2020-05-06 PCD Weekly Meeting notes

Date

06 May 2020

Attendees

• Beyers, Matthew (NIH/NCI) [C]

• Henry Rodriguez, Chris Kinsinger, Erika Kim, John Otridge, Anand Basu, Rajesh, Deepak Signhai, Karen Ketchum, Mike MacCoss, Paul Rudnick, Michael Holck, Gilberto

Agenda

• Ongoing work  
• Data release 
• HNSCC from CPTAC3
• GDC and TCIA linking - received
• Study description and embargo date? - received
• Lung Cancer dataset of Academia Sinica - from ICPC, MacCoss 
• Initial review of the metadata done
• Study IDs reserved and sent
• Release of Simplified study identifiers and external references - now in stage
• Identifiers.org
• Support
• 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)
• Lung Cancer dataset of Academia Sinica - from ICPC, MacCoss - (Late May to early June)
• 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
• NCI Updates

Discussion items

Action items

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