Annotation Conf. Call 2017-07-25

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Meeting URL - NOTE CHANGE TO ZOOM

Agenda

Annotation Guidelines for Modified-Protein Binding

  • Pascale and Sylvain will present the guidelines for annotating to modified-protein binding terms

GO Slims

  • AGR is including a GO slim on the gene pages
  • Launch date for AGR 1.0 is October 2017
  • Need feedback on GO Slim and ribbon display on gene pages
  • Mary Dolan will provide an overview of the methodology used to generate the slim

Alliance JIRA ticket, curators comment here: https://agr-jira.atlassian.net/browse/AGR-470

Signaling Project

  • Update on what pathways have been claimed
  • Update on progress to date, github tickets
    • MAPK - David H.
      • 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: David H., Edith, Emily, Giulia, Harold, Helen, Jim, Mary, Midori, Pascale, Paul T., Penelope, Petra, Rob, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Sylvain, Tanya, Tom

Annotation Guidelines for Modified-Protein Binding

  • Discussion began at USC meeting in November 2016
  • Question: How to correctly annotate when binding to a protein is modification-dependent?
    • For example, a protein binding ubiquitin vs protein binding that depends on ubiquitin modification
  • Solution: create new terms, using the most common types of protein binding that reflect the dependency
    • Less frequent modifications would be annotated to the parent term, modification-dependent protein binding
  • Comments on term usage have been added to the terms in the ontology
  • Full documentation will be added to the go-annotation github repository
  • Sylvain reviewed annotation errors
    • For example, targets of post-translational modifications should not be added to the BP term for the modification
  • Annotations that may have been affected by these terms are recorded in the github ticket for this issue
    • Curators can review these annotations to make sure that we didn't lose information by merging into the parent term, protein binding

GO Slims

  • Mary presented slides on construction of AGR GO slim
  • Started with experimental annotations for all organisms included in AGR + human
  • Select terms based on number of annotations, depth in DAG, information content using an algorithm
    • Select terms
      • Tended to select terms that had between 200 - 1000 annotations (don't want terms with 30000 annotations)
      • Selected terms that are generally 4-7 levels down in the DAG - note that we can always select a parent if a child term is too specific and doesn't have many annotations
    • Eliminate parent-child terms
    • Then manually analyze the list
      • Analyze what terms are in and out
      • Analyze what genes are in and out
        • It might be worthwhile to include an 'Other' category to capture the genes that don't currently map to a slim
        • In AGR, the ribbon display is the main way, right now, that GO annotations will be displayed
    • Gene products can fall into more than one bucket of the slim
  • Map selected terms onto the graph view of GO terms to see what is/is not included
  • Mary also has a view that shows the breakdown of annotations based on contributing group
  • Question about terms in F list
    • How many reflect the overall function vs part of the mechanism of the function
      • For example, metal ion binding - what types of gene products are annotated to these terms? Transporters? Others?
  • Mary will make slides available here on the wiki
  • Relevant github tickets:
  • Alliance JIRA ticket:
  • The AGR slim will be available to all as part of the ontology
  • What are the plans, if any, for integrating the AGR slim with the generic GO slim?
  • Overall workload - not too time-consuming to generate a slim, much of this can be automated
    • Manual review takes a bit more time but is not unbearable (An hour or so for reviewing the whole slim)
  • The slim could also be used also to compare what annotations are used in PAINT propagation

Signaling Project

  • Overview
    • Signaling projects are being tracked in github go-annotation projects page
    • This high-level page is for tracking tasks that need to be done, not for in-depth discussion of specific issues
    • So far, three pathways have been claimed:
      • Canonical Wnt
      • MAPK
      • GPCR
      • Ca2+-mediated fertilization
    • Reviewed workflow for canonical Wnt signaling
      • Review annotations
      • Review ontology term definitions, parentage
        • For example, where does the pathway start and end? What regulates the pathway?
      • Create a GO-CAM model
    • For canonical Wnt signaling, spreadsheets and docs are all in GO's Google drive