Manager Call 2020-09-16

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  • Present: Judy, Laurent-Philippe, David, Huaiyu, Kimberly, Seth, Suzi, Pascale, Chris, Pascale
  • Regrets:


Projects updates

Anyone has blocking issues/delays/changes in project scope they need to report to managers /PIs?

Nothing new to report at the moment.

GAF 2.2 (#4h) and GPAD/GPI 2.0 (#4i)(Kimberly)

  • When do we want to make an announcement to the user community?
    • This seems dependent upon a firm date for switchover - do we have that?
    • We should also supply a test file for developers and include its location in the announcement.
    • MGI and WB are nearly ready with their files; based on 2020-09-15 annotation call, other groups are coming along
    • Propose a meeting between David, Kimberly, Helen, Penelope, and Alex to discuss UniProt files wrt timing of new file release and relations used
    • Expect that we will need to continue to provide support (questions, clarifications) to groups as we get closer to the switchover


  • specifications are out, waiting for feedback. WormBase and MGI nearly ready.
  • out by end of year or early next year
  • possibly start an announcement and supply a test file (available in the GH ticket)
  • GAF 2.2 will be required, GPAD/GPI2.0 seems more flexible
  • can we make this transition even simpler ?
  • we can try to provide a 2.0 to 2.2 converter

Action items:

  • Kimberly will do the announcement and provide a link to the test file
  • Mention also we'll provide a 2.0 -> 2.2 converter
  • Goal: end of year

Ongoing projects updates

  • Noctua Imports (#3a)
    • MGI/Wormbase imports
      • Dustin has a new import on his USC server where David and Kimberly can check models for a select number (15-20) of genes, but code is still using GPAD 1.2 for import. Upshot: this will allow us to check the current state of the import rules for any errors, but does not reflect what the final import will include, e.g. annotation metadata
    • GPAD/GPI 2.0
    • Minerva and GPAD output
      • We need to schedule a virtual working meeting to focus on the GO-CAM GPAD output. Proposal: David and Kimberly create an agenda so we can schedule a meeting knowing what specific work needs to get done, and then find a good time for everyone. This meeting will required Ben, Jim, and Seth. Also Eric? Dustin?
  • Legacy data (#6)

Pascale, Laurent-Philippe

    • testing and release framework
    • Minerva support for noctua
  • Pipeline (ongoing) (#4a)
  • Pathways2GO paper (#1bi)