Manager Call 2020-09-09

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Meta

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

Agenda

Update on SARS-CoV-2 GPI and GPAD/GAF (Chris)

  • What should go in Col 2 ? The 'gene' is the polyprotein, so Alex is putting that in Col 2. Chris thinks the biologically relevant entity is the CHAIN.
  • Sylvain Poux mentioned that in human CHAINS are getting better and better characterized.
  • Suggest to do a breakout at GO meting: Alex, Patrick, Judy, Chris: decide what we need to annotate, how to extract them, and how to represent them in the GPI.
    • Deliverable: GAF/GPI guidelines for CHAINS / also mention operons (for viruses but also other non-viral genes)

BP annotations / regulates closure

  • From Chris: As far as I can tell at this stage we do not have a strong empirical case for excluding regulates in BP annotations.
  • Paul: We do have a strong case for MF. Next week Val will attend the managers' call and give her use cases.
  • Huaiyu: there is also an annotation issue - since the usage of regulates has not been consistent in the past.
    • We need to think about whether it's better to introduce false positives or false negatives.
    • For next grant: Use Panther and other heuristics to populate 'involved' relations, to try to have more direct annotations which should false positives in enrichment analysis

NAR paper update (Laurent-Philippe)

https://docs.google.com/document/d/1yJQFnT6bb-CAx52Z9YdX5OBcpWpiMuwBSaFT4GvrAtg/edit?usp=sharing

GO Meeting Agenda

https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI/edit#

Notes from Chris:

  • can people self-assign themselves? We can also assign on the call tomorrow. Also indicate how much time you think you need.
  • we have a folder for presentations but it's currently empty https://drive.google.com/drive/folders/18BUCjmSzTuy4MkVaYYQ74SNccQHlJ3HW -- we should get cracking on this!
  • some of the times are a bit cryptic: "pipeline reminder". What does reminder mean here? Maybe we can flesh things out tomorrow.

goals are for each project here: https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#

Projects updates

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

GAF 2.2 and GPAD/GPI 2.0 (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 (if not already) ready for this, but we need to assess where other groups are at

Ongoing projects updates

  • Noctua Imports (#3a)
    • MGI/wormbase imports
    • GPAD/GPI 2.0
    • Minerva/gpad output
      • I think we need to schedule a virtual working meeting to focus on the GO-CAM GPAD output. Propose that David and I create an agenda so we can determine who needs to be at the meeting, what specific work needs to get done, and then find a good time for everyone. (Kimberly)
  • Legacy data (#6)

Pascale, Laurent-Philippe

https://github.com/geneontology/noctua-annotation-review/issues/21

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