small molecules are returned while genes are asked

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small molecules are returned while genes are asked #754

Closed TranslatorIssueCreator closed 2 months ago

TranslatorIssueCreator commented 6 months ago

Type: Bug Report

URL: https://ui.test.transltr.io/main/results?l=Acetylcholine&i=PUBCHEM.COMPOUND:187&t=3&r=0&q=27730ac2-b19e-4edd-b146-7a79551965b0

ARS PK: 27730ac2-b19e-4edd-b146-7a79551965b0

Steps to reproduce:

What gene may be upregulated by acetylcholine? select small molecule filter

Screenshots:

sandrine-muller commented 6 months ago

These are two results returned by ARAX as lookups from semmed:

sierra-moxon commented 6 months ago

@edeutsch @saramsey @andrewsu - should we do another SEMMEDDB curation effort for MVP2,3?

edeutsch commented 6 months ago

Do we think this is really a problem? Angiotensin II is complicated. okay, it's not a gene. And maybe not a protein depending on how you define protein. But it is a small polypeptide hormone that comes from a gene after substantial processing. And I think we all agreed to officially conflate genes and proteins. So I'm thinking that if Angiotensin II is regulated by acetylcholine, then it is well worth showing, and it is a very minor offence to call Angiotensin II a small molecule, when it is really a polypeptide or maybe a microprotein or maybe a hormone or something that is ultimately a gene product.

andrewsu commented 2 months ago

I agree with @edeutsch's comment -- on the scale of issues we're juggling, I think this can be a "won't fix"...

Given we have a proposal and a "second", I'm going to close the issue. But feel free to reopen if someone feels passionately about this...