From 6cd1700750412da6dbe99ca0e2060a2c68dad364 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 9 Nov 2023 13:30:26 -0800 Subject: [PATCH] revise children of 'myopathy caused by variation in FKRP' (#6853) * revise children of 'myopathy caused by variation in FKRP' - exclude superclasses and add new super class to - exclude superclasses from 'muscular dystrophy-dystroglycanopathy, type A' close #6851 * exclude superclasses * fix subclsses * rename muscular dystrophy-dystroglycanopathy (limb-girdle), type C5 * exclude QC * relabel MONDO:0011787 per Shruthi's request --- src/ontology/mondo-edit.obo | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index ef75ef4be6..31dcb6610f 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -1520,14 +1520,14 @@ xref: Orphanet:899 {source="MONDO:equivalentTo"} xref: SCTID:111504002 {source="MONDO:equivalentTo"} xref: UMLS:C0265221 {source="NCIT:C99109", source="Orphanet:899", source="MONDO:notFoundInDiseaseSubset"} xref: UMLS:CN239483 {source="MONDO:equivalentTo"} -is_a: MONDO:0016156 {source="Orphanet:899"} ! qualitative or quantitative defects of FKRP -is_a: MONDO:0016184 {source="Orphanet:899"} ! qualitative or quantitative defects of protein O-mannosyltransferase 1 -is_a: MONDO:0016185 {source="Orphanet:899"} ! qualitative or quantitative defects of protein O-mannosyltransferase 2 is_a: MONDO:0018276 {source="https://orcid.org/0000-0001-5208-3432"} ! muscular dystrophy-dystroglycanopathy -is_a: MONDO:0018869 ! cobblestone lissencephaly -is_a: MONDO:0020247 {source="Orphanet:899"} ! congenital vitreoretinal dysplasia -is_a: MONDO:0700066 ! myopathy caused by variation in FKRP -is_a: MONDO:0700068 ! myopathy caused by variation in POMGNT1 +relationship: excluded_subClassOf MONDO:0016156 {source="Orphanet:899"} ! qualitative or quantitative defects of FKRP +relationship: excluded_subClassOf MONDO:0016184 {source="Orphanet:899"} ! qualitative or quantitative defects of protein O-mannosyltransferase 1 +relationship: excluded_subClassOf MONDO:0016185 {source="Orphanet:899"} ! qualitative or quantitative defects of protein O-mannosyltransferase 2 +relationship: excluded_subClassOf MONDO:0018869 ! cobblestone lissencephaly +relationship: excluded_subClassOf MONDO:0020247 {source="Orphanet:899"} ! congenital vitreoretinal dysplasia +relationship: excluded_subClassOf MONDO:0700066 ! myopathy caused by variation in FKRP +relationship: excluded_subClassOf MONDO:0700068 ! myopathy caused by variation in POMGNT1 relationship: has_characteristic MONDO:0021140 ! congenital relationship: has_characteristic MONDO:0021152 {source="OMIMPS:236670"} ! inherited property_value: confidence "0.5294117647058822" xsd:double @@ -232647,7 +232647,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0011787 name: autosomal recessive limb-girdle muscular dystrophy type 2I -def: "Autosomal recessive limb-girdle muscular dystrophy type 2I (LGMD2I) is a subtype of autosomal recessive limb-girdle muscular dystrophy that presents a highly variable age of onset and phenotypic spectrum typically characterized by slowly progressive proximal weakness of the pelvic and shoulder girdle musculature (predominantly affecting the lower limbs), frequently associated with waddling gait, scapular winging, calf and tongue hypertrophy, exercise-induced myalgia, and myoglobinuria and/or elevated creatine kinase serum levels. Abdominal muscle weakness, cardiomyopathy, respiratory muscle involvement and various brain abnormalities have also been reported." [Orphanet:34515] +def: "A subtype of autosomal recessive limb-girdle muscular dystrophy that presents a highly variable age of onset and phenotypic spectrum typically characterized by slowly progressive proximal weakness of the pelvic and shoulder girdle musculature (predominantly affecting the lower limbs), frequently associated with waddling gait, scapular winging, calf and tongue hypertrophy, exercise-induced myalgia, and myoglobinuria and/or elevated creatine kinase serum levels. Abdominal muscle weakness, cardiomyopathy, respiratory muscle involvement and various brain abnormalities have also been reported." [Orphanet:34515] subset: ordo_disease {source="Orphanet:34515"} synonym: "autosomal recessive limb-girdle muscular dystrophy caused by mutation in FKRP" EXACT [MONDO:design_pattern] synonym: "FKRP autosomal recessive limb-girdle muscular dystrophy" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene] @@ -232661,6 +232661,7 @@ synonym: "muscular dystrophy, limb-girdle, type 2I" RELATED [OMIM:607155] synonym: "muscular dystrophy-dystroglycanopathy (limb-girdle) type C 5" EXACT [DOID:0110299] synonym: "muscular dystrophy-dystroglycanopathy (Limb-girdle) type C, 5" EXACT [NCIT:C126739] synonym: "muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 5" RELATED [MONDO:Lexical, OMIM:607155] +synonym: "muscular dystrophy-dystroglycanopathy (limb-girdle), type C5" EXACT [OMIM:607155] synonym: "muscular dystrophy-dystroglycanopathy limb-girdle FRKP-related" EXACT [DOID:0110299] synonym: "muscular dystrophy-dystroglycanopathy, limb-girdle, Frkp-related" RELATED [OMIM:607155] xref: DOID:0110299 {source="MONDO:equivalentTo"} @@ -242490,6 +242491,7 @@ is_a: MONDO:0020121 {source="DOID:0110297/inferred", source="EFO:0009145/inferre is_a: MONDO:0700070 {source="https://clinicalgenome.org/affiliation/50061/"} ! myopathy caused by variation in POMT1 intersection_of: MONDO:0015152 ! autosomal recessive limb-girdle muscular dystrophy intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9202 ! POMT1 +relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql relationship: has_characteristic MONDO:0021140 ! congenital relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9202 {source="MONDO:mim2gene_medgen"} ! POMT1 property_value: confidence "21.666666666666735" xsd:double @@ -261378,6 +261380,7 @@ xref: Orphanet:588 {source="OMIM:613153"} xref: Orphanet:899 {source="MONDO:relatedTo", source="OMIM:613153"} xref: UMLS:C3150413 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:613153"} is_a: MONDO:0000171 {source="OMIM:613153", source="Orphanet:899/btnt"} ! muscular dystrophy-dystroglycanopathy, type A +is_a: MONDO:0016156 {source="https://orcid.org/0000-0001-5208-3432"} ! qualitative or quantitative defects of FKRP is_a: MONDO:0018939 {source="https://orcid.org/0000-0002-4142-7153"} ! muscle-eye-brain disease relationship: has_characteristic MONDO:0021140 {source="https://orcid.org/0000-0002-4142-7153"} ! congenital relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17997 {source="MONDO:mim2gene_medgen"} ! FKRP @@ -261506,6 +261509,7 @@ is_a: MONDO:0016185 {source="Orphanet:206559"} ! qualitative or quantitative def is_a: MONDO:0700071 {source="https://clinicalgenome.org/affiliation/50061/"} ! myopathy caused by variation in POMT2 intersection_of: MONDO:0015152 ! autosomal recessive limb-girdle muscular dystrophy intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/19743 ! POMT2 +relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql relationship: has_characteristic MONDO:0021140 ! congenital relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/19743 {source="MONDO:mim2gene_medgen"} ! POMT2 property_value: confidence "14.999999999999948" xsd:double @@ -351027,7 +351031,7 @@ synonym: "MEB disease with bilateral multicystic leucodystrophy" EXACT [Orphanet xref: ICD10CM:G71.2 {source="Orphanet:370997/attributed", source="Orphanet:370997/ntbt", source="Orphanet:370997"} xref: Orphanet:370997 {source="MONDO:equivalentTo"} is_a: MONDO:0018276 ! muscular dystrophy-dystroglycanopathy -is_a: MONDO:0018869 ! cobblestone lissencephaly +is_a: MONDO:0018869 {source="Orphanet:370997"} ! cobblestone lissencephaly relationship: has_characteristic MONDO:0021140 ! congenital property_value: confidence "0.5294117647058822" xsd:double @@ -361836,12 +361840,13 @@ xref: ICD9:742.4 {source="MONDO:relatedTo", source="MONDO:i2s"} xref: Orphanet:588 {source="MONDO:equivalentTo"} xref: SCTID:277950001 {source="MONDO:equivalentTo"} xref: UMLS:C0457133 {source="Orphanet:588", source="Orphanet:588/e", source="MONDO:notFoundInDiseaseSubset"} -is_a: MONDO:0015327 ! developmental anomaly of metabolic origin -is_a: MONDO:0016185 {source="Orphanet:588"} ! qualitative or quantitative defects of protein O-mannosyltransferase 2 -is_a: MONDO:0018276 ! muscular dystrophy-dystroglycanopathy -is_a: MONDO:0018869 ! cobblestone lissencephaly -is_a: MONDO:0700066 ! myopathy caused by variation in FKRP -is_a: MONDO:0700068 ! myopathy caused by variation in POMGNT1 +is_a: MONDO:0019950 {source="https://orcid.org/0000-0001-5208-3432"} ! congenital muscular dystrophy +relationship: excluded_subClassOf MONDO:0015327 ! developmental anomaly of metabolic origin +relationship: excluded_subClassOf MONDO:0016185 {source="Orphanet:588"} ! qualitative or quantitative defects of protein O-mannosyltransferase 2 +relationship: excluded_subClassOf MONDO:0018276 ! muscular dystrophy-dystroglycanopathy +relationship: excluded_subClassOf MONDO:0018869 ! cobblestone lissencephaly +relationship: excluded_subClassOf MONDO:0700066 ! myopathy caused by variation in FKRP +relationship: excluded_subClassOf MONDO:0700068 ! myopathy caused by variation in POMGNT1 relationship: has_characteristic MONDO:0021140 ! congenital property_value: confidence "0.5294117647058822" xsd:double property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/156/muscle-eye-brain-disease" xsd:anyURI {source="GARD:0000156"} @@ -455230,6 +455235,7 @@ def: "Any myopathy in which the cause of the disease is a variation in the FKRP synonym: "FKRP myopathy" EXACT [MONDO:patterns/disease_series_by_gene] synonym: "FKRP-related myopathy" EXACT CLINGEN_PREFERRED [https://clinicalgenome.org/affiliation/50061/, MONDO:patterns/disease_series_by_gene] synonym: "myopathy caused by mutation in FKRP" EXACT [MONDO:patterns/disease_series_by_gene] +is_a: MONDO:0016156 {source="https://orcid.org/0000-0001-5208-3432"} ! qualitative or quantitative defects of FKRP intersection_of: MONDO:0005336 ! myopathy intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17997 ! FKRP relationship: disease_has_basis_in_disruption_of GO:0006493 ! protein O-linked glycosylation