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revise children of 'myopathy caused by variation in FKRP' (#6853)
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* 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
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@nicolevasilevsky
nicolevasilevsky authored Nov 9, 2023
1 parent 9fd3e7d commit 6cd1700
Showing 1 changed file with 21 additions and 15 deletions.
36 changes: 21 additions & 15 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand All @@ -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"}
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -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
Expand Down

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