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Address cases of multiple gene associations #8330

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merged 4 commits into from
Nov 21, 2024
Merged

Address cases of multiple gene associations #8330

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9596be5
handle cases of multiple gene associations
twhetzel Nov 12, 2024
118c537
update annotations on MONDO:0100188
twhetzel Nov 13, 2024
4dd1d5d
remove gene associations from MONDO:0011974
twhetzel Nov 13, 2024
a46eef6
updated the definition for retinitis pigmentosa 7
sabrinatoro Nov 14, 2024
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13 changes: 5 additions & 8 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -269682,10 +269682,6 @@ 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 @@ -271426,6 +271422,7 @@ is_a: MONDO:1040055 {source="https://clinicalgenome.org/working-groups/clinical-
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
relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-multiple-gene-associations.sparql
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I don't think this is correct.
According to OMIM, this record refers to the disease for which the RDS gene (PRPH2) is mutated, however, "A digenic form of retinitis pigmentosa resulting from a mutation in the RDS gene (179605.0004) and a null mutation of the ROM1 gene (see 180721.0001) has been reported."

Therefore, for this record, we cannot say that in 100% of the case, the disease is caused by a mutation in both genes (or in a mutation in only one gene).

The gene annotations should be removed for this disease.

Note: the definition for this disease should also be changed to make this disease concept not specific to the mutation in the PRPH2 gene.

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Thanks Sabrina. I agree and will make the changes.

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Updated

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 @@ -534297,6 +534294,7 @@ 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 @@ -536514,14 +536512,13 @@ 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

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