename to src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml index eec290ec..88550154 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml @@ -1,6 +1,6 @@ pattern_name: abnormallyDilatedImmaterialAnatomicalEntity -pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedImmaterialAnatomicalEntity.yaml +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntity.yaml 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 not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.' diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml index 728830af..b6bb065f 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntityLumen.yaml @@ -2,7 +2,7 @@ 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 abnormallyDilatedImmaterialAnatomicalEntity pattern.' +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 From c89b80a4ed79fdfc43d9489863910e81f64a5987 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Tue, 7 Oct 2025 13:56:32 -0400 Subject: [PATCH 5/5] working on #1002 fixing typos --- src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml index 88550154..94e16af4 100644 --- a/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml @@ -2,7 +2,7 @@ pattern_name: abnormallyDilatedImmaterialAnatomicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntity.yaml -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 not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.' +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 @@ -27,7 +27,7 @@ annotationProperties: exact_synonym: oio:hasExactSynonym vars: - immaterial_anatomical_entity: "'immaterial anatomical_entity'" + immaterial_anatomical_entity: "'immaterial_anatomical_entity'" name: text: "abnormally dilated %s"