2020-04-29 PDC Weekly Meeting notes

Date

29 Apr 2020

Attendees

• Beyers, Matthew (NIH/NCI) [C]

Agenda

• Ongoing work  
• Simplified study identifiers and external references - now in stage 
  • Identifiers.org
• Support (continuing)
  • Clustergram tutorial video
• Portal and workspace related improvements
  • Workspace usability improvement 
    • Ability to add labels/annotations to files during upload time, that can later be used in the study creation
• Next data sets / releases in pipeline
  
  • HNSCC from CPTAC3  (May)
    • GDC and TCIA linking
    • Study description and embargo date?
  • Lung Cancer dataset of Academia Sinica - from ICPC, MacCoss - (Late May to early June)  
    • Initial review of the metadata done
    • Study IDs reserved and sent
• LSCC from CPTAC3 (July)
• PDA from CPTAC3
• LUAD confirmatory from CPTAC3   
  
• APOLLO
• Georgetown lung dataset
• Organoid dataset from PNNL
• Other items
  • PDC Advisory committee
  • ASMS and AACR virtual conferences
• External interactions
  • SevenBridges + Univ of Michigan - Philosopher integration with SBG
  • ISB-CGC - providing protein quant data through APIs
  • PRIDE SDRF format -  Sample and Data Relationship Format (SDRF) -  https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects
    • Annotate a CPTAC dataset for PRIDE 
    • Evaluate the new PRIDE format - 
• CCDH
• Sam Payne
• User feedback

“ It is very comprehensive sources ”  - by a researcher from Duke Cancer Institute

• NCI Updates

Action items

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