Annotation Conf. Call 2017-02-14: Difference between revisions

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***See [http://link.springer.com/protocol/10.1007%2F978-1-4939-3743-1_17 Huntley and Lovering, 2016] and [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039540/ Huntley et al., 2014]
***See [http://link.springer.com/protocol/10.1007%2F978-1-4939-3743-1_17 Huntley and Lovering, 2016] and [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039540/ Huntley et al., 2014]
**In LEGO models, relations describe the context in which activities (GO MFs) occur and how activities relate to one another
**In LEGO models, relations describe the context in which activities (GO MFs) occur and how activities relate to one another
***[http://noctua.berkeleybop.org/editor/graph/gomodel:5323da1800000002 NEDD4 and the DNA damage response]
=== New Relations for Modifying a Gene's Role in a Biological Process ===
=== New Relations for Modifying a Gene's Role in a Biological Process ===
[https://github.com/geneontology/go-annotation/issues/1517 Link to github Discussion]
[https://github.com/geneontology/go-annotation/issues/1517 Link to github Discussion]

Revision as of 10:44, 14 February 2017

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.
  • We have talked about doing something like this for a long time, with the overall goal being a more accurate representation of biology.
  • These relations will also allow us to better translate LEGO models into conventional GO annotations.
  • The current proposal is to add:
    • 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
  • 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

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