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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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MVP2 - What genes' activity is up/downregulated - Changes to the input node #782

Closed sstemann closed 3 months ago

sstemann commented 4 months ago

https://ui.test.transltr.io/main/results?l=Metformin&i=PUBCHEM.COMPOUND:4091&t=3&r=0&q=ffb1d29d-2e2e-4aff-85ba-09c12cf7736c

if you expand ATP8A2 PROTEIN, HUMAN APP ROS1 NOS3

You will see that the chemical input node has changed for the Unsecret results

image
kaiwenho commented 3 months ago

The "M [Preparations]" concept, which has a UMLS semantic type of Classification (STY:T185), was causing the problem. 

"UMLS:C2267095" ("M [Preparations]") -"biolink:subclass_of"-> "UMLS:C0025598" ("metformin")
"UMLS:C0025424" ("Mercury") -"biolink:subclass_of"->  "UMLS:C2267095" ("M [Preparations]")

We have implemented a filter to avoid using nodes with this UMLS semantic type in the reasoning process. This should resolve all related issues. The update is in Unsecret CI and Test.

cbizon commented 3 months ago

I ran the query in TEST and can confirm that this is fixed.