From d85e13a5a7125b7015953227933f2345a3ef99e8 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Fri, 15 Dec 2023 12:49:37 -0800 Subject: [PATCH] unobsolete MONDO:0016980 and MONDO:0036042 Fixes #6572 I reversed the obsoletion of this term by reversing to their September 2023 version (including their children). I also ran a normalization step --- src/ontology/mondo-edit.obo | 38 +++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 48d6cb72d8..55589dc978 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -221209,6 +221209,7 @@ xref: UMLS:C1845055 {source="NCIT:C118631", source="MONDO:equivalentTo", source= is_a: MONDO:0002254 {source="MONDO:Redundant", source="NCIT:C118631", source="https://orcid.org/0000-0002-5002-8648"} ! syndromic disease is_a: MONDO:0005039 {source="https://orcid.org/0000-0001-9310-0163"} ! reproductive system disorder is_a: MONDO:0005151 ! endocrine system disorder +is_a: MONDO:0016980 {source="Orphanet:847"} ! ATR-X-related syndrome is_a: MONDO:0020040 ! 46,XY disorder of sex development is_a: MONDO:0020119 {source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability relationship: has_characteristic HP:0001417 ! X-linked inheritance @@ -225591,6 +225592,7 @@ xref: UMLS:C0796003 {source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoun xref: UMLS:C4759781 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0016980 {source="Orphanet:847"} ! ATR-X-related syndrome relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/886 {source="MONDO:mim2gene_medgen"} ! ATRX property_value: confidence "37.50000000000002" xsd:double property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -369723,19 +369725,20 @@ property_value: confidence "2.461538461538462" xsd:double [Term] id: MONDO:0016980 -name: obsolete ATR-X-related syndrome -synonym: "ATR-X-related syndrome" EXACT CLINGEN_PREFERRED [] -xref: Orphanet:263355 {source="MONDO:obsoleteEquivalentObsolete"} +name: ATR-X-related syndrome +comment: The obsoletion of this term has been reversed in the Mondo release of January 2024. +subset: disease_grouping +subset: ordo_group_of_disorders {source="Orphanet:263355"} +synonym: "ATR-X-related syndrome" EXACT [] +xref: Orphanet:263355 {source="MONDO:equivalentObsolete"} +xref: UMLS:CN202282 {source="MONDO:equivalentTo"} +is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:263355"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:263355"} ! X-linked syndromic intellectual disability -property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"} +property_value: exactMatch http://linkedlifedata.com/resource/umls/id/CN202282 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6752" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6877" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6878" xsd:anyURI -is_obsolete: true +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6572" xsd:string [Term] id: MONDO:0016981 @@ -490717,17 +490720,16 @@ is_a: MONDO:0029000 {source="Orphanet:240839"} ! poisoning [Term] id: MONDO:0036042 -name: obsolete KAT6B-related multiple congenital anomalies syndrome -subset: gard_rare {source="GARD:22399"} -subset: nord_rare {source="MONDO:NORD"} +name: KAT6B-related multiple congenital anomalies syndrome +comment: The obsoletion of this term has been reversed in the Mondo release of January 2024. +subset: ordo_group_of_disorders synonym: "KAT6B-related disorder" EXACT [Orphanet:597749] -xref: GARD:22399 {source="MONDO:obsoleteEquivalent", source="Orphanet:597749"} -xref: Orphanet:597749 {source="MONDO:obsoleteEquivalent"} -property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"} +xref: Orphanet:597749 {source="MONDO:equivalentTo"} +is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-4142-7153"} ! syndromic disease +is_a: MONDO:0015159 {source="Orphanet:597749"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability +property_value: exactMatch Orphanet:597749 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6876" xsd:anyURI -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6878" xsd:anyURI -is_obsolete: true +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6572" xsd:anyURI [Term] id: MONDO:0036045