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New term TRIP11 related skeletal dysplasia #7873

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New term TRIP11 related skeletal dysplasia #7873

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10 changes: 10 additions & 0 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -71,6 +71,14 @@ property_value: IAO:0000700 MONDO:0021125
property_value: IAO:0000700 MONDO:0021178
property_value: IAO:0000700 MONDO:0042489

[Term]
id: MONDO:0000000
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name: TRIP11 related skeletal dysplasia
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for all of the gene related diseases, we usually write them as TRIP11-related skeletal dysplasia (with a dash), could you please revise this as such and add this label as an exact synonym? Thanks!

def: "TRIP11 related skeletal dysplasia describes both achondrogenesis type 1a and ondontochondrodysplasia. Reduced protein function in TRIP11 causes a spectrum of skeletal symptoms from a more mild phenotype, called ondontochondrodysplasia, with features including short stature and joint laxity to a more severe phenotype, called achondrogenesis type 1a, which presents as a lethal prenatal or neonatal skeletal dysplasia. The clinical severity of achondrogenesis compared to ondontochondrodysplasia is related to the residual function of the gene which is not currently possible to anticipate based on genotype alone. The phenotype cannot fully be predicted by genotype alone, evidenced by variants being reported with both phenotypes." [PMID:20089971, PMID:30728324, PMID:31903676]
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type 1A should be capitalized

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For the definition, the definitions should start with the parent class and not mention the disease label, because they can change. This disease should also follow this pattern: https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/disease_series_by_gene.yaml

I suggest revising the definition to:

Any skeletal dysplasia in which the cause of the disease is a variation in the TRIP11 gene. Reduced protein function in TRIP11 causes a spectrum of skeletal symptoms from a more mild phenotype, called ondontochondrodysplasia, with features including short stature and joint laxity to a more severe phenotype, called achondrogenesis type 1A, which presents as a lethal prenatal or neonatal skeletal dysplasia. The clinical severity of achondrogenesis compared to ondontochondrodysplasia is related to the residual function of the gene which is not currently possible to anticipate based on genotype alone. The phenotype cannot fully be predicted by genotype alone, evidenced by variants being reported with both phenotypes." [PMID:20089971, PMID:30728324, PMID:31903676]

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Note, I don't think it is necessary to mention "TRIP11 related skeletal dysplasia describes both achondrogenesis type 1a and ondontochondrodysplasia." because these are subclasses and that is implied.

is_a: MONDO:0018230 ! skeletal dysplasia
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there should be a source on the parent class

property_value: http://purl.org/dc/elements/1.1/date "2024-06-27T14:50:03Z" xsd:dateTime
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-0587-4693

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please add the term tracker item (link to the GitHub URL for this term):
https://mondo.readthedocs.io/en/latest/editors-guide/f-entities/#term-tracker-item

[Term]
id: MONDO:0000001
name: disease
Expand Down Expand Up @@ -180604,6 +180612,7 @@ xref: Orphanet:932 {source="OMIM:200600"}
xref: Orphanet:93299 {source="MONDO:equivalentTo", source="OMIM:200600"}
xref: SCTID:42725006 {source="MONDO:equivalentTo"}
xref: UMLS:C0265273 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:78546"}
is_a: MONDO:0000000 {source="PMID:20089971", source="PMID:31903676"} ! TRIP11 related skeletal dysplasia
is_a: MONDO:0019648 {source="DC-OMIM:200600", source="DOID:0080054", source="OMIM:200600", source="Orphanet:93299"} ! achondrogenesis
is_a: MONDO:0800080 {source="PMID:31633310"} ! severe spondylodysplastic dysplasia
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/12305 {source="MONDO:mim2gene_medgen"} ! TRIP11
Expand Down Expand Up @@ -500878,6 +500887,7 @@ subset: rare
xref: MEDGEN:411198 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: OMIMPS:184260 {source="MONDO:equivalentTo"}
xref: UMLS:C2745953 {source="MEDGEN:411198", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0000000 {source="PMID:30728324", source="PMID:31903676"} ! TRIP11 related skeletal dysplasia
is_a: MONDO:0016763 {source="Orphanet:166272"} ! spondylometaphyseal dysplasia
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:184260"} ! inherited

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