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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Source for Edge with Primary KS not Displayed #178

Closed sstemann closed 1 year ago

sstemann commented 1 year ago

I think this issue is because of a mismatch between the primary KS value tag "hetio" and the infores catalog, which is automat-hetio or hetionet image image image image

Steps:

  1. Use the Test UI > What gene is upregulated by "lisdexamfetamine"

  2. View the first result slc6a3

  3. on the first/shortest result, click the edge "Affected by +5"

  4. note that the "showing evidence for" lists Slc6a3 Directly Physically Interacts With Lisdexamfetamine image

  5. Note: the publications tab does not have relationship Directly Physically Interacts With, neither does the Sources tab image

  6. In ARAX UI, it looks like this edge is coming from BTE> primary KS > Hetio: https://arax.ncats.io/?r=761ba21f-3935-479a-85c4-c8384264adc6 image

  7. It's also coming back from Robokop:

image

sierra-moxon commented 1 year ago

from TAQA: mismatch between infores:hetio and infores:automat-hetio. hetio is a source should be the primary, automat should be the aggregator should be fixed in test; but we will check. infores:hetio-net and infores:automat-hetio-net Sierra: infores catalog is broken AGAIN.

sierra-moxon commented 1 year ago

update: infores catalog has been migrated to YAML (old TSV is still in the repository to help folks transition without breaking BMT installations). https://github.com/biolink/biolink-model/pull/1318 addresses the hetio-net consistency issue brought up last time.

sierra-moxon commented 1 year ago

retested - 06/22/23 on ci. https://ui.ci.transltr.io/results?l=Lisdexamfetamine&t=3&q=37271f9d-7cb9-48b9-aed3-d12f2915197b https://arax.ncats.io/?r=37271f9d-7cb9-48b9-aed3-d12f2915197b

No longer seeing "affects 5+" in the slc6a3 result. Image

I see the "directly physically interacts with" predicate in the evidence display for the first, direct edge.

I think this is working now :) closing as complete.