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Fix broken PMID links in CX2 output #45

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merged 3 commits into from
Jan 23, 2025
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Fixes #44

The proximate cause of the issue (PMIDs not being expanded into URLs correctly) was that the local project I use to do the CX2 conversion and upload to NDEx was using prefixmaps version 0.2.5. That version does not have a PMID expansion in the GO context. The change here is to bump the minimum required version of prefixmaps up to 0.2.6, which has the necessary PMID expansion. With this change, resyncing my local upload project's environment got prefixmaps version 0.2.6 and the PubMed links come out correctly in the CX2.

Ancillary changes:

  • Feedback from NDEx was also to not link ECO terms. With these changes only the term label is shown, unlinked.
  • Since we expanded the set of GO-CAMs uploaded to NDEx to include human + pathogen models, these changes add a flag to not issue warnings about genes symbols that don't match IQuery's regex (which is designed for human gene symbols).

@pkalita-lbl pkalita-lbl changed the title Do not link to ECO terms Fix broken PMID links in CX2 output Jan 23, 2025
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@pkalita-lbl pkalita-lbl merged commit 2c1c03f into main Jan 23, 2025
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@pkalita-lbl pkalita-lbl deleted the issue-44-evidence-links branch January 23, 2025 20:54
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PubMed links not rendering correctly in CX2
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