Annotation Conf. Call 2019-09-24

From GO Wiki
Revision as of 11:27, 24 September 2019 by Stacia (talk | contribs) (→‎Minutes)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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: David H, Dustin, Edith, Harold, Justin, Kimberly, Laurent-Philippe, Li, Michele, Midori, Pascale, Patrick M, Petra, Rob, Sabrina, Seth, Stacia, Stan, Suzi A, Tanya