Annotation Conf. Call 2019-09-24

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October GOC Meeting - Berkeley


  • 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
  • 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


  • Present: