MONDO and MESH IDs where labels and equivalent IDs aren't being retrieved (response is null)

TranslatorSRI / Babel

Babel creates cliques of equivalent identifiers across many biomedical vocabularies.

MIT License

9 stars 2 forks source link

MONDO and MESH IDs where labels and equivalent IDs aren't being retrieved (response is null) #71

Open colleenXu opened 2 years ago

colleenXu commented 2 years ago

MONDO:0008345 idiopathic pulmonary fibrosis
MONDO:0004955 metabolic syndrome
MONDO:0021668 disorder involving pain
MONDO:0005569 cartilage disease
MESH:D000375 Aging

colleenXu commented 2 years ago

Note that on the ITRB prod instance...only one is also null:

MONDO:0008345

The rest resolve to entities with human-readable names and equivalent IDs

cbizon commented 2 years ago

Another one: MONDO:0009410 Addison's disease

See https://github.com/NCATSTranslator/DataGaps/issues/8

gaurav commented 1 year ago

I think all of those MONDO terms have been deprecated, which is why they're no longer present in NodeNorm.

Term	Label	Replaced by	Label
MONDO:0008345	obsolete idiopathic pulmonary fibrosis	MONDO:0800029	interstitial lung disease 2
MONDO:0004955	obsolete metabolic syndrome	MONDO:0000816	abdominal obesity-metabolic syndrome
MONDO:0021668	obsolete disorder involving pain	MONDO:0700057	neurological pain disorder
MONDO:0005569	obsolete cartilage disease	MONDO:0003900	connective tissue disorder
MONDO:0009410	obsolete Addison disease	MONDO:0015129	chronic primary adrenal insufficiency

I'm still trying to figure out what's up with MESH:D000375 -- on ITRB-prod it is merged into UMLS:C0231337 ("senility"), but on RENCI-dev we have the identical clique, EXCEPT that it excludes MESH:D000375.

cbizon commented 1 year ago

That makes sense. Do we need to rethink how we handle obsolete terms?

I think it makes sense that MESH:D000375 doesn't merge with senility, but it does seem like it should be somewhere. I guess it's probably not getting picked up in whatever query we are doing to get phenotypes from mesh (if we are even doing that).

colleenXu commented 1 year ago

hmmm....BTE / Service Provider may be using data from APIs that still uses the obsolete MONDO terms.

gaurav commented 3 months ago

FWIW MONDO publishes a list of mappings from obsolete IDs to current IDs that we might want to incorporate into NodeNorm: https://github.com/monarch-initiative/mondo/blob/4753018179c28f6a0bb6c35ab67a7623f65a4a5f/reports/obsoletes.tsv#L1722

colleenXu commented 3 months ago

This is an old issue, and maybe some digging would be needed to see how much of a problem this still is.

I imagine that for Service Provider/BTE, it depends on whether we've updated the resources we use to their latest versions, and if those resources are using some-current/up-to-date versions of ID namespaces like MONDO.