Annotation Conf. Call 2017-08-22

Meeting URL

• https://stanford.zoom.us/j/976175422

Agenda

Cambridge Meeting, October 2-4, 2017

• 2017 Cambridge GOC Meeting Logistics
  • Registrration - 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
        • Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common
          • Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology
            • Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 2 (?) Drosophila frizzleds, 4 C. elegans frizzleds
            • Only 8 experimental annotations to Frizzled-2 binding
          • Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse and Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface
        • 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
  • 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: