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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Node Norm Label for Thiamine #695

Closed sstemann closed 4 months ago

sstemann commented 9 months ago

In UI Test, I ran MVP1 for Myopathy, Lactic Acidosis, And Sideroblastic Anemia

Filtered on Chebi Role > Metabolite - and noticed this substance:3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium

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Click on the Node of the substance and you end up here: https://pubchem.ncbi.nlm.nih.gov/compound/1130

I plugged PUBCHEM.COMPOUND:1130 into Node Norm - maybe I have an out of date node norm bookmarked - and it got the crazy label for Pubchem which I dont think is what Pubchem is using, the other identifier labels use some form of Thiamine

I dont know where this decision is made - so tagging UI Front End, ARS and Node Norm.

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Adding a second example: MVP2, what may upregulate Mapk8ip3

Result S-adenosylmethionine - links to PubChem Ademetionine.
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Node Norm PubChem label is S-adenosylmethionine, other identifiers in node norm are using ADEMETIONINE

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dnsmith124 commented 9 months ago

3-(4-Amino-2-methyl... is the label returned to the UI FE for that result, @gprice1129 do we call node norm now that we aren't doing merging, or is that the label we receive from the ARS?

gprice1129 commented 9 months ago

The ARS does node normalization before its merging step so it should not matter which version of merging is being used.

andrewsu commented 9 months ago

I think the root of this one is a difference between PROD and TEST node norm:

dnsmith124 commented 9 months ago

Great find @andrewsu, @gaurav see the above comment.

gaurav commented 4 months ago

NodeNorm now returns "thiamine" as the label for CHEBI:18385 (previously PUBCHEM.COMPOUND:1130) and "ademetionine" as the label for CHEBI:15414 (previously PUBCHEM.COMPOUND:34755). This is true on:

I think that closes this ticket.