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

Cambridge meeting discussion

  • Oct 2-4 (M-W)
  • sign up now if you are going and haven't signed up yet. Final numbers are needed soon.
  • Registration will be paid in cash; final fee will be determined soon
  • Add ideas/suggestions for agenda items to the agenda page and they'll be sorted/organized later
  • Might be better to have small working groups/break out sessions earlier in the meeting and reports at the end of the meeting
  • Discussion of one of the suggested working group topics - 'Representing biologists' view of biology - discussed about what evidence shows and what biologists expect.
    • ACTION ITEM: Form a working group to discuss this before the Cambridge meeting. Paul, Suzi, Judy, and Karen are interested/volunteered. Before Cambridge, group should examine/discuss specific cases where curators don’t feel comfortable making an IDA annotation just based on a particular experiment; cases where people need to take more than 1 piece of evidence to make an assertion. Haven’t been consistent, try to come up with guidelines.
  • Meeting will be streamed; Please add name to agenda to get an estimate of who to expect remotely

Signaling pathway workshop on Oct 1

  • Four pathways are being worked on; suggestion for presentations from all pathway working groups, plus a wrap up
  • Suggested content in presentations - analysis, summary, what led to specific proposals
  • Groups are experiencing similar annotation issues

Signaling pathway reports

  • Wnt pathway (Helen, Kimberly)
    • focusing on canonical pathway
    • Google docs should be accessible; please e-mail Kimberly if you can't access and want to.
    • Wnts - looking at MF annotations; seeing inconsistencies about how we are annotating MF
      • inconsistency being defined as: given a certain assay, curators are choosing different terms
      • would like to come up with guidelines for choosing terms
      • cytokine - may want to work on definition or usage notes
  • MAPK (Sabrina)
    • spreadsheet with all annotations to MAPK pathway; looking at gene product annotations to process terms, but no expt evidence for MF annotations
    • Found some problematic annotations
      • most experiments that authors report - look at phosphorylation of a member of the pathway or target; some annotations are made to MF of kinase activity
    • looking into examples of good papers with evidence to make annotations to the pathways, specifically to MF terms
      • many have been based on sequence similarities to genes a different species; difficult to find an original paper where there is enough evidence to make MF annotation
    • coming up with guidelines for making MF annotations
    • looking at scaffold proteins - how these should be annotated, where they should be in the GO-CAM model; if they are regulating the pathway or part of the pathway
    • MAP kinase import into nucleus term - haven't found evidence that there is active transport into the nucleus; looking to see if we should have this term or be obsoleted
    • Paul has a GO-CAM example with scaffolding protein in it; will dig it up.
  • Sept 12 call will start with Ca2+ Signaling and GPCR