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Add QC check and report for ClinGen labels #7244

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@matentzn matentzn commented Feb 6, 2024

@sabrinatoro found out during curation that there are some Mondo terms with multiple ClinGen labels. We already know from #7027 that there were times when ClinGen labels made it into the curation pipeline which where not exact.

This PR

  1. Adds a QC check to ensure that there are Mondo terms with multiple ClinGen labels and non non-exact ClinGen labels.
  2. Adds a report to generate all current ClinGen labels as a nice table

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sabrinatoro commented Feb 8, 2024

@matentzn This looks good to me, but it appears that the QC fails because the new QC test works. I guess we need to wait for ClinGen to review the list we shared with them when we met (Wed, Feb 7th).
Is this a correct assessment of the state of this PR?

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matentzn commented Feb 8, 2024

Yes, they need to provide fixes for the 26 conflicts..

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@sabrinatoro can you follow up with ClinGen when they plan to supply the fixes?

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@twhetzel I assigned this PR to you as you voiced interest in manually fixing the 25 clingen conflicts.

@matentzn matentzn marked this pull request as draft May 24, 2024 16:24
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Without tickets/PRs on the latest Mondo release board, it's longer before I see these. Is there still something to be done here or is any work in this PR now included in #6903?

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The thing that needs to be done on this PR is to fix the QC, i.e. fixing the ClinGen preferred labels. I thought you mentioned you were going to do this because there are few? See #7630

make some changes to kickoff the qc checks again since logs expired
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twhetzel commented Jun 1, 2024

Adding my Slack comment here:
Are we in agreement these Mondo terms that have >1 synonym annotated with CLINGEN_LABEL can be fixed by reviewing the ClinGen web site to see what "Name" they list on their site and then make sure that this is the synonym in Mondo with the CLINGEN_LABEL?

For example, the error line for:
http://purl.obolibrary.org/obo/MONDO_0014564,congenital bile acid synthesis defect 5,ABCD3 congenital bile acid synthesis defect
would have "congenital bile acid synthesis defect 5" as the CLINGEN_LABEL based on the ClinGen web site page for: https://search.clinicalgenome.org/kb/conditions/MONDO:0014564

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4 participants