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add new term RNU4ATAC spectrum disorder (#7543)
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* add new term RNU4ATAC spectrum disorder

and reclassify children
close #7497

* fix syn scope

* update parent new ID (updated from conflict resolution)

---------

Co-authored-by: Sabrina Toro <sabrina@tislab.org>
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@nicolevasilevsky @sabrinatoro
nicolevasilevsky and sabrinatoro committed Apr 8, 2024
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Showing 1 changed file with 31 additions and 17 deletions.
48 changes: 31 additions & 17 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -176685,18 +176685,18 @@ def: "A microcephalic osteodysplastic primordial dwarfism that has material basi
subset: gard_rare {source="GARD:15144"}
subset: nord_rare {source="MONDO:NORD"}
subset: rare
synonym: "Brachymelic primordial dwarfism" RELATED [OMIM:210710]
synonym: "brachymelic primordial dwarfism" EXACT [OMIM:210710]
synonym: "brachymelic primordial dwarfism" EXACT [DOID:0060608]
synonym: "Cephaloskeletal dysplasia" RELATED [OMIM:210710]
synonym: "cephaloskeletal dysplasia" EXACT [DOID:0060608]
synonym: "cephaloskeletal dysplasia" EXACT [OMIM:210710]
synonym: "low-birth-weight dwarfism with skeletal dysplasia" EXACT [DOID:0060608, OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type 1" RELATED [OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type I" RELATED [MONDO:Lexical, OMIM:210710]
synonym: "MOPD 1" RELATED [OMIM:210710]
synonym: "MOPD1" RELATED ABBREVIATION [MONDO:Lexical, OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type 1" EXACT [OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type I" EXACT [MONDO:Lexical, OMIM:210710]
synonym: "MOPD 1" EXACT [OMIM:210710]
synonym: "MOPD1" EXACT ABBREVIATION [MONDO:Lexical, OMIM:210710]
synonym: "osteodysplastic primordial dwarfism type I" EXACT [DOID:0060608]
synonym: "osteodysplastic primordial dwarfism, type 1" RELATED [OMIM:210710]
synonym: "Taybi-Linder syndrome" RELATED [DOID:0060608, OMIM:210710]
synonym: "osteodysplastic primordial dwarfism, type 1" EXACT [OMIM:210710]
synonym: "Taybi-Linder syndrome" EXACT [DOID:0060608, OMIM:210710]
xref: DOID:0060608 {source="MONDO:equivalentTo"}
xref: GARD:15144 {source="OMIM:210710"}
xref: ICD10CM:Q87.1 {source="DOID:0060608"}
Expand All @@ -176707,12 +176707,14 @@ xref: UMLS:C1859452 {source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoun
is_a: MONDO:0000060 {source="DC-OMIM:210710", source="MONDO:Entailed", source="MONDO:Redundant"} ! microcephalic osteodysplastic primordial dwarfism
is_a: MONDO:0005516 {source="DOID:0060608"} ! osteochondrodysplasia
is_a: MONDO:0016994 {source="Orphanet:2636/btnt"} ! microcephalic osteodysplastic primordial dwarfism types I and III
is_a: MONDO:0100558 {source="https://clinicalgenome.org/affiliation/40065/"} ! RNU4ATAC spectrum disorder
is_a: MONDO:0800063 {source="PMID:31633310"} ! primordial dwarfism and slender bone disorder
intersection_of: MONDO:0000060 ! microcephalic osteodysplastic primordial dwarfism
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/34016 ! RNU4ATAC
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/34016 {source="MONDO:mim2gene_medgen"} ! RNU4ATAC
property_value: confidence "1.8124999999999996" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7497" xsd:anyURI

[Term]
id: MONDO:0008872
Expand Down Expand Up @@ -184845,11 +184847,11 @@ subset: ordo_disease {source="Orphanet:1824"}
subset: orphanet_rare {source="Orphanet:1824"}
subset: rare
synonym: "epiphyseal dysplasia, microcephaly and nystagmus" RELATED [GARD:0000264]
synonym: "epiphyseal dysplasia, microcephaly, and NYSTAGMUS" RELATED [OMIM:226960]
synonym: "epiphyseal dysplasia, multiple, with microcephaly and retinal dystrophy" EXACT [OMIM:226960]
synonym: "epiphyseal dysplasia-microcephaly-nystagmus syndrome" EXACT [Orphanet:1824]
synonym: "Lowry Wood syndrome" RELATED [GARD:0000264]
synonym: "Lowry Wood syndrome" EXACT [GARD:0000264]
synonym: "Lowry-Wood syndrome" EXACT [OMIM:226960]
synonym: "LWS" RELATED ABBREVIATION [GARD:0000264]
synonym: "LWS" EXACT ABBREVIATION [GARD:0000264]
xref: GARD:264 {source="Orphanet:1824"}
xref: ICD10CM:Q87.5 {source="Orphanet:1824", source="Orphanet:1824/attributed", source="Orphanet:1824/ntbt"}
xref: MedDRA:10062600 {source="Orphanet:1824/e", source="Orphanet:1824"}
Expand All @@ -184858,9 +184860,11 @@ xref: OMIM:226960 {source="Orphanet:1824/e", source="MONDO:equivalentTo", source
xref: Orphanet:1824 {source="OMIM:226960", source="MONDO:equivalentTo"}
xref: SCTID:721975004 {source="MONDO:equivalentTo"}
xref: UMLS:C0796021 {source="Orphanet:1824/e", source="OMIM:226960", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="Orphanet:1824"}
is_a: MONDO:0100558 {source="https://clinicalgenome.org/affiliation/40065/"} ! RNU4ATAC spectrum disorder
is_a: MONDO:0800063 {source="PMID:31633310"} ! primordial dwarfism and slender bone disorder
property_value: confidence "3.666666666666667" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7497" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/264/lowry-wood-syndrome" xsd:anyURI {source="GARD:0000264"}

[Term]
Expand Down Expand Up @@ -324349,11 +324353,10 @@ subset: nord_rare {source="MONDO:NORD"}
subset: ordo_disease {source="Orphanet:353298"}
subset: orphanet_rare {source="Orphanet:353298"}
subset: rare
synonym: "RFMN" RELATED ABBREVIATION [OMIM:616651]
synonym: "ROIFMAN syndrome" RELATED [OMIM:616651]
synonym: "RFMN" EXACT ABBREVIATION [OMIM:616651]
synonym: "Roifman syndrome" EXACT [OMIM:616651]
synonym: "spondyloepiphseal dysplasia, retinal dystrophy and antibody deficiency" RELATED [GARD:0009163]
synonym: "spondyloepiphyseal dysplasia, retinal dystrophy, and antibody deficiency" RELATED [OMIM:616651]
synonym: "spondyloepiphyseal dysplasia, retinal dystrophy, and antibody deficiency" EXACT [OMIM:616651]
synonym: "spondyloepiphyseal dysplasia-retinal dystrophy-immunodeficiency syndrome" EXACT [Orphanet:353298]
xref: GARD:9163 {source="Orphanet:353298"}
xref: ICD10CM:Q77.7 {source="Orphanet:353298/attributed", source="Orphanet:353298/ntbt", source="Orphanet:353298"}
Expand All @@ -324365,12 +324368,14 @@ xref: UMLS:C1846059 {source="Orphanet:353298", source="MONDO:equivalentTo", sour
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0005046 {source="https://orcid.org/0000-0001-8216-5084"} ! immune system disorder
is_a: MONDO:0016761 {source="Orphanet:353298"} ! spondyloepiphyseal dysplasia
is_a: MONDO:0100558 {source="https://clinicalgenome.org/affiliation/40065/"} ! RNU4ATAC spectrum disorder
is_a: MONDO:0800063 {source="PMID:31633310"} ! primordial dwarfism and slender bone disorder
relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:353298", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/34016 {source="MONDO:mim2gene_medgen"} ! RNU4ATAC
property_value: confidence "3.0625" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6747" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7497" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/9163/roifman-syndrome" xsd:anyURI {source="GARD:0009163"}

[Term]
Expand Down Expand Up @@ -370212,8 +370217,8 @@ subset: nord_rare {source="MONDO:NORD"}
subset: ordo_malformation_syndrome {source="Orphanet:2636"}
subset: orphanet_rare {source="Orphanet:2636"}
subset: rare
synonym: "Brachymelic primordial dwarfism" RELATED [GARD:0005120]
synonym: "Cephaloskeletal dysplasia" RELATED [GARD:0005120]
synonym: "brachymelic primordial dwarfism" RELATED [GARD:0005120]
synonym: "cephaloskeletal dysplasia" RELATED [GARD:0005120]
synonym: "low-birth-weight dwarfism with skeletal dysplasia" RELATED [GARD:0005120]
synonym: "microcephalic osteodysplastic primordial dwarfism type 1" RELATED [GARD:0005120]
synonym: "microcephalic osteodysplastic primordial dwarfism types 1 and 3" RELATED [GARD:0005120]
Expand All @@ -370222,7 +370227,7 @@ synonym: "MOPD 1" RELATED [GARD:0005120]
synonym: "MOPD types I and III" EXACT [Orphanet:2636]
synonym: "osteodysplastic primordial dwarfism type I" RELATED [GARD:0005120]
synonym: "primordial microcephalic dwarfism, Crachami type" EXACT [GARD:0005120, Orphanet:2636]
synonym: "Taybi-Linder syndrome" EXACT [Orphanet:2636]
synonym: "Taybi-Linder syndrome" NARROW [Orphanet:2636]
xref: GARD:5120 {source="Orphanet:2636"}
xref: ICD10CM:Q87.1 {source="Orphanet:2636", source="Orphanet:2636/attributed", source="Orphanet:2636/ntbt"}
xref: Orphanet:2636 {source="MONDO:equivalentTo", source="GARD:0005120"}
Expand Down Expand Up @@ -513947,6 +513952,15 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6461" xsd:anyURI

[Term]
id: MONDO:0100558
name: RNU4ATAC spectrum disorder
def: "A syndromic disease characterized by growth restriction, microcephaly, skeletal dysplasia, and cognitive impairment. Less common but variable findings include brain anomalies, seizures, strokes, immunodeficiency, and cardiac anomalies, as well as ophthalmologic, skin, renal, gastrointestinal, hearing, and endocrine involvement. The term includes Microcephalic osteodysplastic primordial dwarfism type I/III (MOPDI), Taybi-Linder syndrome, Lowry-Wood syndrome, and Roifman syndrome." [https://clinicalgenome.org/affiliation/40065/]
is_a: MONDO:0002254 {source="https://clinicalgenome.org/affiliation/40065/"} ! syndromic disease
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/34016 {source="https://clinicalgenome.org/affiliation/40065/"} ! RNU4ATAC
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7497" xsd:anyURI

[Term]
id: MONDO:0100557
name: RBFOX2-related congenital heart disorder
Expand Down

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