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BladderPDO and Schema Fixes #365

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Merged
merged 6 commits into from
May 21, 2025
Merged

BladderPDO and Schema Fixes #365

merged 6 commits into from
May 21, 2025

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jjacobson95
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@jjacobson95 jjacobson95 commented Apr 24, 2025

This PR will fix all known issues in BladderPDO, the Schema, and current build.

BladderPDO

  • model type mapping updated in samples file
  • additional samples added from GEO
  • transcriptomics now maps correctly to all samples
  • fixed transcriptomics column name (values to transcriptomics)
  • deleted extra files generated and ensured that files were correctly named
    • deleted bladderpdo_dosresponse.tsv
    • changed bladderpdo_copynumber.csv to bladderpdo_copy_number.csv
    • changed bladderpdo_experiments.tsv.0 to bladderpdo_experiments.tsv

Schema
Additionally, I added bladderpdo and sarcpdo to the Validation schema checker. Previously these had been left out of the schema/expected_files.yaml. This is what allowed the data discrepancies to sneak by in the first place.
And I added 'xenograft derived organoid' to the model types as this is used and described in the bladderpdo paper.

Overall Build
The cross build mapping files have been updated as well. These should not change until the next version.

  • build/improve_drug_mapping.json
  • build/improve_sample_mapping.json
  • All bladderpdo and sarcpdo (because it it downstream of bladderpdo in build) files have been re-uploaded to figshare.

@jjacobson95 jjacobson95 marked this pull request as ready for review April 24, 2025 14:22
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jjacobson95 commented Apr 24, 2025

This will address #358 and #360.

@jjacobson95 jjacobson95 requested a review from RubyFore April 24, 2025 18:54
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Conflicts resolved. Ready to be reviewed/merged.

@sgosline sgosline merged commit e237db5 into main May 21, 2025
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