Alignment OMIM for September release (#8061)

* Alignment OMIM for September release * added new omim terms * addressed QC fails - incorrect Annotation property was updated ("excluded from QC", and not "excluded subclass of") - One of the OMIMPS concept already existed in Mondo. I added the x-ref and removed the newly created term
monarch-initiative · Aug 12, 2024 · 5dd8c16 · 5dd8c16
1 parent ba0c0e7
commit 5dd8c16
Showing 1 changed file with 95 additions and 3 deletions.
diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo
@@ -222692,12 +222692,14 @@ xref: ICD10CM:E03.1 {source="Orphanet:95716/attributed", source="Orphanet:95716/
 xref: MEDGEN:903446 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: MESH:C564766 {source="MONDO:equivalentTo"}
 xref: NCIT:C121751 {source="MONDO:equivalentTo"}
+xref: OMIMPS:274400 {source="MONDO:equivalentTo"}
 xref: Orphanet:95716 {source="MONDO:equivalentTo", source="OMIM:274400"}
 xref: SCTID:718183003 {source="MONDO:equivalentTo"}
 xref: UMLS:C4273748 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:903446"}
 is_a: MONDO:0018612 {source="DOID:0112183", source="MESH:C564766", source="MONDO:Redundant", source="NCIT:C121751", source="Orphanet:95716/inferred"} ! congenital hypothyroidism
 relationship: disease_has_basis_in_disruption_of GO:0042403 ! thyroid hormone metabolic process
 relationship: has_characteristic MONDO:0021140 ! congenital
+relationship: has_characteristic MONDO:0021152 {source="OMIMPS:274400"} ! inherited
 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/642" xsd:anyURI
 
 [Term]
@@ -465326,14 +465328,14 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
 
 [Term]
 id: MONDO:0020716
-name: familial thyroid dyshormonogenesis 1
+name: thyroid dyshormonogenesis 1
 subset: gard_rare {source="GARD:18188", source="MONDO:GARD"}
 subset: nord_rare {source="MONDO:NORD"}
 subset: rare
+synonym: "familial thyroid dyshormonogenesis 1" EXACT [OMIM:274400]
 synonym: "hypothyroidism, congenital, due to dyshormonogenesis, 1" EXACT [OMIM:274400]
 synonym: "iodine accumulation, transport, or trapping defect" EXACT [OMIM:274400]
 synonym: "TDH1" EXACT ABBREVIATION [MONDO:Lexical, OMIM:274400]
-synonym: "thyroid dyshormonogenesis 1" EXACT [MONDO:Lexical, OMIM:274400]
 synonym: "thyroid dyshormonogenesis type 1" EXACT [MONDORULE:1, OMIM:274400]
 synonym: "thyroid hormonogenesis, genetic defect in, 1" EXACT [OMIM:274400]
 xref: DOID:0112185 {source="MONDO:equivalentTo"}
@@ -504890,6 +504892,7 @@ xref: DOID:0060952 {source="MONDO:equivalentTo"}
 xref: MEDGEN:1823995 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIM:620056 {source="MONDO:equivalentTo"}
 xref: UMLS:C5774222 {source="MONDO:equivalentTo", source="MEDGEN:1823995", source="MONDO:MEDGEN"}
+is_a: MONDO:0004691 {source="OMIM:620056", source="https://orcid.org/0000-0002-4142-7153"} ! autosomal dominant polycystic kidney disease
 is_a: MONDO:0020642 {source="OMIM:620056"} ! polycystic kidney disease
 
 [Term]
@@ -558378,9 +558381,10 @@ is_a: MONDO:0043878 {source="OMIM:620550"} ! hereditary optic atrophy
 
 [Term]
 id: MONDO:0957825
-name: deafness, autosomal recessive 121
+name: hearing loss, autosomal recessive 121
 subset: gard_rare {source="MONDO:GARD"}
 subset: rare
+synonym: "deafness, autosomal recessive 121" NARROW [OMIM:620551]
 xref: OMIM:620551 {source="MONDO:equivalentTo"}
 is_a: MONDO:0003847 {source="OMIM:620551"} ! hereditary disease
 is_a: MONDO:0019588 {source="OMIM:620551"} ! hearing loss, autosomal recessive
@@ -560690,6 +560694,94 @@ subset: rare
 xref: OMIM:620865 {source="MONDO:equivalentTo"}
 is_a: MONDO:0020066 {source="OMIM:620865", source="https://orcid.org/0000-0002-4142-7153"} ! Ehlers-Danlos syndrome
 
+[Term]
+id: MONDO:0971149
+name: spastic paraplegia 30b, autosomal recessive
+xref: OMIM:620607 {source="MONDO:equivalentTo"}
+is_a: MONDO:0019064 {source="OMIM:620607", source="https://orcid.org/0000-0002-4142-7153"} ! hereditary spastic paraplegia
+
+[Term]
+id: MONDO:0971150
+name: neuronopathy, distal hereditary motor, autosomal recessive 11, with spasticity
+xref: OMIM:620854 {source="MONDO:equivalentTo"}
+is_a: MONDO:0015363 {source="OMIM:620854", source="https://orcid.org/0000-0002-4142-7153"} ! neuronopathy, distal hereditary motor, autosomal recessive
+
+[Term]
+id: MONDO:0971151
+name: immunodeficiency 122
+xref: OMIM:620869 {source="MONDO:equivalentTo"}
+is_a: MONDO:0021094 {source="OMIM:620869", source="https://orcid.org/0000-0002-4142-7153"} ! immunodeficiency disease
+
+[Term]
+id: MONDO:0971152
+name: hearing loss, autosomal recessive 125
+synonym: "deafness, autosomal recessive 125" NARROW [https://orcid.org/0000-0002-4142-7153, OMIM:620877]
+xref: OMIM:620877 {source="MONDO:equivalentTo"}
+is_a: MONDO:0019588 {source="OMIM:620877", source="https://orcid.org/0000-0002-4142-7153"} ! hearing loss, autosomal recessive
+relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-omim-subsumption.sparql
+
+[Term]
+id: MONDO:0971170
+name: prostate cancer, hereditary, X-linked 3
+xref: OMIM:301120 {source="MONDO:equivalentTo"}
+is_a: MONDO:0015356 {source="OMIM:301120", source="https://orcid.org/0000-0002-4142-7153"} ! hereditary neoplastic syndrome
+
+[Term]
+id: MONDO:0971171
+name: muscular dystrophy, limb-girdle, autosomal recessive 29
+xref: OMIM:620793 {source="MONDO:equivalentTo"}
+is_a: MONDO:0015152 {source="OMIM:620793", source="https://orcid.org/0000-0002-4142-7153"} ! autosomal recessive limb-girdle muscular dystrophy
+
+[Term]
+id: MONDO:0971172
+name: neurodevelopmental disorder with hypotonia, brain anomalies, distinctive facies, and absent language
+xref: OMIM:620851 {source="MONDO:equivalentTo"}
+is_a: MONDO:0003847 {source="OMIM:620851", source="https://orcid.org/0000-0002-4142-7153"} ! hereditary disease
+is_a: MONDO:0700092 {source="OMIM:620851", source="https://orcid.org/0000-0002-4142-7153"} ! neurodevelopmental disorder
+
+[Term]
+id: MONDO:0971173
+name: autoinflammation with arthritis and vasculitis
+xref: OMIM:620880 {source="MONDO:equivalentTo"}
+is_a: MONDO:0003847 {source="OMIM:620880", source="https://orcid.org/0000-0002-4142-7153"} ! hereditary disease
+
+[Term]
+id: MONDO:0971174
+name: multiple mitochondrial dysfunctions syndrome 9b
+xref: OMIM:620887 {source="MONDO:equivalentTo"}
+is_a: MONDO:0017338 {source="OMIM:620887", source="https://orcid.org/0000-0002-4142-7153"} ! fatal multiple mitochondrial dysfunctions syndrome
+
+[Term]
+id: MONDO:0971175
+name: cardiomyopathy, dilated, 2K
+xref: OMIM:620894 {source="MONDO:equivalentTo"}
+is_a: MONDO:0016333 {source="OMIM:620894", source="https://orcid.org/0000-0002-4142-7153"} ! familial dilated cardiomyopathy
+
+[Term]
+id: MONDO:0971176
+name: ovarian dysgenesis 11
+xref: OMIM:620897 {source="MONDO:equivalentTo"}
+is_a: MONDO:0009299 {source="OMIM:620897", source="https://orcid.org/0000-0002-4142-7153"} ! 46 XX gonadal dysgenesis
+
+[Term]
+id: MONDO:0971177
+name: immunodeficiency 123 with HPV-related verrucosis
+xref: OMIM:620901 {source="MONDO:equivalentTo"}
+is_a: MONDO:0021094 {source="OMIM:620901", source="https://orcid.org/0000-0002-4142-7153"} ! immunodeficiency disease
+
+[Term]
+id: MONDO:0971178
+name: polycystic kidney disease 8
+xref: OMIM:620903 {source="MONDO:equivalentTo"}
+is_a: MONDO:0004691 {source="OMIM:620903", source="https://orcid.org/0000-0002-4142-7153"} ! autosomal dominant polycystic kidney disease
+is_a: MONDO:0020642 {source="OMIM:620903", source="https://orcid.org/0000-0002-4142-7153"} ! polycystic kidney disease
+
+[Term]
+id: MONDO:0971179
+name: arterial tortuosity-bone fragility syndrome
+xref: OMIM:620908 {source="MONDO:equivalentTo"}
+is_a: MONDO:0002254 {source="OMIM:620908", source="https://orcid.org/0000-0002-4142-7153"} ! syndromic disease
+
 [Term]
 id: MONDO:1010000
 name: pythiosis