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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Reads Diabetes <Treats or Applied or Study to Treat> Compound Name #786

Closed sstemann closed 5 months ago

sstemann commented 5 months ago

https://ui.test.transltr.io/main/results?l=Diabetes%20Mellitus&i=MONDO:0005015&t=0&r=99ac263a&q=8ccea6d0-5bd1-4969-b41c-45581214283e

MVP1 in Test > Glyburide the paths look like the diease is treating a compound - I can't view the ARAGORN results in the ARAX GUI.

image

edeutsch commented 5 months ago

I can't view the ARAGORN results in the ARAX GUI

why not? Seems to work okay for me? https://arax.ci.transltr.io/?r=a22c86b0-c93c-4001-920f-d71aa7415a47

image

cbizon commented 5 months ago

Yeah, this one loaded for me in ARAX as well. The results are a bit confusing, I think because of the way subclasses are being handled. So I won't say for sure yet that the ARAGORN result is properly formatted. But I don't see any results with the treatsor... edges pointed the wrong way:

image

cbizon commented 5 months ago

I think that this is probably an application of the rule: (A)-[treats_or]->(B) AND (A)-[similar_to]->(C)-[treats_or]->(B) SUGGESTS (A)-[treats]->(B)

But it looks funny because while B=Diabetes mellitus, we are getting some subclasses of that back for the two [treats_or] links.

sstemann commented 5 months ago

I can't view the ARAGORN results in the ARAX GUI

why not? Seems to work okay for me? https://arax.ci.transltr.io/?r=a22c86b0-c93c-4001-920f-d71aa7415a47

image

my apologies - it was these PK, which were run in UI - CI 294a214d-674c-410d-86cb-1932b7447d03
9a0f94e2-f0eb-4560-8150-d77bed72bf0b

edeutsch commented 5 months ago

For the first one 294a214d-674c-410d-86cb-1932b7447d03, the validator reports invalid TRAPI: https://arax.ci.transltr.io/?r=294a214d-674c-410d-86cb-1932b7447d03

image

It looks like there are KG Edge.object entries with no corresponding KG Node entry. Invalid TRAPI is known to cause rendering problems in the ARAX GUI.

Would be good to fix the TRAPI and then it should render.

cbizon commented 5 months ago

I don't think that there is an edge pointing the direction that the UI is showing in the results. @Genomewide do you think this is a UI issue?

Genomewide commented 5 months ago

Looking at the raw data, I think it could be. I don't see any edges that have the disease treating the drug. @dnsmith124 @gprice1129 thoughts?

sstemann commented 5 months ago

resolved in TEST