2020-12-09 PDC-Scientific Committee Meeting notes

• Pau R presented data harmonization - CDAP, APIs, Gene summary page related topics

Here are some comments from the discussion:

• Sam P: As a follow up to the topic on David Fenyo's work Seven Bridges genomics platform using PDC data, Sam Payne asked if we (users) can build a pipeline for RNA splice data and Antigen data? The SBG platform allows bringing in new tools. 
• Henry R pointed that it is important to capture end user experience and requested Mandy P and Oliver B to chime in to provide a cancer biologist view that is different from proteomic informatics specialists. He also suggested to take an end user perspective - ask a simple query by Cancer Biologists and retrieve results.
• Mandy P suggested tumor type comparison rather than normal to tumor for BRCA studies is more meaningful. She also said, we may be complicating this and should just build a simple gene query interface and add filters.
• Oliver B suggested to think of
  • How can we enhance Training such as more on the Science side of data (Control vs Disease).
  • What are the scientific questions being studied and user type accessing the system?
  • Gene and Protein lookup is overwhelming for researchers. Should we hand hold them?
• Mike MacCoss (MM): We should conduct webinars targeted to different audience such as computational savvy and Protein view and understand what users want more from the data.
• MM: We have the metadata that has gone through QC, curated and in the system now. We are at a point to do more on the system now.
• Henry R: How do we begin bringing the right people onboard to help?
• Bing Zhang: This is a 2 step process: 1)Get data and make it accessible 2) Serving Biologists – If we can get good access to data and then leverage existing tools while enabling others to build their own tools.
• MM: We started off first with Managing Data followed by Processing and Display. Now we are taking the results and working with groups having the expertise and can leverage other pipelines to run the data.

Action Items:

Follow up calls with Amanda and Oliver to gather details and determine ways to incorporate in PDC.