LEGO November 16, 2015

Agenda

• 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:
      • Gluconeogenesis - likely conserved, but different isozymes in different tissues; each participant could model what is known in their organism- http://www.ncbi.nlm.nih.gov/pubmed/6311081
      • Annotating transcription regulatory networks and annotating isoforms - http://www.ncbi.nlm.nih.gov/pubmed/25148942
      • Annotating ligand-receptor interactions and annotating from cross-species experiments - http://www.ncbi.nlm.nih.gov/pubmed/8861902

Minutes

• 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
    • Link to documentation
    • https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit#