Annotation Conf. Call 2019-09-24

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Agenda

October GOC Meeting - Berkeley

Pipeline

  • There have been some glitches with the GOC pipeline.
  • New ontology terms may not be available for use yet.
  • Software team is aware of the issues and working on restoring the pipeline to its regular schedule.
  • Any updates here?

GO-CAMs and Annotation Extensions

  • Update on relations allowed for GO-CAM as specified in ShEx (Shape Expressions)
  • Approach:
    • Examine relations used in GO
      • Annotations extensions
      • Ontology
    • Some relations are in the Relations Ontology (RO), others have just been in gorel (relations only used in the Gene Ontology)
    • Trying to move towards using only RO relations, using a smaller set of relations to make curation easier (but still maintain accurate representation of the biology)
  • Relations Usage
    • Definitely in
    • In, but usage restricted to specific ontology terms and their children
    • Out for now (need further discussion)
    • Definitely out


  • Biological Process
    • Definitely in:
      • part_of
      • has_input
      • has_output
      • occurs_in
      • transports_or_maintains_localization_of
      • has_target_end_location (Reactome)
      • has_target_start_location (Reactome)
      • regulates
      • negatively_regulates
      • positively_regulates
    • In but usage restricted to extending from 'activity regulating processes', e.g. transcription, translation:
      • causally_upstream_of
      • causally_upstream_of_negative_effect
      • causally_upstream_of_positive_effect
    • Out for now (need further discussion)
      • results in.....
        • curators would request appropriate terms for now
      • others
    • Definitely out
      • chained relations, e.g. regulates_o_occurs_in
        • annotations using these relations will be modeled in GO-CAM but the relations won't be used in the GO-CAM models themselves
      • others


  • Molecular Function
    • Definitely in:
      • enabled_by
      • part_of
      • occurs_in
      • has_output
      • has_input
      • regulates
      • negatively_regulates
      • positively_regulates
      • directly_regulates
      • directly_negatively_regulates
      • directly_positively_regulates
      • causally_upstream_of_or_within
      • causally_upstream_of_or_within_negative_effect
      • causally_upstream_of_or_within_positive_effect
      • causally_upstream_of
      • causally_upstream_of_negative_effect
      • causally_upstream_of_positive_effect
      • happens_during
    • In but usage restricted to specific function terms
      • directly_provides_input_for
    • Out for now (need further discussion)
      • occurs_at
      • compound function relations
    • Definitely out


  • Cellular Component
    • Definitely in:
      • part_of
    • In but usage restricted to specific component terms
      • adjacent_to
        • extracellular region
      • overlaps
        • cell junction-type terms
    • Out for now (need further discussion)
      • produced_by
    • Definitely out:


  • GO-CAM GPAD outputs
    • Still work to be done here
      • Should we limit the AEs generated and if so, how?
      • Should we try to get chained annotation extension relations back out of GO-CAM models?
      • How do we want to propagate 'contributes to'?

Minutes

  • Present: Dustin, Edith, Harold, Justin, Kimberly, Li, Michele, Midori, Pascale, Patrick, Sabrina, Seth, Stan