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 note that this is generally an underused term
            • Definition:Interacts with receptors such that the proportion of receptors in the active form is increased.
            • For the experiments that we are annotating, it is unlikely that the assay will directly measure the “proportion of receptors in the active form”. Rather, the assay will examine an endpoint of signaling, such as activation of a TCF/LEF transcriptional reporter. Is this sufficient evidence to annotate to a 'receptor agonist activity' term?
            • If so, do we want more specific child terms?
            • 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
            • Is this a generally reasonable and sustainable approach for describing the molecular functions of signaling ligands and their receptors?
            • Related issues: look at parent terms of 'signal transducer activity' and 'receptor activator activity'. Some inconsistencies with our current annotation guidelines.
          • 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 receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'
            • The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?
              • Some preliminary Textpresso searchers (Wnt AND cytokine) suggest that they are thought of as distinct activities.
        • 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: Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Liz, Midori, Penelope, Rob, Sabrina, Shur-Jen, Stacia, Stan, Suzi, Terry