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Updated UniProt mapping notebook to include Agora nominated targets #166

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Updated UniProt mapping notebook to include Agora nominated targets #166

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@jaclynbeck-sage jaclynbeck-sage commented Dec 17, 2024 •
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This PR addresses AG-1577 to update the Ensembl to Uniprot mapping file:

  • Adds a new column, "OPTIONAL_INFORMATION", which contains the string "Agora Nominated Target for Alzheimer’s Disease" if the gene/protein is a nominated target
  • Removes cell output from the notebook for future cleaner diffs
  • Changes the Synapse version of this file in the configs to v5 (latest update)
  • Updates the Pharos class file, which uses this uniprot file as input (no code changes required)
  • Changes the Synapse version of the Pharos class file in the configs to v2 (latest update)

Human-readable notebook:
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@jaclynbeck-sage jaclynbeck-sage marked this pull request as ready for review December 18, 2024 20:54
@jaclynbeck-sage jaclynbeck-sage requested a review from a team as a code owner December 18, 2024 20:54
BWMac
BWMac approved these changes Dec 18, 2024
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LGTM, just a NIT comment

data_analysis/agora/notebooks/preprocessing/preprocessing_utils.py Outdated Show resolved Hide resolved
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Quality Gate Passed Quality Gate passed

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0.0% Coverage on New Code
0.0% Duplication on New Code

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