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Source for Edge with Primary KS not Displayed #178

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sstemann opened this issue May 12, 2023 · 3 comments
Closed

Source for Edge with Primary KS not Displayed #178

sstemann opened this issue May 12, 2023 · 3 comments
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@sstemann
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sstemann commented May 12, 2023

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

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

@sierra-moxon sierra-moxon added this to the June 30 milestone May 25, 2023
@sierra-moxon
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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.
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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.

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