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Pico hgnc updates #194

Merged
merged 4 commits into from
Jun 11, 2023
Merged

Pico hgnc updates #194

merged 4 commits into from
Jun 11, 2023

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AlexanderPico
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Updated a handful of outdated "previous symbols" using the HGNC website as reference.

@AlexanderPico
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AlexanderPico commented May 30, 2023

Hmm. I intended to PR two branches, but it looks like my TLE and ICAM family additions made it into this same branch somehow.

Will this work for you?

@bgyori
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bgyori commented May 30, 2023

Yes, I can sort it out from here, thanks for the contribution!

@bgyori
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bgyori commented Jun 10, 2023

@AlexanderPico thanks again for the contribution. Unfortunately I'm not able to push to this PR to complete the changes that are needed - usually there is a checkbox that is checked by default when you open a PR, allowing maintainers to push to the PR branch. If you look at this page now, do you still see that perhaps? If not, I will open a new PR with the changes.

@AlexanderPico
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Sorry for the hassle. Looks like this is a commonly requested feature for organization-owned forks like this case, https://github.com/orgs/community/discussions/5634.

I will add you as a collaborator to our org as a possible workaround.

Also feel free to make a PR to our fork, which I will then merge, which I think is how @cthoyt got around this same issues.

@bgyori bgyori merged commit 22d2a4c into sorgerlab:master Jun 11, 2023
@bgyori
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bgyori commented Jun 11, 2023

Thanks @AlexanderPico, after you gave access to the repo, things worked. To recap the changes:

  • Updating HGNC resource version required a corresponding change in INDRA to make the validation script not error.
  • New FamPlex terms are also listed in the entities.csv file
  • I added a couple of synonyms in the grounding_map.csv. This is not strictly necessary but useful. I found TLE to be ambiguous and most often used to represent something other than the protein family so I didn't include "TLE" as a synonym.
  • I update all the exports

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2 participants