Annotation Conf. Call 2017-02-14

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Bluejeans URL

Agenda

Meeting Reminder

  • Next Consortium Meeting: June 1-3, 2017 in Corvallis, Oregon
  • Noctua Workshop on June 4th
  • Reactome Workshop on June 5th

Qualifiers and Relations in GO

  • Qualifiers are used in GAF and GPAD
  • Relations are used in GPAD, Annotation Extensions, and LEGO models
    • In GPAD, the explicit relations between a gene/gene product and GO terms are ontology-specific:
      • involved_in a BP
      • enables a MF
      • part_of a CC
    • Annotation extension relations 'extend' the meaning of the GO term, providing additional biological context
    • In LEGO models, relations describe the context in which activities (GO MFs) occur and how activities relate to one another

New Relations for Modifying a Gene's Role in a Biological Process

Link to github Discussion

  • This issue is about adding more relations to the list that curators currently use to describe the relationship between a gene/gene product and a BP GO term, again, with the overall goal being a more accurate representation of biology.
  • We have talked about doing something like this for some time wrt conventional annotations, and we need them to translate LEGO annotations back to GPAD/GAF formats.
  • The current proposal is to add the following relations to the 'qualifier' column of GAF and GPAD to better describe the relationship between a gene product and a GO term:
    • acts_upstream_of_or_within
      • acts_upstream_of
        • involved_in_regulation_of
      • involved_in_or_involved_in_regulation_of
        • involved_in
        • involved_in_regulation_of
          • involved_in_negative_regulation_of
          • involved_in_positive_regulation_of
  • Note the differences between the relations for GAF/GPAD and the relations used in LEGO models due to the nature of what is being related, i.e. gene to GO term in the former and GO term to another GO term in LEGO.
    • Example translation:
      • LEGO: 'causally upstream of'
      • GAF/GPAD: 'acts upstream of'
  • For discussion:
    • Use of 'within' vs 'involved_in'
      • 'within' is used in the top level relation, but 'involved_in' in child terms
      • Should one or the other be used throughout?
    • Definitions
      • Necessary formal definitions exist, but curators would like guidance on how experimental results inform selection of a given relation
      • For example, 'causally upstream of or within' has a formal definition:
        • p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
        • This relation has a related synonym - 'affects'
    • LEGO GPAD outputs
      • How will LEGO annotations translate back to GPAD annotations, specifically wrt regulates relations?
      • GAF/GPAD output working group meets on Wednesdays at 7am PST to discuss output of different LEGO models
      • The particular issue wrt regulates and regulation is being worked on
    • Where can curators view all of the relations used in GO, their definitions, and usage statements and examples?
    • We need clear, vetted examples of usage in LEGO.

Jenkins Jobs

February 28th Call

  • Discussion of LEGO Models
    • Sabrina (ZFIN)
    • Midori (PomBase)

Minutes

  • On call: Alice, Chris, David H, David OS, Edith, George, Giulia, Helen, Jim, Kimberly, Midori, Moni, Olivia, Pascale, Petra, Rachael, Stacia, Stan, Suzi, Tanya, Terry, Val

GOC Meeting

  • Corvallis, OR - Please register
  • Need to get more information from Reactome about what their workshop will entail

Ontology Editor Training

  • Berkeley, February 22-24, 2017
  • Chris and David H. will lead the workshop
  • Attending: Karen, Harold, Kimberly, Pascale

Annotation Relations

  • First issue wrt use of 'within' vs 'involved_in'
    • 'acts_upstream_of_or_within' reads acts upstream of or acts within
    • within = involved in
    • No current plans to change relation term name
  • We spent the rest of the call discussing which of the proposed new qualifiers should be included for annotation, what those qualifiers actually mean, and how we might go about developing clear annotation guidelines for their use
  • One of the main use cases to sort out is mutant phenotype-based annotations from multicellular organisms
    • These annotations reflect a broad range of 'directness' with respect to the BP terms selected
  • There are also concerns about how users will either use or ignore these qualifiers in their analysis
    • Enrichment results could be different depending upon which set of annotations someone uses
    • Should GO provide filtered annotation sets based on these qualifiers?
      • There seems to be support for that proposal, but we still need to get to the point of having consistent annotation sets.
      • David OS suggested that the defaul download set would NOT include any of the causally_upstream of qualified annotations
  • Several suggestions for how to go about establishing guidelines for qualifier use:
    • Look at annotation outliers - Val's matrix tool can help with this; Val, David H., and Kimberly working on some examples there
    • PAINT - Pascale noted that the experience of PAINT curators, i.e. what they've chosen to propagate, could be very helpful here for providing examples
    • Helen suggested pathway analysis to determine which genes/gene products should be included
  • ACTION ITEMS:
      • Each annotation group should look at some of their existing BP annotations to see how they would apply the newly proposed qualifiers/relations, particularly acts_upstream_of_or_within, acts_upstream_of, and involved_in_or_involved_in_regulation_of and child terms.
      • Is it always clear which relation to use? If not, when is it not clear?
      • If new information is now available about how a gene product acts, do existing annotations still apply?
      • If there are orthologs in other organisms, what BP annotations exist? What is the overlap?
    • Construct LEGO models to create usage examples for the corresponding relations.