2021-02-16 Best Practices Monthly Meeting notes

• Investigate direct connection with Redcap
• Todd/Phillip to review IO and clin/path can be in database or if they belong in a file
  • Both currently on hold pending ICDC task prioritization
  • For datasets linked to patients, how to provide those datasets
  • Preference for data in a computer readable format, not PDF if possible
  • Flow data probably already in a spreadsheet
  • Canine I/O, flow, immunohistochemistry
  • Identifier for each dog are the same as used for sequence files, ICDC can make the connections

• Best Practices document update
• Will and Heather have been finalizing
• Starting to make available for feedback

• Clinpath largely done
• Some data may be in PDF
• Immunology - Put all in spreadsheet
• Flow data - specify 
• I/O - standardized
• Immunohistochemistry - last to be standardized, need to be converted to spreadsheet
  • Currently in PDF
  • May not be used in analysis, could be hosted as a PDF.

Imaging Update

• No new images
• Add question about images to the standard data intake SOP
  • Probably initial submission request document
  • Looking for standard of care images

• Starting to look at genomic/mutation viewers (OncoGRID in particular)
• Bam file viewer?  JBrowse
• GDC allows users to select which calling method to use
• Do we need to finalize on some use cases and standards?

• 5 studies in various stages of readiness
  • NCATS - data update
  • COTC - data update
  • UBC01 - embargo
  • UBC02 - final updates
  • CCL - in progress
  • OSA- in progress
  • MCG- in progress