Annotation Conf. Call 2020-09-15

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Agenda and Minutes

October Consortium Meeting

  • Virtual meeting
  • October 6th - 8th (SAB on October 9th)
  • Registration
  • Draft agenda
  • We would like to have annotation groups give ~5' flash talks about what their groups is doing wrt GO curation (e.g. annotation, display, tools, outreach). If you need more time, let us know.
  • Please indicate if there are other topics you'd like to discuss and ideas for break-out groups

GAF 2.2 and GPAD/GPI 2.0

GAF 2.2

  • github ticket
  • Specifications
  • Summary:
    • The qualifier field(Column 4) will be mandatory; accordingly, there are additional values for that field
    • Also, required header fields include:
      • file format
      • generated-by
      • date-generated
  • There will be a pipeline check for a value in the qualifier field
    • Proposal: Non-compliant annotations (i.e. those with no value) will be assigned default relations as follows:
      • BP: acts_upstream_of_or_within
      • MF: enables
      • CC: located_in (for non-protein-containing complex terms)
      • CC: part_of (for protein-containing complex terms)



  • GPAD 2.0 has an annotation property 'contributor-id' in which we'd ideally like to capture curators' orcids
  • orcids are captured as metadata (specifically the uri tag) in the users.yaml file
  • BUT, there are cases where a curator does not have an orcid and/or is no longer with the annotation group
  • What to do?
    • If a curator is still active within your group, please have them get an orcid and we can add it to users.yaml
    • If a curator is no longer with your group, they don't have to get an orcid; we can use their GOC:xyz xref as their contributor-id
    • Please DON'T remove anyone from the users.yaml file, though; this file allows us to keep some history of who was involved in GO and with what group in case we ever need to trace something down
    • Organization, although often populated in the users.yaml file, is more of a legacy field. Currently, we want curators to be associated with groups, designated with URLs.
    • There is a tag, previous-groups, in the users.yaml schema
      • Will need to investigate further; sample PR this morning gave an error message
    • 'Collective' users - double-check users.yaml entries for those
  • users.yaml cleanup is fine - check in with Kimberly/Pascale/Seth if you have questions


  • Have had some feedback requesting more specific information and examples about populating the file headers, e.g. optional ontology version fields
  • Will add that to the documentation


  • Wrt the timing and synchronicity of the GAF 2.2 and GPAD/GPI 2.0 changes, we will try to allow a period between the GOC release and when the new files are ingested so we can address any issues before the next release
  • Groups will have to account for some possible asynchronicity in managing their local imports, but the file format should be in the header of each file so the expected format can be dealt with there
  • Berkeley will have parsing scripts available to share and can otherwise assist in helping groups with the transition

GO-CAM Jamboree

  • Dates: Monday, November 16th - Friday, November 20th
  • Goal: focused discussions on GO-CAM modeling of specific topics to train more curators on making GO-CAM models and assess the time and resources needed to create process-centric GO-CAM models
  • Format will be similar to transcription workshop and May GOC meeting, i.e. 1/2-day sessions of presentations, annotation, discussion, breakout rooms
  • Ideally, we'd like to have a representative from each group (although it wouldn't have to be the same person every day)
  • Doodle poll
  • Google spreadsheet for suggesting biological processes to model
  • Please fill out Doodle poll and spreadsheet if you'd like to attend
  • Agenda will be forthcoming

GO-CAM Modeling Calls

  • Reserve annotation call slot on the 2nd and 4th Tuesdays of each month for GO-CAM "office hours"
  • Objective: answer specific questions that curators have about GO-CAM modeling
  • Submit questions or tickets to the agenda by the Friday before the meeting, so we can make best/efficient use of everyone's time on the call


  • On call: David, Dustin, Edith, Giulia, Harold, Judy, Karen, Kimberly, Li, Mahima, Malcolm, Mary, Midori, Pascale, Patrick, Penelope, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Val