From a84bed32e87cc1ed0e61d9a0ecbdb672bef7248f Mon Sep 17 00:00:00 2001 From: Yousif Date: Thu, 14 Nov 2024 10:58:20 -0500 Subject: [PATCH 1/4] Update Synonyms of cholesterol embolism Closes #8049 Cholesterol Embolism primarily occurs in the lower extremities, mainly the toes. However, can arise anywhere - thus 'purple toe syndrome', 'trash foot', and 'warfarin blue toe syndrome' were moved to be synonyms of 'Blue toe syndrome'. Also added term tracker to both --- src/ontology/mondo-edit.obo | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 59c683ffc..81cc475ff 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -31153,11 +31153,15 @@ property_value: IAO:0000589 "bacteriuria (disease)" xsd:string id: MONDO:0001883 name: blue toe syndrome def: "A condition that is caused by recurring atheroembolism in the lower extremities. It is characterized by cyanotic discoloration of the toes, usually the first, fourth, and fifth toes. Discoloration may extend to the lateral aspect of the foot. Despite the gangrene-like appearance, blue toes may respond to conservative therapy without amputation." [MESH:D018438] +synonym: "purple toe syndrome" EXACT [DOID:1461] +synonym: "trash foot" EXACT [DOID:1461] +synonym: "warfarin blue toe syndrome" EXACT [DOID:1416] xref: DOID:14121 {source="MONDO:equivalentTo"} xref: MEDGEN:66940 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D018438 {source="MONDO:equivalentTo", source="DOID:14121"} xref: UMLS:C0242645 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:66940"} is_a: MONDO:0005568 {source="DOID:14121", source="MESH:D018438"} ! cholesterol embolism +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:string [Term] id: MONDO:0001884 @@ -108056,9 +108060,6 @@ def: "Blocking of a blood vessel by cholesterol-rich atheromatous deposits, gene subset: otar {source="MONDO:OTAR"} synonym: "atheroembolism" EXACT [DOID:1461] synonym: "cholesterol crystal embolism" EXACT [DOID:1461] -synonym: "purple toe syndrome" EXACT [DOID:1461] -synonym: "trash foot" EXACT [DOID:1461] -synonym: "warfarin blue toe syndrome" EXACT [DOID:1461] xref: DOID:1461 {source="EFO:0005801", source="MONDO:equivalentTo"} xref: EFO:0005801 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: ICD10CM:I75 {source="DOID:1461"} @@ -108071,6 +108072,7 @@ xref: SCTID:307406004 {source="EFO:0005801", source="MONDO:equivalentTo"} xref: UMLS:C0149649 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:57437"} is_a: MONDO:0005385 {source="DOID:1461", source="MESH:D017700/inferred"} ! vascular disorder relationship: disease_has_location UBERON:0001981 {source="EFO:0000784"} ! blood vessel +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:string [Term] id: MONDO:0005569 From 30b2ff94ac9f01abc5b386bd9b9c8361a0425703 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Thu, 14 Nov 2024 11:31:41 -0800 Subject: [PATCH 2/4] updated synonyms scopes --- src/ontology/mondo-edit.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 81cc475ff..817c24b0d 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -31153,9 +31153,6 @@ property_value: IAO:0000589 "bacteriuria (disease)" xsd:string id: MONDO:0001883 name: blue toe syndrome def: "A condition that is caused by recurring atheroembolism in the lower extremities. It is characterized by cyanotic discoloration of the toes, usually the first, fourth, and fifth toes. Discoloration may extend to the lateral aspect of the foot. Despite the gangrene-like appearance, blue toes may respond to conservative therapy without amputation." [MESH:D018438] -synonym: "purple toe syndrome" EXACT [DOID:1461] -synonym: "trash foot" EXACT [DOID:1461] -synonym: "warfarin blue toe syndrome" EXACT [DOID:1416] xref: DOID:14121 {source="MONDO:equivalentTo"} xref: MEDGEN:66940 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D018438 {source="MONDO:equivalentTo", source="DOID:14121"} @@ -108060,6 +108057,9 @@ def: "Blocking of a blood vessel by cholesterol-rich atheromatous deposits, gene subset: otar {source="MONDO:OTAR"} synonym: "atheroembolism" EXACT [DOID:1461] synonym: "cholesterol crystal embolism" EXACT [DOID:1461] +synonym: "purple toe syndrome" NARROW [DOID:1461] +synonym: "trash foot" NARROW [DOID:1461] +synonym: "warfarin blue toe syndrome" NARROW [DOID:1461] xref: DOID:1461 {source="EFO:0005801", source="MONDO:equivalentTo"} xref: EFO:0005801 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: ICD10CM:I75 {source="DOID:1461"} @@ -309899,7 +309899,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:280576"} subset: orphanet_rare {source="Orphanet:280576"} subset: otar {source="MONDO:OTAR"} subset: rare -synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID:008387] +synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID\:008387] synonym: "Nestor-Guillermo progeria syndrome" EXACT [MONDO:Lexical, OMIM:614008] synonym: "NGPS" EXACT ABBREVIATION [MONDO:Lexical, OMIM:614008, Orphanet:280576] synonym: "progeria syndrome, childhood-onset, with osteolysis" RELATED [OMIM:614008] From 23e8cafdeff2e5c52703d2d1c110b090837e4ffd Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Thu, 14 Nov 2024 11:37:37 -0800 Subject: [PATCH 3/4] Update mondo-edit.obo --- src/ontology/mondo-edit.obo | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 817c24b0d..6d0c59651 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -31153,6 +31153,9 @@ property_value: IAO:0000589 "bacteriuria (disease)" xsd:string id: MONDO:0001883 name: blue toe syndrome def: "A condition that is caused by recurring atheroembolism in the lower extremities. It is characterized by cyanotic discoloration of the toes, usually the first, fourth, and fifth toes. Discoloration may extend to the lateral aspect of the foot. Despite the gangrene-like appearance, blue toes may respond to conservative therapy without amputation." [MESH:D018438] +synonym: "purple toe syndrome" EXACT [https://orcid.org/0000-0002-0587-4693] +synonym: "trash foot" EXACT [https://orcid.org/0000-0002-0587-4693] +synonym: "warfarin blue toe syndrome" EXACT [https://orcid.org/0000-0002-0587-4693] xref: DOID:14121 {source="MONDO:equivalentTo"} xref: MEDGEN:66940 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D018438 {source="MONDO:equivalentTo", source="DOID:14121"} From cb20065ebea91a4549e46ece454ceb582d2381d2 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Thu, 14 Nov 2024 12:24:07 -0800 Subject: [PATCH 4/4] Update mondo-edit.obo --- src/ontology/mondo-edit.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 6d0c59651..7ada6477f 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -31161,7 +31161,7 @@ xref: MEDGEN:66940 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D018438 {source="MONDO:equivalentTo", source="DOID:14121"} xref: UMLS:C0242645 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:66940"} is_a: MONDO:0005568 {source="DOID:14121", source="MESH:D018438"} ! cholesterol embolism -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:string +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:anyURI [Term] id: MONDO:0001884 @@ -108075,7 +108075,7 @@ xref: SCTID:307406004 {source="EFO:0005801", source="MONDO:equivalentTo"} xref: UMLS:C0149649 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:57437"} is_a: MONDO:0005385 {source="DOID:1461", source="MESH:D017700/inferred"} ! vascular disorder relationship: disease_has_location UBERON:0001981 {source="EFO:0000784"} ! blood vessel -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:string +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:anyURI [Term] id: MONDO:0005569 @@ -309902,7 +309902,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:280576"} subset: orphanet_rare {source="Orphanet:280576"} subset: otar {source="MONDO:OTAR"} subset: rare -synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID\:008387] +synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID:008387] synonym: "Nestor-Guillermo progeria syndrome" EXACT [MONDO:Lexical, OMIM:614008] synonym: "NGPS" EXACT ABBREVIATION [MONDO:Lexical, OMIM:614008, Orphanet:280576] synonym: "progeria syndrome, childhood-onset, with osteolysis" RELATED [OMIM:614008]