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TranslatorSRI / Babel

Babel creates cliques of equivalent identifiers across many biomedical vocabularies.
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zinc cliques #224

Open cbizon opened 5 months ago

cbizon commented 5 months ago

In the context of the question "what treats common cold", we are getting back several related concepts around zinc. There's Zinc, Zinc Lozenge, Zinc Gluconate, and Zinc Gluconate Lozenge.

Zinc Gluconate actually merges with its Lozenge in dev.

But Zinc Lozenge (UMLS:C1248424) doesn't seem to link to anything in UMLS or RXNORM. So I'm not sure how we are going to handle this. Do we need to just hand map it?

Also, zinc merges with zinc methionine, why doesn't it merge with zinc gluconate?

cbizon commented 5 months ago

Part of the reason may be that in RxNorm, zinc methionine is a precise ingredient (PIN) with an ingredient of Zinc. But zinc gluconate is an ingredient itself. There is a PIN but that is a more specific thing "zinc gluconate trihydrate". So RxNorm doesn't have any kind of link from Zinc Gluconate to Zinc...

cbizon commented 5 months ago

This may be pointing at the difficulty on relying on rxnorm for this kind of conflation. It would also be very tricky to be based on deconstructing the salt smiles though because using a size way of figuring out what is the important part of the compound would end up merging zinc gluconate with gluconate, not zinc.