Annotation Conf. Call 2020-07-28

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Agenda and Minutes

GAF 2.2 and GPAD/GPI 2.0

  • Check in to see if there is any additional feedback from groups
  • PLEASE review the specs with your developers and provide feedback
  • The plan is still to switch to the new file formats by the end of 2020

GAF 2.2

  • Naming: we won't be changing anything about naming the GAF files, but will need to communicate to users what the change is, i.e. the qualifier field is now mandatory and allowed values have increased
  • There will be a check for the actual relation label used and non-compliant annotations will be flagged/removed - need to confirm what the action will be


  • 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

  • We would like to hold a week-long GO-CAM jamboree this fall (exact dates TBD)
  • The purpose is to have focused discussions on GO-CAM modeling and to assess time and resources needed to create process-centric GO-CAM models
  • Format will be similar to transcription workshop and May GOC meeting, i.e. 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)
  • We want to work on processes that are as broadly relevant as possible, but also correspond to manageable chunks of biology. For example:
    • Signaling pathway
    • Metabolic pathway
    • Regulation of transcription
    • Small molecule activator/inhibitors that affect MFs
  • Coming soon: Doodle poll for selecting a good week and a Google doc for suggesting biological processes to model


  • On call: Birgit, Bob, David, Debby, Dmitry, Dustin, Edith, Giulia, Harold, Judy, Karen, Kimberly, Li, Malcolm, Michelle, Petra, Sabrina, Seth, Stacia, Stan, Suzi