Annotation Conf. Call 2017-08-22

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Meeting URL

Agenda

Cambridge Meeting, October 2-4, 2017

  • 2017 Cambridge GOC Meeting Logistics
    • Registration - confirm pay in cash
  • 2017 Cambridge GOC Meeting Agenda
    • Poster session Monday night
    • Wednesday afternoon hands-on/workshop session. Suggestions:
      • Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.
        • Presentations from Val (PomBase), Mary Dolan (MGI)
      • Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.
        • Conventional annotation display as well as GO-CAM model display
      • Good annotation practice: phenotype vs process
      • Representing biologists’ view of biology
        • Author intent & protein domains; IDA v IC v New evidence code

2017 Cambridge GOC Signalling Workshop, October 1, 2017

  • 2017 Cambridge GOC Signalling Workshop
  • Start thinking about agenda
  • We have four different pathways being worked on
    • Four presentations, and time for a wrap-up?
      • Summary of analysis work, followed by specific proposals?
    • Some of the same annotations issues are surfacing for different pathways

Signaling Project

  • Update on progress to date, github tickets
    • Wnt - Giulia, Helen, Kimberly
      • Google spreadsheet with annotation, ontology analysis
      • Google doc for crystallizing github tickets
      • Annotation and Ontology Issues:
        • Wnts
          • Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but generally an underused term
            • Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'
            • Note that we have terms like 'Wnt-activated receptor activity' to describe receptors
          • Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common
          • Some annotation with terms like 'cytokine activity'
            • Should we have terms in the ontology like 'cytokine agonist activity' as a child of 'receptor agonist activity' and 'cytokine antagonist activity' as a child of 'receptor antagonist activity'
          • General issue: co-annotation vs more terms in the ontology
        • Receptors
          • Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors
          • Most frizzleds, however, do not appear to signal via G-proteins
            • Proposal: Create a specific term for Wnt-activated GPCR activity
    • MAPK - David H. and Sabrina
      • Examining gene products annotated to the process with no experimental support for known MFs
      • Thinking about how to define the beginning and parts of the pathway
    • Ca2+ Signaling
      • Fertilization - Penelope
    • GPCR - Pascale, Petra
      • Some ontology tickets have been addressed
      • Needs global annotation review
      • Needs GO-CAM model
    • Reminder - discussion on specific github tickets, not on project page

Minutes

  • On call: