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A repo for tracking gaps in Translator data and finding ways to fill them.
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biolink:regulates for chemical-to-gene relationships #761

Closed TranslatorIssueCreator closed 2 months ago

TranslatorIssueCreator commented 5 months ago

Type: Bug Report

URL: https://ui.test.transltr.io/main/results?l=Lepirudin&i=PUBCHEM.COMPOUND:118856773&t=4&r=0&q=9c30d7a5-be5f-4f44-a12e-376369954f57

ARS PK: 9c30d7a5-be5f-4f44-a12e-376369954f57

Steps to reproduce:

search for SERPINF2

Screenshots:

sandrine-muller commented 5 months ago

What genes may be downregulated by:Lepirudin

image

Result returned by Unsecret

My understanding of biolink was that chemical-to-gene relationships cannot be used with the predicate biolink:regulates: Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Would this relationship be a qualified biolink:affected_by?

Nonetheless, I went on to look at the mechanism of action of the compound on Drugbank (as stated as the reference KS) to see whether the compound could inhibit the SERPINF2 regulation. Unfortunately, I could not find anything on either the compound card or the protein card. The only relationship I could find is that, on the compound card, we see that one of Lepirudin drug category is "serpins" but that seems too much of a stretch for the statement to be true.

sierra-moxon commented 4 months ago

@kaiwenho - is this something you could investigate as part of the Unsecret team? :) -- we aren't sure quite where the problem lies.

kaiwenho commented 2 months ago

This has been fixed in CI, TEST, and PROD by utilizing the updated KGs.