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'
    • Definitions
      • Formal definitions exist, but curators would like guidance on how experimental results inform selection of a given relation
    • LEGO GPAD outputs
      • How will LEGO annotations translate back to GPAD annotations, specifically wrt regulates relations?
    • Where can curators view all of the relations used in GO, their definitions, and usage statements and examples?
    • See email thread from last week with subject: documentation for AE
      • GO website
        • Annotation Documentation
        • Ontology browser
      • GO wiki
      • github
      • Google docs
      • OLS
      • Protege

Jenkins Jobs

February 28th Call

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

Minutes