From 54ea25d2733c00334a6b2af676bdc8ed7096673f Mon Sep 17 00:00:00 2001 From: katiermullen <102704401+katiermullen@users.noreply.github.com> Date: Thu, 14 Nov 2024 11:18:43 -0700 Subject: [PATCH 1/3] Incorrect ICD10 mapping Closes #7998 Correct mapping for MONDO:0016267 and MONDO:0016266. --- 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..837d71a5d 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -309897,7 +309897,7 @@ 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] @@ -372482,13 +372482,14 @@ subset: rare synonym: "body of uterus squamous cell carcinoma" EXACT [MONDO:patterns/location] synonym: "endometrial squamous cell carcinoma" RELATED [Orphanet:213716] xref: GARD:20479 {source="MONDO:GARD"} -xref: ICD10CM:C50 {source="MONDO:relatedTo", source="Orphanet:213716/ntbt", source="Orphanet:213716"} +xref: ICD10CM:C54.1 {source="MONDO:relatedTo", source="Orphanet:213716/ntbt", source="Orphanet:213716"} xref: MEDGEN:1633992 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: Orphanet:213716 {source="MONDO:equivalentTo"} xref: UMLS:C4707099 {source="MONDO:equivalentTo", source="MEDGEN:1633992", source="MONDO:MEDGEN"} is_a: MONDO:0004992 {source="Orphanet:213716"} ! cancer intersection_of: MONDO:0005096 ! squamous cell carcinoma intersection_of: disease_has_location UBERON:0009853 ! body of uterus +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:anyURI [Term] id: MONDO:0016267 @@ -372502,13 +372503,14 @@ subset: rare synonym: "body of uterus undifferentiated carcinoma" EXACT [MONDO:patterns/location] synonym: "endometrial undifferentiated carcinoma" RELATED [Orphanet:213721] xref: GARD:20480 {source="MONDO:GARD"} -xref: ICD10CM:C50 {source="Orphanet:213721/ntbt", source="MONDO:relatedTo", source="Orphanet:213721"} +xref: ICD10CM:C54.9 {source="Orphanet:213721/ntbt", source="MONDO:relatedTo", source="https://orcid.org/0000-0002-7347-2434", source="Orphanet:213721"} xref: MEDGEN:1638762 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: Orphanet:213721 {source="MONDO:equivalentTo"} xref: UMLS:C4707822 {source="MEDGEN:1638762", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0004992 {source="Orphanet:213721"} ! cancer intersection_of: MONDO:0005617 ! undifferentiated carcinoma intersection_of: disease_has_location UBERON:0009853 ! body of uterus +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:string [Term] id: MONDO:0016268 From fdba760d7ddd9fa0a4df9e97db7c465aa6c70499 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Thu, 14 Nov 2024 13:43:03 -0800 Subject: [PATCH 2/3] remove x-ref --- src/ontology/mondo-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 837d71a5d..ceb65ecb9 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -309897,7 +309897,7 @@ 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 [] 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 bbae156ad9bcd9400671124eb7720024a09fc2c3 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Thu, 14 Nov 2024 13:45:38 -0800 Subject: [PATCH 3/3] updated issue tracker annotation type --- src/ontology/mondo-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index ceb65ecb9..a7d1fe1f4 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -372510,7 +372510,7 @@ xref: UMLS:C4707822 {source="MEDGEN:1638762", source="MONDO:equivalentTo", sourc is_a: MONDO:0004992 {source="Orphanet:213721"} ! cancer intersection_of: MONDO:0005617 ! undifferentiated carcinoma intersection_of: disease_has_location UBERON:0009853 ! body of uterus -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:string +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:anyURI [Term] id: MONDO:0016268