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Node Normalization of conflation for T1D #410

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jaredroach opened this issue Sep 4, 2024 · 0 comments
Open

Node Normalization of conflation for T1D #410

jaredroach opened this issue Sep 4, 2024 · 0 comments

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@jaredroach
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jaredroach commented Sep 4, 2024

When I search for T1D in the autocomplete, in an effort to find "the one node" for type 1 diabetes, it is not clear what phrase to best (or start typing) type into the autocomplete and then which of the options to choose to find the unifying node. Some choices seem to lead to the same (best, probably) choice: MONDO:0005147. But others lead elsewhere. Also, it is not clear that typing "T1D" into autocomplete gets anywhere (e.g., MT1DP is one of the prominently offered choices). And the most obvious or common choice for most users would be "type 1 diabetes" which seems to lead to the wrong node.

diabetes insipidus
MONDO:0004782

type 1 diabetes mellitus
MONDO:0005147

type 1 diabetes	
OMIM:MTHU023582

diabetes, type 1
OMIM:MTHU067663

Which raises the question of what the deuce is "OMIM:MTHU067663"? Goggling is hard, but perhaps not impossible. The ARAX UI leads to a 404 error if one clicks on the provenance link purl.obolibrary.org from https://arax.ci.transltr.io/?r=279518:

	
--
attribute_type_id: | biolink:IriType
value_type_id: | metatype:Uri
value_url: | http://purl.obolibrary.org/obo/OMIM_MTHU067663
value: | http://purl.obolibrary.org/obo/OMIM_MTHU067663
 
attribute_type_id: | biolink:description
value_type_id: | metatype:String
value: | UMLS Semantic Type: STY:T047
 
attribute_type_id: | biolink:category
description: | Categories of all nodes in this synonym set in RTX-KG2.
value_type_id: | metatype:Uriorcurie
value: | biolink:Disease
 
attribute_type_id: | biolink:synonym
description: | Names of all nodes in this synonym set in RTX-KG2.
value_type_id: | metatype:String
value: | Diabetes, type 1
 
attribute_type_id: | biolink:xref
description: | Identifiers of all nodes in this synonym set in RTX-KG2.
value_type_id: | metatype:Nodeidentifier
value: | OMIM:MTHU067663

Google eventually gets here, which seems to be the only reference on the web:
https://bioportal.bioontology.org/ontologies/OMIM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FOMIM%2F243150

This Bioportal page seems to suggest that T1D (aka, "Diabetes, Type 1") is actually "GASTROINTESTINAL DEFECTS AND IMMUNODEFICIENCY SYNDROME 1" which is a source of confusion. Seems to come from conflating the "has manifestation" field from Bioportal with the actual name/concept. And this "has manifestation" field seems to be exceptionally liberal - including anything that has even the slightest increased incidence in folks with any mutations in any gene spanning locus 2p21.

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