LEGO November 16, 2015

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Bluejeans URL:


  • LEGO camp in December
  • Agenda
    • What do we want people to come away with?
    • What annotation issues and topics do we want to make sure we cover?
      • Issues:
        • Annotation workflows
          • Annotating a biological process - specify a process and import from annotations; import from user-specified gene list
            • Source of imported annotations - GOlr database
          • Annotating from a single paper
      • Possible topics:


  • Annotation workflow
    • Annotate simultaneously into Protein2GO and Noctua - or any MOD curation tool and Noctua
    • Need GAFs to exchange data between the two tools
    • Draw out data flow to see how to make this work
    • Short term: each group needs to sort out how they will take in Noctua annotations
    • Long term: think about larger strategy for annotation workflows from GOC to MODs
    • Suzi: Do we have a specific Noctua tag for the GAF?
    • Seth, Heiko: No, not at the moment.
    • David: GOC might be a possibility? This is already used for F-P links.
    • Seth: maybe GAF really isn't the solution; have Noctua files available in a separate location
    • David: indicating in the GAF that an annotation came from Noctua may not be necessary as long as there is a separate directory where people can trace the Noctua annotations
    • Proposed solution: have a Noctua-specific GAF directory
  • Geneva Agenda
    • Introduction to LEGO philosophy
    • Start with a talk at Univ. Geneva (morning of the first day) - Chris, Paul will tag team
      • What LEGO is, what the vision is
    • Mechanics of LEGO annotations
    • Example exercises
      • Provide specific papers as examples
      • Trainers can help new people where they get stuck
    • Training documentation
      • What should the actual physical documentation be?
      • Check current Google doc
      • Attendees: Pascale, David, Val, Suzi, Kimberly, Huaiyu, Stacia, Julia, Chris, Marc, Ruth, Paul T.
      • Need very basic demos for curators who may not have seen any Noctua demos before
      • Use one of the annotation consistency papers as a start - last Zfin paper? also SGD paper that had simpler MF annotations
      • Other possible straightforward papers - enzyme purification, knock-out demonstrating role in process
    • Logistics
      • Suzi: Is there an upper limit on airfare?
      • Paul T.: Main issue is not airfare, but carriers; participants buy tickets and get reimbursed
    • Showcase Examples
      • Suzi: Do we have examples of where LEGO models improve analysis?
      • Paul T: We need a corpus of models and then we can start network-based analysis which can't be done with GO right now.
    • Review Existing Github Tickets
      • Already arranged into milestones - will review
      • Strategy: a conference call to go over github tickets would be best
    • Conference Calls
      • Keep one call strictly an annotation call
      • Keep one call focused on software development
      • Decide strategy after Geneva meeting
      • Paul T.: Try to put as much into annotation guidelines as possible
    • Future Calls
      • Monday, the 23rd and Monday, the 30th
    • Work on an agenda page