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Samples.md

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A sample in ID3C is "A sample collected from an individual during a specific encounter." See the warehouse schema diagram to visualize how samples are related to encounters and other concepts in ID3C.

REDCap projects

We wait to create Samples in ID3C until the following conditions are met for each project:

SCAN

SCAN ETL

  • Mail

    • post_collection_data_entry_qc is complete and verified
    • return_utm_barcode is not blank

  • In-person (kiosk)

    • nasal_swab_collection is complete and verified
    • utm_tube_barcode_2 is not blank or reenter_barcode == reenter_barcode_2

  • Husky Testing (kiosk)

    • nasal_swab_collection is complete and verified
    • utm_tube_barcode_2 is not blank or reenter_barcode == reenter_barcode_2

SFS

  • Childcare

    • post_collection_data_entry_qc is complete and verified
    • One of the following barcode fields is not blank:
      • return_utm_barcode
      • utm_tube_barcode
      • pre_scan_barcode

  • UW Reopening

    • the sample is a swab-n-send sample and post_collection_data_entry_qc is complete and verified or the sample is a kiosk sample and kiosk_registration_4c7f is complete and verified
    • collect_barcode_kiosk is not blank or return_utm_barcode is not blank or pre_scan_barcode is not blank

  • Kiosk

    • sfs_barcode is not blank or sfs_barcode_manual is not blank

  • Swab & Send

    • return_utm_barcode is not blank, or pre_scan_barcode is not blank, or utm_tube_barcode_2 is not blank, or (barcode_confirm == "No" and corrected_barcode is not blank)

  • Asymptomatic Swab & Send

    • return_utm_barcode is not blank, or pre_scan_barcode is not blank, or (utm_tube_barcode is not blank, or (check_barcodes == "No" and corrected_barcode is not blank)

  • Swab & Send + Home Flu

    • return_utm_barcode is not blank, or pre_scan_barcode is not blank, or utm_tube_barcode_2 is not blank, or utm_tube_barcode_2_st is not blank, or ((barcode_confirm or barcode_confirm_st == "No") and (corrected_barcode is not blank or corrected_barcode_st is not blank))

FHIR

We represent an ID3C Sample in HL7 FHIR vocabulary as a Specimen Resource.

Identifying Sample Origin or Project

Collection Barcode

  • Year1 - all collection barcodes were in the same identifier set
  • Year2 and on - Collection barcodes are assigned to specific collection identifier set that matches to projects/sub-projects
  • UW retrospectives do not have collection barcodes
  • Should be the ultimate source of truth of a sample's origin/project

Lab AQ Sheet

  • sample_origin - matches to big projects
  • swab_site - matches to specific sites within projects
  • currently a dropdown box in Excel sheet
  • ingested as free text into ID3C without any verification
  • used as backup for identifying sample's origin

Site from Encounter metadata

  • sites linked to encounter when ingesting participant metadata
  • specific site of collection, there may be multiple sites per project
  • site is missing for samples that do not have encounter data ingested