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Missing susceptibility classifications #8618

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matentzn opened this issue Jan 21, 2025 · 0 comments
Open

Missing susceptibility classifications #8618

matentzn opened this issue Jan 21, 2025 · 0 comments

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@matentzn
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To look for terms that look like susceptibility that are not classified as such I used the following query on Ubergraph (for Mondo, remember to add the + signs to both rdfs:subclassOf predicates).

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX pattern: <http://purl.obolibrary.org/obo/mondo/patterns/>
PREFIX MONDO: <http://purl.obolibrary.org/obo/MONDO_>
SELECT DISTINCT ?entity ?label WHERE {
  ?entity rdfs:label ?label .
  ?entity rdfs:subClassOf MONDO:0000001 .
  FILTER NOT EXISTS {
	  ?entity rdfs:subClassOf MONDO:0042489 .
  }
  FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
  FILTER(regex(str(?label), "susceptib") || regex(str(?label), "predisposit") )
}
ORDER BY ?entity

I get the following 11 results:

entity label
http://purl.obolibrary.org/obo/MONDO_0012075 oligodontia-cancer predisposition syndrome
http://purl.obolibrary.org/obo/MONDO_0012530 palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome
http://purl.obolibrary.org/obo/MONDO_0013599 autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome
http://purl.obolibrary.org/obo/MONDO_0013607 monocytopenia with susceptibility to infections
http://purl.obolibrary.org/obo/MONDO_0030970 immunodeficiency 106, susceptibility to viral infections
http://purl.obolibrary.org/obo/MONDO_0031030 immunodeficiency 107, susceptibility to invasive staphylococcus aureus infection
http://purl.obolibrary.org/obo/MONDO_0032848 immunodeficiency 65, susceptibility to viral infections
http://purl.obolibrary.org/obo/MONDO_0042982 GATA2 deficiency with susceptibility to MDS/AML
http://purl.obolibrary.org/obo/MONDO_0100216 DICER1-related tumor predisposition
http://purl.obolibrary.org/obo/MONDO_0975761 immunodeficiency 126, susceptibility to
http://purl.obolibrary.org/obo/MONDO_1040020 methicillin-susceptible staphylococcus aureus infectious disease

Can we determine if these should be classified as susceptibilities? This is in the context of some work in Matrix where I want to use the susceptibility classification for removing tagging some classes to be excluded from the disease list:

everycure-org/matrix-disease-list#36

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