From 30d7a6d3f83db73169fbcc3cb845c2c8a20a61a9 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Sat, 22 Feb 2025 16:51:47 -0800 Subject: [PATCH 1/2] add superclass to neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline (MONDO:0030028) and related classes (assert as child of neurodegenerative disorder) - remove duplicate synonyms - revise synonym scope close #8492 --- src/ontology/mondo-edit.obo | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index f8d244382..2a670fa57 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -346044,6 +346044,7 @@ xref: MEDGEN:934660 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:617145 {source="MONDO:equivalentTo"} xref: UMLS:C4310693 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:934660"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11280 {source="MONDO:mim2gene_medgen", source="OMIM:617145"} ! SQSTM1 [Term] @@ -499102,13 +499103,14 @@ id: MONDO:0030028 name: neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline subset: otar {source="MONDO:OTAR"} synonym: "CONATOC" EXACT ABBREVIATION [OMIM:618868] -synonym: "NEURODEGENERATION, CHILDHOOD-ONSET, WITH ATAXIA, TREMOR, OPTIC ATROPHY, AND COGNITIVE DECLINE" EXACT [OMIM:618868] synonym: "neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline" EXACT [OMIM:618868] xref: MEDGEN:1715031 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618868 {source="MONDO:equivalentTo"} xref: UMLS:C5394335 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1715031"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-6330-7526"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/18798 {source="OMIM:618868"} ! SLC44A1 +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8492" xsd:anyURI [Term] id: MONDO:0030029 @@ -504128,7 +504130,7 @@ subset: nord_rare {source="MONDO:NORD"} subset: ordo_disorder {source="Orphanet:610573"} subset: orphanet_rare {source="Orphanet:610573"} subset: rare -synonym: "CONRIBA" EXACT ABBREVIATION [] +synonym: "CONRIBA" EXACT ABBREVIATION [OMIM:619173] synonym: "neurodegeneration, childhood-onset, hypotonia, respiratory insufficiency and brain imaging abnormalities" EXACT [] xref: GARD:18023 {source="MONDO:GARD"} xref: MEDGEN:1781967 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} @@ -504136,6 +504138,7 @@ xref: OMIM:619173 {source="MONDO:equivalentTo"} xref: Orphanet:610573 {source="MONDO:equivalentTo"} xref: UMLS:C5543020 {source="MEDGEN:1781967", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2024 {source="OMIM:619173"} ! CLCN6 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -504746,6 +504749,7 @@ xref: MEDGEN:1779901 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:619259 {source="MONDO:equivalentTo"} xref: UMLS:C5543254 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1779901"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10680 {source="OMIM:619259"} ! SDHA [Term] @@ -507157,12 +507161,12 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0032650 name: neurodegeneration, childhood-onset, with cerebellar atrophy -synonym: "CONDCA" RELATED ABBREVIATION [] -synonym: "NEURODEGENERATION, CHILDHOOD-ONSET, WITH CEREBELLAR ATROPHY" RELATED [] +synonym: "CONDCA" EXACT ABBREVIATION [OMIM:618276] xref: MEDGEN:1648286 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618276 {source="MONDO:equivalentTo"} xref: UMLS:C4748934 {source="MEDGEN:1648286", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:618276"} ! hereditary disease +is_a: MONDO:0005559 ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17258 {source="OMIM:618276"} ! AGTPBP1 [Term] @@ -508612,12 +508616,12 @@ relationship: curated_content_resource https://search.clinicalgenome.org/kb/cond [Term] id: MONDO:0032758 name: neurodegeneration, early-onset, with choreoathetoid movements and microcytic anemia -synonym: "NDCAMA" RELATED ABBREVIATION [] -synonym: "NEURODEGENERATION, EARLY-ONSET, WITH CHOREOATHETOID MOVEMENTS AND MICROCYTIC ANEMIA" RELATED [] +synonym: "NDCAMA" EXACT ABBREVIATION [OMIM:618451] xref: MEDGEN:1676579 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618451 {source="MONDO:equivalentTo"} xref: UMLS:C5193104 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1676579"} is_a: MONDO:0003847 {source="OMIM:618451"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6115 {source="OMIM:618451"} ! IREB2 [Term] @@ -513092,14 +513096,14 @@ is_a: MONDO:0018158 {source="DOID:0070450", source="OMIM:618972"} ! mitochondria id: MONDO:0033546 name: neurodegeneration, infantile-onset, biotin-responsive subset: otar {source="MONDO:OTAR"} -synonym: "NERIB" RELATED ABBREVIATION [] -synonym: "NEURODEGENERATION, INFANTILE-ONSET, BIOTIN-RESPONSIVE" RELATED [] -synonym: "Smvt Deficiency" RELATED [] -synonym: "Sodium-Dependent Multivitamin Transporter Deficiency" RELATED [] +synonym: "NERIB" EXACT ABBREVIATION [OMIM:618973] +synonym: "SMVT deficiency" EXACT [OMIM:618973] +synonym: "sodium-dependent multivitamin transporter deficiency" EXACT [OMIM:618973] xref: MEDGEN:1771692 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618973 {source="MONDO:equivalentTo"} xref: UMLS:C5436520 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1771692"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11041 {source="OMIM:618973"} ! SLC5A6 [Term] @@ -536819,7 +536823,7 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-520 [Term] id: MONDO:0100095 name: neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures -def: "Autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development, with cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable. The cause is mutations in the ADPRHL2 gene." [https://orcid.org/0000-0002-4650-631X, PMID:3010008, PMID:30401461] +def: "An autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development, with cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable. The cause is mutations in the ADPRHL2 gene." [https://orcid.org/0000-0002-4650-631X, PMID:3010008, PMID:30401461] subset: gard_rare {source="MONDO:GARD"} subset: otar {source="MONDO:OTAR"} subset: rare @@ -536831,7 +536835,7 @@ xref: OMIM:618170 {source="MONDO:equivalentTo"} xref: UMLS:C4748527 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1648391"} is_a: MONDO:0003847 {source="OMIM:618170"} ! hereditary disease is_a: MONDO:0006025 {source="DOID:0070352"} ! autosomal recessive disease -is_a: MONDO:0024237 ! inherited neurodegenerative disorder +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_characteristic HP:0000007 {source="PMID:30401461"} ! Autosomal recessive inheritance relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/21304 {source="OMIM:618170"} ! ADPRS property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432 @@ -558731,6 +558735,7 @@ xref: MEDGEN:1841021 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620306 {source="MONDO:equivalentTo"} xref: UMLS:C5830385 {source="MEDGEN:1841021", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:620306"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11016 {source="OMIM:620306"} ! SLC31A1 [Term] @@ -560781,6 +560786,7 @@ xref: MEDGEN:1847831 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620636 {source="MONDO:equivalentTo"} xref: UMLS:C5882726 {source="MEDGEN:1847831", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:620636"} ! hereditary disease +is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6743 {source="OMIM:620636"} ! CAPRIN1 [Term] From 11175b5c8cb663122ee86cafef622c0899f2d477 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Mon, 24 Feb 2025 20:05:28 -0800 Subject: [PATCH 2/2] update superclass to 'inherited neurodegenerative disease' --- src/ontology/mondo-edit.obo | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 2a670fa57..66d31927f 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -346044,7 +346044,7 @@ xref: MEDGEN:934660 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:617145 {source="MONDO:equivalentTo"} xref: UMLS:C4310693 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:934660"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11280 {source="MONDO:mim2gene_medgen", source="OMIM:617145"} ! SQSTM1 [Term] @@ -499108,7 +499108,7 @@ xref: MEDGEN:1715031 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618868 {source="MONDO:equivalentTo"} xref: UMLS:C5394335 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1715031"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-6330-7526"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-6330-7526"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/18798 {source="OMIM:618868"} ! SLC44A1 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8492" xsd:anyURI @@ -504138,7 +504138,7 @@ xref: OMIM:619173 {source="MONDO:equivalentTo"} xref: Orphanet:610573 {source="MONDO:equivalentTo"} xref: UMLS:C5543020 {source="MEDGEN:1781967", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2024 {source="OMIM:619173"} ! CLCN6 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -504749,7 +504749,7 @@ xref: MEDGEN:1779901 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:619259 {source="MONDO:equivalentTo"} xref: UMLS:C5543254 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1779901"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10680 {source="OMIM:619259"} ! SDHA [Term] @@ -507166,7 +507166,7 @@ xref: MEDGEN:1648286 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618276 {source="MONDO:equivalentTo"} xref: UMLS:C4748934 {source="MEDGEN:1648286", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:618276"} ! hereditary disease -is_a: MONDO:0005559 ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17258 {source="OMIM:618276"} ! AGTPBP1 [Term] @@ -508621,7 +508621,7 @@ xref: MEDGEN:1676579 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618451 {source="MONDO:equivalentTo"} xref: UMLS:C5193104 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1676579"} is_a: MONDO:0003847 {source="OMIM:618451"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6115 {source="OMIM:618451"} ! IREB2 [Term] @@ -513103,7 +513103,7 @@ xref: MEDGEN:1771692 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618973 {source="MONDO:equivalentTo"} xref: UMLS:C5436520 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1771692"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11041 {source="OMIM:618973"} ! SLC5A6 [Term] @@ -558735,7 +558735,7 @@ xref: MEDGEN:1841021 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620306 {source="MONDO:equivalentTo"} xref: UMLS:C5830385 {source="MEDGEN:1841021", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:620306"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11016 {source="OMIM:620306"} ! SLC31A1 [Term] @@ -558820,7 +558820,7 @@ xref: MEDGEN:1841069 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620327 {source="MONDO:equivalentTo"} xref: UMLS:C5830433 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1841069"} is_a: MONDO:0003847 {source="OMIM:620327"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/32687 {source="OMIM:620327"} ! MED11 [Term] @@ -560786,7 +560786,7 @@ xref: MEDGEN:1847831 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620636 {source="MONDO:equivalentTo"} xref: UMLS:C5882726 {source="MEDGEN:1847831", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003847 {source="OMIM:620636"} ! hereditary disease -is_a: MONDO:0005559 {source="https://orcid.org/0000-0001-5208-3432"} ! neurodegenerative disease +is_a: MONDO:0024237 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited neurodegenerative disorder relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6743 {source="OMIM:620636"} ! CAPRIN1 [Term]