From db0bbaca2a2cfa982b1eaac4bbfc82d417eadde8 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Tue, 10 Dec 2024 22:07:22 -0500 Subject: [PATCH 1/5] immunological diseases - see robot template [here-"ROBOT template 241210" tab](https://docs.google.com/spreadsheets/d/1kmCCaUIfTTrHrucoLDyXMdWQ_GJOX1Blu2-FDEzNxvs/edit?gid=2088980721#gid=2088980721) - addresses #8090 --- src/ontology/mondo-edit.obo | 456 ++++++++++++++++++++++++++++++++++++ 1 file changed, 456 insertions(+) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 2decbd910..82564876c 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -340323,6 +340323,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:477814"} subset: orphanet_rare {source="Orphanet:477814"} subset: otar {source="MONDO:OTAR"} subset: rare +synonym: "DIAPH1 deficiency" EXACT [PMID:33662367, PMID:39120629] synonym: "SCBMS" EXACT ABBREVIATION [OMIM:616632] synonym: "seizures, cortical blindness, and microcephaly syndrome" RELATED [] synonym: "seizures, cortical blindness, microcephaly syndrome" EXACT [] @@ -340333,8 +340334,10 @@ xref: Orphanet:477814 {source="MONDO:equivalentTo"} xref: UMLS:C5567650 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1799073"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease is_a: MONDO:0021147 ! disorder of development or morphogenesis +is_a: MONDO:0700289 {source="PMID:33662367", source="PMID:39120629"} ! combined immunodeficiency with associated or syndromic feature relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2876 {source="MONDO:mim2gene_medgen", source="OMIM:616632"} ! DIAPH1 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6744" xsd:anyURI +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI [Term] id: MONDO:0014715 @@ -547964,6 +547967,457 @@ relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4142-7153 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7921" xsd:anyURI +[Term] +id: MONDO:0700284 +name: NUDCD3-related immunodeficiency +def: "A T-B- severe combined immunodeficiency in which the cause of the disease is a variation in the NUDCD3 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "NUDCD3 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0017855 {source="https://orcid.org/0000-0003-4018-1646"} ! T-B- severe combined immunodeficiency +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/22208 {source="https://orcid.org/0000-0003-4018-1646"} ! NUDCD3 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700285 +name: IRF4-related immunodeficiency +def: "A combined immunodeficiency in which the cause of the disease is a variation in the IRF4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0015131 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6119 {source="https://orcid.org/0000-0003-4018-1646"} ! IRF4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700286 +name: NFATC1-related immunodeficiency +def: "A combined immunodeficiency in which the cause of the disease is a variation in the NFATC1 gene." [MONDO:patterns/disease_series_by_gene, PMID:37249233] +synonym: "NFATC1 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0015131 {source="PMID:37249233"} ! combined immunodeficiency +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7775 {source="PMID:37249233"} ! NFATC1 + +[Term] +id: MONDO:0700287 +name: POLD2-related immunodeficiency +def: "A non-severe combined immunodeficiency due to polymerase delta deficiency in which the cause of the disease is a variation in the POLD2 gene." [MONDO:patterns/disease_series_by_gene, PMID:31449058] +synonym: "Polymerase D2 deficiency" BROAD [PMID:31449058] +is_a: MONDO:0800145 {source="PMID:31449058"} ! non-severe combined immunodeficiency due to polymerase delta deficiency +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9176 {source="PMID:31449058"} ! POLD2 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700288 +name: POLD3-related immunodeficiency +def: "A combined immunodeficiency in which the cause of the disease is a variation in the POLD3 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "Polymerase D3 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0015131 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/20932 {source="https://orcid.org/0000-0003-4018-1646"} ! POLD3 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700289 +name: combined immunodeficiency with associated or syndromic feature +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency." [doi:10.1016/B978-0-12-821028-4.00008-7] +synonym: "CID syndrome" EXACT [doi:10.1016/B978-0-12-821028-4.00008-7] +is_a: MONDO:0015131 {source="doi:10.1016/B978-0-12-821028-4.00008-7"} ! combined immunodeficiency +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700290 +name: IKZF2-related immunodeficiency +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the IKZF2 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0700289 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency with associated or syndromic feature +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/13177 {source="https://orcid.org/0000-0003-4018-1646"} +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700291 +name: GINS4-related immunodeficiency +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the GINS4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "GINS4 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0700289 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency with associated or syndromic feature +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/28226 {source="https://orcid.org/0000-0003-4018-1646"} ! GINS4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700292 +name: CD28-related immunodeficiency +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the CD28 gene." [MONDO:patterns/disease_series_by_gene, PMID:37249233] +synonym: "CD28 deficiency" BROAD [PMID:37249233] +is_a: MONDO:0700289 {source="PMID:37249233"} ! combined immunodeficiency with associated or syndromic feature +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/1653 {source="PMID:37249233"} +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700293 +name: FLT3LG-related immunodeficiency +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the FLT3LG gene." [MONDO:patterns/disease_series_by_gene, PMID:31449058] +synonym: "FLT3L deficiency" BROAD [PMID:31449058] +is_a: MONDO:0700289 {source="PMID:31449058"} ! combined immunodeficiency with associated or syndromic feature +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/3766 {source="PMID:31449058"} ! FLT3LG +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700294 +name: PTCRA-related immunodeficiency +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the PTCRA gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "PTCRA deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0700289 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency with associated or syndromic feature +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/21290 {source="https://orcid.org/0000-0003-4018-1646"} ! PTCRA +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700295 +name: CHARGE syndrome due to SEMA3E deficiency +def: "#REF!" [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0008965 {source="https://orcid.org/0000-0003-4018-1646"} ! CHARGE syndrome +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10727 {source="https://orcid.org/0000-0003-4018-1646"} ! SEMA3E +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700296 +name: CHARGE syndrome due to CHD7 deficiency +def: "#REF!" [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0008965 {source="OMIM:214800", source="https://orcid.org/0000-0003-4018-1646"} ! CHARGE syndrome +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/20626 {source="https://orcid.org/0000-0003-4018-1646"} ! CHD7 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700297 +name: PTEN-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the PTEN gene." [MONDO:patterns/disease_series_by_gene, PMID:27426521, PMID:37178059] +synonym: "PTEN deficiency" BROAD [PMID:27426521, PMID:37178059] +is_a: MONDO:0021094 {source="PMID:27426521", source="PMID:37178059"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="PMID:27426521", source="PMID:37178059"} ! PTEN +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700298 +name: TNFSF12-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFSF12 gene." [MONDO:patterns/disease_series_by_gene, PMID:23493554] +synonym: "TWEAK deficiency" BROAD [PMID:23493554] +is_a: MONDO:0021094 {source="PMID:23493554"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11927 {source="PMID:23493554"} ! TNFSF12 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700299 +name: INO80-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the INO80 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "INO80 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/26956 {source="https://orcid.org/0000-0003-4018-1646"} ! INO80 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700300 +name: FAAP24-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the FAAP24 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "FAAP24 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/28467 {source="https://orcid.org/0000-0003-4018-1646"} ! FAAP24 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700301 +name: GIMAP6-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the GIMAP6 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "GIMAP6 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/21918 {source="https://orcid.org/0000-0003-4018-1646"} ! GIMAP6 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700302 +name: CD274-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the CD274 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "PD-L1 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17635 {source="https://orcid.org/0000-0003-4018-1646"} ! CD274 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700303 +name: ERN1-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the ERN1 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IRE1a deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/3449 {source="https://orcid.org/0000-0003-4018-1646"} ! ERN1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700304 +name: SH2B3-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the SH2B3 gene." [MONDO:patterns/disease_series_by_gene, PMID:37206266, PMID:37277724] +synonym: "SH2B3 deficiency" BROAD [PMID:37206266, PMID:37277724] +is_a: MONDO:0021094 {source="PMID:37206266", source="PMID:37277724"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/29605 {source="PMID:37206266", source="PMID:37277724"} ! SH2B3 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700305 +name: NFAT5-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the NFAT5 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "NFAT5 haploinsufficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7774 {source="https://orcid.org/0000-0003-4018-1646"} ! NFAT5 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700306 +name: TNFSF6-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFSF6 gene." [MONDO:patterns/disease_series_by_gene, PMID:22857792] +synonym: "ALPS-FASLG" EXACT [PMID:22857792] +synonym: "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation" EXACT [PMID:22857792] +is_a: MONDO:0021094 {source="PMID:22857792"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11936 {source="PMID:22857792"} ! FASLG +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700307 +name: IL27RA-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IL27RA gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IL-27RA deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17290 {source="https://orcid.org/0000-0003-4018-1646"} ! IL27RA +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700308 +name: TNFRSF9-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFRSF9 gene." [MONDO:patterns/disease_series_by_gene, PMID:37144041] +synonym: "41BB deficiency" BROAD [PMID:37144041] +synonym: "CD137 deficiency" BROAD [PMID:37144041] +is_a: MONDO:0021094 {source="PMID:37144041"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11924 {source="PMID:37144041"} ! TNFRSF9 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700309 +name: TNFSF9-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFSF9 gene." [MONDO:patterns/disease_series_by_gene, PMID:35657354] +synonym: "4-1 BBL deficiency" BROAD [PMID:35657354] +synonym: "CD137L deficiency" BROAD [PMID:35657354] +is_a: MONDO:0021094 {source="PMID:35657354"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11939 {source="PMID:35657354"} ! TNFSF9 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700310 +name: DBF4-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the DBF4 gene." [MONDO:patterns/disease_series_by_gene, PMID:36841265] +synonym: "DBF4 deficiency" BROAD [PMID:36841265] +is_a: MONDO:0021094 {source="PMID:36841265"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17364 {source="PMID:36841265"} ! DBF4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700311 +name: Shwachman Diamond syndrome due to DNAJC21 deficiency +def: "A Shwachman Diamond syndrome in which the cause of the disease is a variation in the DNAJC21 gene." [MONDO:patterns/disease_series_by_gene, PMID:28062395] +is_a: MONDO:0021094|MONDO:0009833 {source="PMID:28062395"} +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/27030 {source="PMID:28062395"} ! DNAJC21 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700312 +name: SRP19-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the SRP19 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "SRP19 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11300 {source="https://orcid.org/0000-0003-4018-1646"} ! SRP19 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700313 +name: SRPRA-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the SRPRA gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "SRPRA deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11307 {source="https://orcid.org/0000-0003-4018-1646"} ! SRPRA +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700314 +name: IL12RB2-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IL12RB2 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IL-12Rb2 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/5972 {source="https://orcid.org/0000-0003-4018-1646"} ! IL12RB2 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700315 +name: NOS2-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the NOS2 gene." [MONDO:patterns/disease_series_by_gene, PMID:31995689] +synonym: "NOS2 deficiency" BROAD [PMID:31995689] +is_a: MONDO:0021094 {source="PMID:31995689"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7873 {source="PMID:31995689"} ! NOS2 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700316 +name: OAS2-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the OAS2 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "OAS2 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/8087 {source="https://orcid.org/0000-0003-4018-1646"} ! OAS2 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700317 +name: POLR3C-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the POLR3C gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "RNA polymerase III deficiency due to POLR3C defects" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/30076 {source="https://orcid.org/0000-0003-4018-1646"} ! POLR3C +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700318 +name: ATG4A-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the ATG4A gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "ATG4A deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/16489 {source="https://orcid.org/0000-0003-4018-1646"} ! ATG4A +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700319 +name: GTF3A-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the GTF3A gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "GTF3A deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/4662 {source="https://orcid.org/0000-0003-4018-1646"} ! GTF3A +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700320 +name: IKBKE-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IKBKE gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IKBKE deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/14552 {source="https://orcid.org/0000-0003-4018-1646"} ! IKBKE +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700321 +name: MAP1LC3B2-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the MAP1LC3B2 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "MAP1LC3B2 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/34390 {source="https://orcid.org/0000-0003-4018-1646"} ! MAP1LC3B2 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700322 +name: RIPK3-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the RIPK3 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "RIPK3 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10021 {source="https://orcid.org/0000-0003-4018-1646"} ! RIPK3 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700323 +name: TLR4-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TLR4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "TLR4 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11850 {source="https://orcid.org/0000-0003-4018-1646"} ! TLR4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700324 +name: LY96-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the LY96 gene." [MONDO:patterns/disease_series_by_gene, PMID:36462957] +synonym: "MD2 deficiency" BROAD [PMID:36462957] +is_a: MONDO:0021094 {source="PMID:36462957"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17156 {source="PMID:36462957"} ! LY96 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700325 +name: IRAK1-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IRAK1 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IRAK1 deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6112 {source="https://orcid.org/0000-0003-4018-1646"} ! IRAK1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700326 +name: IRAK4-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IRAK4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "IRAK4 disorder" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17967 {source="https://orcid.org/0000-0003-4018-1646"} ! IRAK4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700327 +name: IRF4-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IRF4 gene." [MONDO:patterns/disease_series_by_gene, PMID:36917008] +synonym: "IRF4 haplosufficiency" BROAD [PMID:36917008] +is_a: MONDO:0021094 {source="PMID:36917008"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6119 {source="PMID:36917008"} ! IRF4 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700328 +name: STING1-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the STING1 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "STING-like disease" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/27962 {source="https://orcid.org/0000-0003-4018-1646"} ! STING1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700329 +name: C8G-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the C8G gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +synonym: "C8G deficiency" BROAD [https://orcid.org/0000-0003-4018-1646] +is_a: MONDO:0021094 {source="https://orcid.org/0000-0003-4018-1646"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/1354 {source="https://orcid.org/0000-0003-4018-1646"} ! C8G +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700330 +name: PTEN-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the PTEN gene." [MONDO:patterns/disease_series_by_gene, PMID:27426521, PMID:37178059] +synonym: "PTEN Deficiency (LOF)" BROAD [PMID:27426521, PMID:37178059] +is_a: MONDO:0021094 {source="PMID:27426521", source="PMID:37178059"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="PMID:27426521", source="PMID:37178059"} ! PTEN +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700331 +name: TNFSF12-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFSF12 gene." [MONDO:patterns/disease_series_by_gene, PMID:23493554] +synonym: "TWEAK deficiency" BROAD [PMID:23493554] +is_a: MONDO:0021094 {source="PMID:23493554"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11927 {source="PMID:23493554"} ! TNFSF12 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700332 +name: SH2B3-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the SH2B3 gene." [MONDO:patterns/disease_series_by_gene, PMID:37277724] +synonym: "SH2B3 deficiency" BROAD [PMID:37277724] +is_a: MONDO:0021094 {source="PMID:37277724"} ! immunodeficiency disease +relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/29605 {source="PMID:37277724"} ! SH2B3 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700333 +name: Aicardi-Goutieres syndrome 1, autosomal dominant +def: "Autosomal dominant form of Aicardi-Goutieres syndrome 1." [MONDO:patterns/autosomal_dominant, PMID:30561700] +is_a: MONDO:0009165 {source="PMID:30561700"} ! Aicardi-Goutieres syndrome 1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + +[Term] +id: MONDO:0700334 +name: Aicardi-Goutieres syndrome 1, autosomal recessive +def: "Autosomal recessive form of Aicardi-Goutieres syndrome 1." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/autosomal_recessive] +is_a: MONDO:0009165 {source="https://orcid.org/0000-0003-4018-1646"} ! Aicardi-Goutieres syndrome 1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + [Term] id: MONDO:0800001 name: delayed sleep phase syndrome, susceptibility to @@ -561966,7 +562420,9 @@ id: MONDO:0970994 name: immunodeficiency 120 xref: OMIM:620836 {source="MONDO:equivalentTo"} is_a: MONDO:0021094 {source="OMIM:620836", source="https://orcid.org/0000-0002-4142-7153"} ! immunodeficiency disease +is_a: MONDO:0800145 {source="PMID:31449058"} ! non-severe combined immunodeficiency due to polymerase delta deficiency relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9175 {source="OMIM:620836"} ! POLD1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI [Term] id: MONDO:0970995 From 325c27c8cc9418f71b74ab931a0e6832f0397bd1 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Wed, 11 Dec 2024 09:13:26 -0500 Subject: [PATCH 2/5] removed duplicated term --- src/ontology/mondo-edit.obo | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 82564876c..c2e6a12f5 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -548386,24 +548386,6 @@ is_a: MONDO:0021094 {source="PMID:27426521", source="PMID:37178059"} ! immunodef relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="PMID:27426521", source="PMID:37178059"} ! PTEN property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI -[Term] -id: MONDO:0700331 -name: TNFSF12-related immunodeficiency -def: "A immunodeficiency disease in which the cause of the disease is a variation in the TNFSF12 gene." [MONDO:patterns/disease_series_by_gene, PMID:23493554] -synonym: "TWEAK deficiency" BROAD [PMID:23493554] -is_a: MONDO:0021094 {source="PMID:23493554"} ! immunodeficiency disease -relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11927 {source="PMID:23493554"} ! TNFSF12 -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI - -[Term] -id: MONDO:0700332 -name: SH2B3-related immunodeficiency -def: "A immunodeficiency disease in which the cause of the disease is a variation in the SH2B3 gene." [MONDO:patterns/disease_series_by_gene, PMID:37277724] -synonym: "SH2B3 deficiency" BROAD [PMID:37277724] -is_a: MONDO:0021094 {source="PMID:37277724"} ! immunodeficiency disease -relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/29605 {source="PMID:37277724"} ! SH2B3 -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI - [Term] id: MONDO:0700333 name: Aicardi-Goutieres syndrome 1, autosomal dominant From 1017c92ba97c5c3e04d7205b37712268e41a87f9 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Wed, 11 Dec 2024 09:36:45 -0500 Subject: [PATCH 3/5] Updated definitions + updated CHARGE syndrome x-ref --- src/ontology/mondo-edit.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index c2e6a12f5..b60a247a8 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -189608,7 +189608,6 @@ xref: NANDO:1200464 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0 xref: NANDO:2200972 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NCIT:C75100 {source="MONDO:equivalentTo", source="DOID:0050834"} xref: NORD:920 {source="MONDO:NORD"} -xref: OMIM:214800 {source="Orphanet:138", source="MONDO:equivalentTo", source="DOID:0050834", source="GARD:0000029", source="Orphanet:138/e"} xref: Orphanet:138 {source="MONDO:equivalentTo", source="DOID:0050834", source="GARD:0000029", source="OMIM:214800"} xref: SCTID:394529000 {source="DOID:0050834"} xref: SCTID:47535005 {source="MONDO:equivalentTo", source="DOID:0050834"} @@ -548065,7 +548064,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0700295 name: CHARGE syndrome due to SEMA3E deficiency -def: "#REF!" [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the SEMA3E gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] is_a: MONDO:0008965 {source="https://orcid.org/0000-0003-4018-1646"} ! CHARGE syndrome relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10727 {source="https://orcid.org/0000-0003-4018-1646"} ! SEMA3E property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI @@ -548073,7 +548072,8 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0700296 name: CHARGE syndrome due to CHD7 deficiency -def: "#REF!" [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +def: "A combined immunodeficiency in which other clinical features are present in addition to immunodeficiency, and in which the cause of the disease is a variation in the CHD7 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +xref: OMIM:214800 {source="MONDO:equivalentTo"} is_a: MONDO:0008965 {source="OMIM:214800", source="https://orcid.org/0000-0003-4018-1646"} ! CHARGE syndrome relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/20626 {source="https://orcid.org/0000-0003-4018-1646"} ! CHD7 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI From f1e0c88653a5c46a6a1db4f9db7cf66e3f5cf590 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Tue, 17 Dec 2024 15:25:07 -0800 Subject: [PATCH 4/5] updated definitions --- src/ontology/mondo-edit.obo | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index b60a247a8..49a69d35c 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -165143,6 +165143,8 @@ synonym: "Lhermitte-Duclos syndrome" EXACT [] synonym: "multiple hamartoma syndrome" RELATED [] synonym: "Proteus-like syndrome" RELATED [] synonym: "PTEN Cowden disease" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene] +synonym: "PTEN deficiency" BROAD [PMID:27426521, PMID:37178059] +synonym: "PTEN-related immunodeficiency" BROAD [PMID:27426521, PMID:37178059] xref: GARD:16450 {source="MONDO:GARD"} xref: OMIM:158350 {source="MONDO:equivalentTo"} xref: Orphanet:201 {source="OMIM:158350"} @@ -165154,6 +165156,7 @@ intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.o relationship: has_characteristic HP:0000006 {source="MONDO:HPOA", source="OMIM:158350"} ! Autosomal dominant inheritance relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="MONDO:mim2gene_medgen"} ! PTEN property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:string [Term] id: MONDO:0008022 @@ -547977,8 +547980,8 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0700285 -name: IRF4-related immunodeficiency -def: "A combined immunodeficiency in which the cause of the disease is a variation in the IRF4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] +name: IRF4-related multimorphic immunodeficiency +def: "A combined immunodeficiency in which the cause of the disease is the heterozygous germline mutation p.T95R in the DNA binding domain (DBD) of the IRF4 gene." [https://orcid.org/0000-0003-4018-1646, MONDO:patterns/disease_series_by_gene] is_a: MONDO:0015131 {source="https://orcid.org/0000-0003-4018-1646"} ! combined immunodeficiency relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6119 {source="https://orcid.org/0000-0003-4018-1646"} ! IRF4 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI @@ -548078,15 +548081,6 @@ is_a: MONDO:0008965 {source="OMIM:214800", source="https://orcid.org/0000-0003-4 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/20626 {source="https://orcid.org/0000-0003-4018-1646"} ! CHD7 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI -[Term] -id: MONDO:0700297 -name: PTEN-related immunodeficiency -def: "A immunodeficiency disease in which the cause of the disease is a variation in the PTEN gene." [MONDO:patterns/disease_series_by_gene, PMID:27426521, PMID:37178059] -synonym: "PTEN deficiency" BROAD [PMID:27426521, PMID:37178059] -is_a: MONDO:0021094 {source="PMID:27426521", source="PMID:37178059"} ! immunodeficiency disease -relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="PMID:27426521", source="PMID:37178059"} ! PTEN -property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI - [Term] id: MONDO:0700298 name: TNFSF12-related immunodeficiency @@ -548352,8 +548346,8 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0700327 -name: IRF4-related immunodeficiency -def: "A immunodeficiency disease in which the cause of the disease is a variation in the IRF4 gene." [MONDO:patterns/disease_series_by_gene, PMID:36917008] +name: IRF4, interferon activation domain-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the interferon activation domain of the IRF4 gene." [MONDO:patterns/disease_series_by_gene, PMID:36917008] synonym: "IRF4 haplosufficiency" BROAD [PMID:36917008] is_a: MONDO:0021094 {source="PMID:36917008"} ! immunodeficiency disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6119 {source="PMID:36917008"} ! IRF4 @@ -548379,13 +548373,23 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0700330 -name: PTEN-related immunodeficiency -def: "A immunodeficiency disease in which the cause of the disease is a variation in the PTEN gene." [MONDO:patterns/disease_series_by_gene, PMID:27426521, PMID:37178059] +name: PTEN loss-of-function-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a loss-of-function mutation in the PTEN gene." [MONDO:patterns/disease_series_by_gene, PMID:27426521, PMID:37178059] synonym: "PTEN Deficiency (LOF)" BROAD [PMID:27426521, PMID:37178059] is_a: MONDO:0021094 {source="PMID:27426521", source="PMID:37178059"} ! immunodeficiency disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 {source="PMID:27426521", source="PMID:37178059"} ! PTEN property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI +[Term] +id: MONDO:0700331 +name: IRF4-related immunodeficiency +def: "A immunodeficiency disease in which the cause of the disease is a variation in the IRF4 gene." [MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0021094 ! immunodeficiency disease +intersection_of: MONDO:0021094 ! immunodeficiency disease +intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6119 ! IRF4 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4142-7153 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI + [Term] id: MONDO:0700333 name: Aicardi-Goutieres syndrome 1, autosomal dominant From 4f0bad65e7b11bb0f26ef33f0b9028a5017aeccc Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Tue, 17 Dec 2024 16:19:56 -0800 Subject: [PATCH 5/5] Update mondo-edit.obo --- src/ontology/mondo-edit.obo | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 49a69d35c..4cbee66c7 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -548205,7 +548205,8 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0700311 name: Shwachman Diamond syndrome due to DNAJC21 deficiency def: "A Shwachman Diamond syndrome in which the cause of the disease is a variation in the DNAJC21 gene." [MONDO:patterns/disease_series_by_gene, PMID:28062395] -is_a: MONDO:0021094|MONDO:0009833 {source="PMID:28062395"} +is_a: MONDO:0009833 {source="PMID:28062395"} ! Shwachman-Diamond syndrome +is_a: MONDO:0021094 {source="PMID:28062395"} ! immunodeficiency disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/27030 {source="PMID:28062395"} ! DNAJC21 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8090" xsd:anyURI