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feat: add UniProt identifiers #349

Merged
merged 3 commits into from
Aug 22, 2023
Merged

feat: add UniProt identifiers #349

merged 3 commits into from
Aug 22, 2023

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cheng-yu-zhang
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@cheng-yu-zhang cheng-yu-zhang commented Aug 4, 2023 •
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Main improvements in this PR:

All files and codes are in yeast-GEM/add_uniprot_id.

  1. get_uniprot_id.py is for getting uniprot ids from the uniprot website.
  2. SGD_with_Uniprot.csv is the output of get_uniprot_id.py with gene names and its uniprot ids.
  3. SGDgeneNames.tsv is originally in yeast-GEM/data/database.
  4. addUniprotID.m was used to add uniprot ids into yeast-GEM.

I hereby confirm that I have:

  • Selected develop as a target branch (top left drop-down menu)

feiranl
feiranl reviewed Aug 5, 2023
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@edkerk edkerk changed the base branch from main to develop August 19, 2023 14:09
edkerk
edkerk approved these changes Aug 19, 2023
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I rebased the PR to develop, refactored the code to use RAVEN's editMiriam and removed duplicate SGDgeneNames.tsv. Otherwise, LGTM.

feiranl
feiranl approved these changes Aug 22, 2023
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LGTM!

@edkerk edkerk changed the title add uniprot id feat: add UniProt identifiers Aug 22, 2023
@edkerk edkerk merged commit 4cc1498 into develop Aug 22, 2023
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@edkerk edkerk deleted the add-uniprot-id branch August 22, 2023 16:12
@edkerk edkerk linked an issue Oct 16, 2023 that may be closed by this pull request
feat: Uniprot annotations for all genes #320
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@edkerk edkerk mentioned this pull request Oct 16, 2023
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@feiranl feiranl feiranl approved these changes

@edkerk edkerk edkerk approved these changes

@hongzhonglu hongzhonglu Awaiting requested review from hongzhonglu

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feat: Uniprot annotations for all genes
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