From 9596be569cc9c56bf00f63a939e76ae8ee530494 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Mon, 11 Nov 2024 20:54:51 -0800 Subject: [PATCH 1/4] handle cases of multiple gene associations --- src/ontology/mondo-edit.obo | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 56e4661f4c..3a02bcd25e 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -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] @@ -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 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"} @@ -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] @@ -536520,8 +536518,6 @@ 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 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 From 118c5370cb45ff00f1d1238dcaa17131658130cd Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Tue, 12 Nov 2024 17:34:59 -0800 Subject: [PATCH 2/4] update annotations on MONDO:0100188 --- src/ontology/mondo-edit.obo | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 3a02bcd25e..84a75f912f 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -536512,12 +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="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 From 4dd1d5d67a2e083c6452629edd2f34a5bae976bb Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Tue, 12 Nov 2024 21:33:59 -0800 Subject: [PATCH 3/4] remove gene associations from MONDO:0011974 --- src/ontology/mondo-edit.obo | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 84a75f912f..d83fd84056 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -271397,7 +271397,7 @@ 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 pigmentosa that results in a progressive retinal degeneration. It has been found to be caused by heterozygous mutation in the RDS gene (PRPH2) on chromosome 6p21. 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 @@ -271419,10 +271419,6 @@ 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 -relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-multiple-gene-associations.sparql 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"} From a46eef675c2326e8734b3e83ca737be04275b638 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Wed, 13 Nov 2024 20:54:38 -0800 Subject: [PATCH 4/4] updated the definition for retinitis pigmentosa 7 --- src/ontology/mondo-edit.obo | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index d83fd84056..cf2c42c9c4 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -271397,16 +271397,14 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0011974 name: retinitis pigmentosa 7 -def: "A retinitis pigmentosa that results in a progressive retinal degeneration. It has been found to be caused by heterozygous mutation in the RDS gene (PRPH2) on chromosome 6p21. 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] +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]