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Display dbGap study in sample view and add dbGap tab #1198

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ao508 opened this issue Jun 20, 2024 · 0 comments
Open

Display dbGap study in sample view and add dbGap tab #1198

ao508 opened this issue Jun 20, 2024 · 0 comments

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@ao508
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ao508 commented Jun 20, 2024

Tasks:

  • Add dbGap to displayed data on sample table
  • Add a tab for viewing dbGap data
  • When in dbGap view, allow PMs to export data for submitting to dbGap

The data collected/exported for dbGap should include:

  • SUBJECT_ID (CMO patient ID)
  • SAMPLE_ID (Sample CMO label)
  • SEX (from sample metadata
  • RACE (do not have yet)
  • CANCER_TYPE (from sample metadata)
  • BODY_SITE (from sample metadata)
  • ANALYTE_TYPE (may be resolved from existing sample metadata)
  • IS_TUMOR (from sample metadata)
  • SAMPLE_TYPE (from sample metadata)
  • HISTOLOGICAL_TYPE (from sample metadata)
  • HISTOLOGICAL_SUBTYPE (do not have yet)
  • SEQUENCING_PANEL (from sample metadata)
  • PLATFORM (do not have yet but might be able to get mapping from Voyager team)
  • INSTRUMENT_MODEL (do not have yet but might be able to get mapping from Voyager team)
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