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.

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

  • When do we want to make an announcement to the community?
    • This seems dependent upon a firm date for switchover - do we have that?
    • 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)