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epilepsy branch revisions (#7569)
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* epilepsy branch revisions

- reinstate obsolete term: myoclonic epilepsy in infancy
- add synonym to 'self-limited familial neonatal-infantile epilepsy'

address #5957

* add obsoletion reason

* add dxref

* revise def

* remove synonym

* fix qc

* revise defs, add syns

* add superclass axioms to benign childhood occipital epilepsy, Panayiotopoulos type

and benign childhood occipital epilepsy, Gastaut type

* revise defs, syn

* revise definition

* add superclass

* exclude superclass

* remove superclasses from 'MERRF syndrome'

* revise def

* add ORCID

* update ID for myoclonic epilepsy in infancy

* normalization

---------

Co-authored-by: Sabrina Toro <sabrina@tislab.org>
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nicolevasilevsky and sabrinatoro committed Apr 10, 2024
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91 changes: 51 additions & 40 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -176685,10 +176685,8 @@ def: "A microcephalic osteodysplastic primordial dwarfism that has material basi
subset: gard_rare {source="GARD:15144"}
subset: nord_rare {source="MONDO:NORD"}
subset: rare
synonym: "brachymelic primordial dwarfism" EXACT [OMIM:210710]
synonym: "brachymelic primordial dwarfism" EXACT [DOID:0060608]
synonym: "cephaloskeletal dysplasia" EXACT [DOID:0060608]
synonym: "cephaloskeletal dysplasia" EXACT [OMIM:210710]
synonym: "brachymelic primordial dwarfism" EXACT [DOID:0060608, OMIM:210710]
synonym: "cephaloskeletal dysplasia" EXACT [DOID:0060608, OMIM:210710]
synonym: "low-birth-weight dwarfism with skeletal dysplasia" EXACT [DOID:0060608, OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type 1" EXACT [OMIM:210710]
synonym: "microcephalic osteodysplastic primordial dwarfism, type I" EXACT [MONDO:Lexical, OMIM:210710]
Expand Down Expand Up @@ -180138,10 +180136,8 @@ name: hypoplasminogenemia
def: "A rare multi-system disease characterized by markedly impaired extracellular fibrinolysis leading to the formation of ligneous (fibrin-rich) pseudomembranes on mucosae." [Orphanet:722]
subset: gard_rare {source="GARD:4380"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_disease {source="Orphanet:97231"}
subset: ordo_disease {source="Orphanet:722"}
subset: orphanet_rare {source="Orphanet:722"}
subset: orphanet_rare {source="Orphanet:97231"}
subset: ordo_disease {source="Orphanet:722", source="Orphanet:97231"}
subset: orphanet_rare {source="Orphanet:722", source="Orphanet:97231"}
subset: rare
synonym: "hypoplasminogenemia" EXACT CLINGEN_LABEL []
synonym: "ligneous conjunctivitis" RELATED [https://orcid.org/0000-0001-9310-0163, OMIM:217090]
Expand Down Expand Up @@ -229049,12 +229045,11 @@ xref: UMLS:C0162672 {source="OMIM:545000", source="NCIT:C84889", source="Orphane
is_a: MONDO:0002254 {source="NCIT:C84889"} ! syndromic disease
is_a: MONDO:0004069 ! inborn mitochondrial metabolism disorder
is_a: MONDO:0004675 {source="DOID:310", source="MESH:D017243"} ! mitochondrial encephalomyopathy
is_a: MONDO:0016022 {source="DC-OMIM:545000"} ! early myoclonic encephalopathy
is_a: MONDO:0016333 ! familial dilated cardiomyopathy
is_a: MONDO:0020127 ! hereditary peripheral neuropathy
is_a: MONDO:0044970 {source="https://orcid.org/0000-0001-5208-3432"} ! mitochondrial disease
is_a: MONDO:0100033 {source="https://www.epilepsydiagnosis.org/aetiology/metabolic-groupoverview.html"} ! metabolic epilepsy
relationship: excluded_subClassOf MONDO:0016022 {source="DC-OMIM:545000", source="https://orcid.org/0000-0001-5208-3432"} ! early myoclonic encephalopathy
relationship: excluded_subClassOf MONDO:0020074 {source="MESH:D017243", source="Orphanet:551", source="https://orcid.org/0000-0001-5208-3432"} ! progressive myoclonus epilepsy
property_value: confidence "3.666666666666666" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0010791
Expand Down Expand Up @@ -282010,7 +282005,7 @@ is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditar
[Term]
id: MONDO:0012999
name: guanidinoacetate methyltransferase deficiency
def: "Guanidinoacetate methyltransferase (GAMT) deficiency is a creatine deficiency syndrome characterized by global developmental delay/intellectual disability (DD/ID), prominent speech delay, autistic/hyperactive behavioral disorders, seizures, and various types of pyramidal and/or extra-pyramidal manifestations." [Orphanet:382]
def: "A creatine deficiency syndrome characterized by global developmental delay/intellectual disability (DD/ID), prominent speech delay, autistic/hyperactive behavioral disorders, seizures, and various types of pyramidal and/or extra-pyramidal manifestations." [https://orcid.org/0000-0001-5208-3432, Orphanet:382]
subset: gard_rare {source="GARD:2578"}
subset: nord_rare {source="MONDO:NORD", source="NORD:1967"}
subset: ordo_disease {source="Orphanet:382"}
Expand Down Expand Up @@ -342234,7 +342229,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
[Term]
id: MONDO:0015584
name: febrile infection-related epilepsy syndrome
def: "Febrile infection-related epilepsy syndrome (FIRES) describes an explosive-onset, potentially fatal acute epileptic encephalopathy that develops in previously healthy children and adolescents following the onset of a non-specific febrile illness." [Orphanet:163703]
def: "A rare, potentially fatal, epileptic encephalopathy characterized by explosive-onset of recurrent multifocal and bilateral tonic-clonic seizures following an unspecific febrile illness. The syndrome develops without a clear acute structural, toxic or metabolic cause, in a patient without previous epilepsy. FIRES is a subgroup of new-onset refractory status epilepticus (NORSE), and requires a preceding febrile infection as a mandatory feature." [https://orcid.org/0000-0001-5208-3432, Orphanet:163703]
subset: gard_rare {source="GARD:11005"}
subset: nord_rare {source="MONDO:NORD", source="NORD:1889"}
subset: ordo_disease {source="Orphanet:163703"}
Expand All @@ -342258,6 +342253,7 @@ xref: Orphanet:163703 {source="MONDO:equivalentTo"}
xref: SCTID:725413002 {source="MONDO:equivalentTo"}
xref: UMLS:C4049262 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0020072 {source="MONDO:0018200-obsoleted", source="https://github.com/monarch-initiative/mondo/pull/2571/"} ! childhood-onset epilepsy syndrome
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/11005/febrile-infection-related-epilepsy-syndrome" xsd:anyURI {source="GARD:0011005"}

[Term]
Expand Down Expand Up @@ -350602,8 +350598,7 @@ subset: orphanet_rare {source="Orphanet:1929"}
subset: rare
synonym: "CFE" EXACT ABBREVIATION [NCIT:C125384]
synonym: "chronic focal encephalitis" EXACT [NCIT:C125384]
synonym: "Rasmussen Encephalitis" EXACT [NORD:1649]
synonym: "Rasmussen encephalitis" EXACT [NCIT:C125384]
synonym: "Rasmussen encephalitis" EXACT [NCIT:C125384, NORD:1649]
synonym: "Rasmussen syndrome" EXACT [Orphanet:1929]
synonym: "RE" RELATED ABBREVIATION [GARD:0007527]
xref: GARD:18752 {source="Orphanet:1929"}
Expand Down Expand Up @@ -381577,7 +381572,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
[Term]
id: MONDO:0017615
name: benign familial infantile epilepsy
def: "Benign familial infantile epilepsy (BFIE) is a genetic epileptic syndrome characterized by the occurrence of afebrile repeated seizures in healthy infants, between the third and eighth month of life." [Orphanet:306]
def: "A genetic epileptic syndrome characterized by the occurrence of afebrile repeated seizures in healthy infants, between the third and eighth month of life." [https://orcid.org/0000-0001-5208-3432, Orphanet:306]
subset: clingen
subset: gard_rare {source="GARD:857"}
subset: nord_rare {source="MONDO:NORD"}
Expand Down Expand Up @@ -393542,7 +393537,7 @@ synonym: "GEFS+" EXACT [DOID:0060170, Orphanet:36387]
synonym: "generalised epilepsy with febrile seizures-plus" RELATED OMO:0003005 []
synonym: "generalized epilepsy with febrile seizures plus" EXACT CLINGEN_LABEL []
synonym: "generalized epilepsy with febrile seizures-plus" RELATED [Orphanet:36387]
synonym: "genetic epilepsy with febrile seizures plus" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40005/, Orphanet:36387]
synonym: "genetic epilepsy with febrile seizures plus" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40005/, https://www.epilepsydiagnosis.org/syndrome/fbp-overview.html, Orphanet:36387]
synonym: "genetic epilepsy with febrile seizures-plus" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40005/, Orphanet:36387]
xref: DOID:0060170 {source="MONDO:equivalentTo"}
xref: GARD:18641 {source="Orphanet:36387"}
Expand All @@ -393559,6 +393554,7 @@ relationship: disease_has_feature HP:0002373 ! Febrile seizure (within the age r
relationship: excluded_subClassOf MONDO:0005579 {source="DOID:0060170", source="MESH:C565808", source="NCIT:C122811", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-6601-2165"} ! epilepsy, idiopathic generalized
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:604233"} ! inherited
property_value: confidence "1.1309583424662981" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0018215
Expand Down Expand Up @@ -421099,21 +421095,11 @@ relationship: has_characteristic MONDO:0700005 {source="Orphanet:86908"} ! idiop
[Term]
id: MONDO:0019486
name: obsolete myoclonic epilepsy of infancy
subset: gard_rare {source="GARD:19086"}
subset: nord_rare {source="MONDO:NORD"}
synonym: "benign myoclonic epilepsy of infancy" EXACT [Orphanet:86909]
synonym: "benign myoclonus epilepsy of infancy" EXACT [Orphanet:86909]
xref: GARD:19086 {source="Orphanet:86909", source="MONDO:obsoleteEquivalent"}
xref: ICD10CM:G40.3 {source="Orphanet:86909", source="Orphanet:86909/attributed", source="Orphanet:86909/ntbt"}
xref: Orphanet:86909 {source="MONDO:obsoleteEquivalent"}
xref: UMLS:C0751120 {source="Orphanet:86909", source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:86909/e"}
xref: UMLS:C0917800 {source="Orphanet:86909", source="Orphanet:86909/e"}
relationship: excluded_subClassOf MONDO:0100022 {source="Orphanet:86909", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0001-8486-0558"} ! neonatal/infantile epilepsy syndrome
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5740" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6752" xsd:anyURI
is_obsolete: true
replaced_by: MONDO:0100566

[Term]
id: MONDO:0019487
Expand Down Expand Up @@ -435969,7 +435955,7 @@ replaced_by: MONDO:0011694
[Term]
id: MONDO:0020300
name: autosomal dominant nocturnal frontal lobe epilepsy
def: "Autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) is a seizure disorder characterized by intermittent dystonia and/or choreoathetoid movements that occur during sleep. The clusters of nocturnal motor seizures are often stereotyped and brief." [Orphanet:98784]
def: "A seizure disorder characterized by intermittent dystonia and/or choreoathetoid movements that occur during sleep. The clusters of nocturnal motor seizures are often stereotyped and brief." [https://orcid.org/0000-0001-5208-3432, Orphanet:98784]
subset: gard_rare {source="GARD:11918"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_disease {source="Orphanet:98784"}
Expand Down Expand Up @@ -436080,7 +436066,7 @@ replaced_by: MONDO:0008572
[Term]
id: MONDO:0020307
name: benign childhood occipital epilepsy, Panayiotopoulos type
def: "Benign childhood occipital epilepsy, Panayiotopoulos type is a rare, genetic neurological disorder characterized by late infancy to early-adolescence onset of prolonged, nocturnal seizures which begin with autonomic features (e.g. vomiting, pallor, sweating) and associate tonic eye deviation, impairment of consciousness and may evolve to a hemi-clonic or generalized convulsion. Autonomic status epilepticus may be the only clinical event in some cases." [Orphanet:98815]
def: "A rare, genetic neurological disorder characterized by late infancy to early-adolescence onset of prolonged, nocturnal seizures which begin with autonomic features (e.g. vomiting, pallor, sweating) and associate tonic eye deviation, impairment of consciousness and may evolve to a hemi-clonic or generalized convulsion. Autonomic status epilepticus may be the only clinical event in some cases." [https://orcid.org/0000-0001-5208-3432, Orphanet:98815]
subset: gard_rare {source="GARD:19581"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_clinical_subtype {source="Orphanet:98815"}
Expand All @@ -436095,22 +436081,29 @@ xref: Orphanet:98815 {source="MONDO:equivalentTo"}
xref: SCTID:230387008 {source="MONDO:equivalentTo"}
xref: UMLS:C0393676 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0007558 {source="Orphanet:98815"} ! benign occipital epilepsy
is_a: MONDO:0020072 {source="https://www.epilepsydiagnosis.org/syndrome/panayiotopoulos-overview.html"} ! childhood-onset epilepsy syndrome
relationship: has_characteristic HP:0011463 {source="https://www.epilepsydiagnosis.org/syndrome/panayiotopoulos-overview.html"} ! Childhood onset
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0020308
name: benign childhood occipital epilepsy, Gastaut type
def: "Benign childhood occipital epilepsy, Gastaut type is a rare, genetic neurological disorder characterized by childhood to mid-adolescence onset of frequent, brief, diurnal simple partial seizures which usually begin with visual hallucinations (e.g. phosphenes) and/or ictal blindness and may associate non visual seizures (such as deviation of the eyes, oculoclonic seizures), forced eyelid closure and blinking and sensory hallucinations. Post-ictal headache is common while impairment of consciousness is rare." [Orphanet:98816]
def: "A rare, genetic neurological disorder characterized by childhood to mid-adolescence onset of frequent, brief, diurnal simple partial seizures which usually begin with visual hallucinations (e.g. phosphenes) and/or ictal blindness and may associate non visual seizures (such as deviation of the eyes, oculoclonic seizures), forced eyelid closure and blinking and sensory hallucinations. Post-ictal headache is common while impairment of consciousness is rare." [https://orcid.org/0000-0001-5208-3432, Orphanet:98816]
subset: gard_rare {source="GARD:19582"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_clinical_subtype {source="Orphanet:98816"}
subset: orphanet_rare {source="Orphanet:98816"}
subset: rare
synonym: "childhood occipital epilepsy (Gastaut type)" EXACT [https://www.epilepsydiagnosis.org/syndrome/late-childhood-occipital-overview.html]
synonym: "late-onset benign childhood occipital epilepsy" EXACT [Orphanet:98816]
xref: GARD:19582 {source="Orphanet:98816"}
xref: ICD10CM:G40.0 {source="Orphanet:98816/attributed", source="Orphanet:98816/ntbt", source="Orphanet:98816"}
xref: Orphanet:98816 {source="MONDO:equivalentTo"}
xref: UMLS:C0393677 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0007558 {source="Orphanet:98816"} ! benign occipital epilepsy
is_a: MONDO:0020072 {source="https://www.epilepsydiagnosis.org/syndrome/late-childhood-occipital-overview.html"} ! childhood-onset epilepsy syndrome
relationship: has_characteristic HP:0011463 {source="https://www.epilepsydiagnosis.org/syndrome/late-childhood-occipital-overview.html"} ! Childhood onset
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0020309
Expand Down Expand Up @@ -506245,7 +506238,7 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-520
[Term]
id: MONDO:0100027
name: obsolete febrile seizures plus, genetic epilepsy with febrile seizures plus
property_value: IAO:0000231 OMO:0001000
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeNonDisease"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3442" xsd:anyURI
is_obsolete: true
consider: MONDO:0018214
Expand Down Expand Up @@ -506285,11 +506278,12 @@ name: adolescent/adult onset autosomal dominant epilepsy with auditory features
def: "A genetic focal epilepsy, with focal sensory auditory seizures seen in family members. Seizures often comprise such mild symptoms that they are undiagnosed. There are no implications expected for development or learning and seizures are typically infrequent and well controlled." [https://www.epilepsydiagnosis.org/syndrome/adeaf-overview.html]
subset: inferred_rare
subset: rare
synonym: "autosomal dominant partial/lateral temporal epilepsy with auditory features" EXACT []
synonym: "autosomal dominant partial/lateral temporal epilepsy with auditory features" EXACT [https://www.epilepsydiagnosis.org/syndrome/adeaf-overview.html]
is_a: MONDO:0010898 {source="https://github.com/monarch-initiative/mondo/issues/1764"} ! autosomal dominant epilepsy with auditory features
is_a: MONDO:0100030 {source="https://orcid.org/0000-0001-8486-0558"} ! adolescent/adult-onset epilepsy syndrome
property_value: http://purl.org/dc/elements/1.1/date "2018-06-23T01:47:18Z" xsd:dateTime
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/5957" xsd:anyURI

[Term]
id: MONDO:0100032
Expand Down Expand Up @@ -508723,6 +508717,7 @@ subset: rare
is_a: MONDO:0100022 {source="https://clinicalgenome.org/affiliation/40005/"} ! neonatal/infantile epilepsy syndrome
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/5793" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0100209
Expand Down Expand Up @@ -513996,6 +513991,15 @@ intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.o
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/7389" xsd:anyURI

[Term]
id: MONDO:0100560
name: ligneous conjunctivitis
def: "A rare form of chronic conjunctivitis characterized by the development of firm fibrin-rich, woody-like pseudomembraneous lesions mainly on the tarsal conjunctivae. Ligneous conjunctivitis is usually the initial and most common manifestation of type I congenital plasminogen deficiency." [OMIM:217090, PMID:12850227]
xref: OMIM:217090 {source="MONDO:includedEntryInOMIM"}
is_a: MONDO:0006170 {source="OMIM:217090"} ! conjunctival disorder
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/7224" xsd:anyURI

[Term]
id: MONDO:0100561
name: HBA1-related alpha thalassemia spectrum
Expand Down Expand Up @@ -514046,13 +514050,20 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-520
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7561" xsd:anyURI

[Term]
id: MONDO:0100560
name: ligneous conjunctivitis
def: "A rare form of chronic conjunctivitis characterized by the development of firm fibrin-rich, woody-like pseudomembraneous lesions mainly on the tarsal conjunctivae. Ligneous conjunctivitis is usually the initial and most common manifestation of type I congenital plasminogen deficiency." [OMIM:217090, PMID:12850227]
xref: OMIM:217090 {source="MONDO:includedEntryInOMIM"}
is_a: MONDO:0006170 {source="OMIM:217090"} ! conjunctival disorder
id: MONDO:0100566
name: myoclonic epilepsy in infancy
subset: gard_rare {source="GARD:19086"}
subset: nord_rare {source="MONDO:NORD"}
synonym: "benign myoclonic epilepsy of infancy" EXACT [Orphanet:86909]
synonym: "benign myoclonus epilepsy of infancy" EXACT [Orphanet:86909]
xref: GARD:19086 {source="Orphanet:86909", source="MONDO:equivalentTo"}
xref: ICD10CM:G40.3 {source="Orphanet:86909", source="Orphanet:86909/attributed", source="Orphanet:86909/ntbt"}
xref: Orphanet:86909 {source="MONDO:equivalentTo"}
xref: UMLS:C0751120 {source="Orphanet:86909", source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:86909/e"}
xref: UMLS:C0917800 {source="Orphanet:86909", source="Orphanet:86909/e"}
is_a: MONDO:0100022 {source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/mei-overview.html"} ! neonatal/infantile epilepsy syndrome
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/7224" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5957" xsd:anyURI

[Term]
id: MONDO:0200000
Expand Down

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