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Address cases of multiple gene associations (#8330)
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* handle cases of multiple gene associations

* update annotations on MONDO:0100188

* remove gene associations from MONDO:0011974

* updated the definition for retinitis pigmentosa 7

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Co-authored-by: Sabrina Toro <[email protected]>
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@twhetzel @sabrinatoro
twhetzel and sabrinatoro authored Nov 21, 2024
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Showing 1 changed file with 6 additions and 15 deletions.
21 changes: 6 additions & 15 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -269696,10 +269696,6 @@ xref: SCTID:445227008 {source="DOID:0050458", source="MONDO:equivalentTo"}
xref: UMLS:C0349639 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:138109"}
is_a: MONDO:0006311 {source="DOID:0050458", source="MONDO:Redundant", source="NCIT:C9233", source="ONCOTREE:JMML"} ! myelodysplastic/myeloproliferative neoplasm
is_a: MONDO:0020311 ! chronic myelomonocytic leukemia
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/1541 {source="OMIM:607785"} ! CBL
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17073 {source="OMIM:607785"} ! ARHGAP26
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7765 {source="OMIM:607785"} ! NF1
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9644 {source="OMIM:607785"} ! PTPN11
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI

[Term]
Expand Down Expand Up @@ -271415,16 +271411,14 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/
[Term]
id: MONDO:0011974
name: retinitis pigmentosa 7
def: "A retinitis pigmentosa that has material basis in mutation in the PRPH2 gene on chromosome 6p21." [DOID:0110383, PMID:1749427]
def: "A retinitis pigmentosain which the cause of the disease is a variation in the RDS gene (PRPH2). A digenic form of retinitis pigmentosa, resulting from a mutation in the RDS gene and a null mutation of the ROM1 gene, has also been reported." [DOID:0110383, OMIM:608133, PMID:1749427]
subset: gard_rare {source="GARD:10386", source="MONDO:GARD"}
subset: nord_rare {source="MONDO:NORD"}
subset: rare
synonym: "Leber congenital amaurosis 18" RELATED [OMIM:608133]
synonym: "leber congenital amaurosis 18, autosomal recessive, autosomal dominant, digenic dominant" EXACT [OMIM:608133, OMIM:genemap2]
synonym: "retinitis pigmentosa 7" EXACT [MONDO:Lexical, OMIM:608133]
synonym: "retinitis pigmentosa 7 and digenic form, autosomal recessive, autosomal dominant, digenic dominant" EXACT [OMIM:608133, OMIM:genemap2]
synonym: "retinitis pigmentosa 7, digenic" RELATED [OMIM:608133]
synonym: "retinitis pigmentosa 7, digenic form, autosomal recessive, autosomal dominant, digenic dominant" EXACT [OMIM:608133, OMIM:genemap2]
synonym: "retinitis pigmentosa 7, digenic form, autosomal recessive, autosomal dominant, digenic dominant" NARROW [OMIM:608133, OMIM:genemap2]
synonym: "retinitis pigmentosa type 7" EXACT [DOID:0110383, MONDORULE:1, OMIM:608133]
synonym: "RP 7" RELATED [GARD:0010386]
synonym: "RP7" EXACT ABBREVIATION [DOID:0110383, MONDO:Lexical, OMIM:608133]
Expand All @@ -271437,9 +271431,6 @@ xref: Orphanet:791 {source="OMIM:608133"}
xref: UMLS:C1842475 {source="MEDGEN:334168", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0019200 {source="DC-OMIM:608133", source="DOID:0110383", source="MONDO:Redundant", source="OMIM:608133"} ! retinitis pigmentosa
is_a: MONDO:1040055 {source="https://clinicalgenome.org/working-groups/clinical-domain/ocular-cdwg/", source="https://orcid.org/0000-0001-5935-2391"} ! PRPH2-related retinopathy
intersection_of: MONDO:0019200 ! retinitis pigmentosa
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10254 ! ROM1
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9942 ! PRPH2
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/10386/retinitis-pigmentosa-7" xsd:anyURI {source="GARD:0010386"}

Expand Down Expand Up @@ -534330,6 +534321,7 @@ is_a: MONDO:0010168 {source="OMIM:601067"} ! Usher syndrome type 1
intersection_of: MONDO:0010168 ! Usher syndrome type 1
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/13733 ! CDH23
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/14674 ! PCDH15
relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-multiple-gene-associations.sparql
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432

[Term]
Expand Down Expand Up @@ -536547,14 +536539,13 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
[Term]
id: MONDO:0100188
name: combined ApoA-I and ApoC-III deficiency
def: "A hypoalphalipoproteinemia that is has its basis in the disruption of ApoA-I and ApoC-III." [MONDO:patterns/inborn_metabolic_disrupts, PMID:3118360]
def: "A hypoalphalipoproteinemia that is has its basis in the disruption of ApoA-I and ApoC-III." [MONDO:patterns/inborn_metabolic_disrupts, PMID:20616715]
subset: gard_rare {source="MONDO:GARD"}
subset: nord_rare {source="MONDO:NORD"}
subset: rare
synonym: "ApoA-I and apoC-III deficiency, combined" EXACT [OMIM:618463]
is_a: MONDO:0017773 {source="PMID:3118360"} ! hypoalphalipoproteinemia
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/600 {source="OMIM:618463"} ! APOA1
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/610 {source="PMID:3118360"} ! APOC3
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/600 {source="PMID:20616715"} ! APOA1
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/610 {source="PMID:20616715"} ! APOC3
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/4925" xsd:anyURI

Expand Down

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