GO-CAM August 9th, 2017

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Zoom URL

https://stanford.zoom.us/j/679970729

Agenda

Update on Proposal for a Tabular Editing Interface

https://github.com/geneontology/noctua/issues/461

Discussion of Models, Inferred Annotations, and GPAD Output

  • Missing inferred annotations
    • This ticket specifically refers to:
      • Generating 'enables' annotations for component function (subfunctions) for compound molecular functions
      • Generating 'contributes_to' annotations in GPAD output for complex members
  • Remove relations from GPAD qualifiers list
    • This ticket specifically refers to:
      • The list of qualifiers that we will use for GPAD output:
        • Cellular Component
          • part_of
        • Molecular Function
          • enables
          • contributes_to
        • Biological Process
          • involved_in
          • acts_upstream_of
            • acts_upstream_of_negatively?
            • acts_upstream_of_positively?
          • acts_upstream_of_or_within
            • acts_upstream_of_or_within_negatively?
            • acts_upstream_of_or_within_positively?
      • Removed:
        • involved_in_regulation_of
        • involved_in_positive_regulation_of
        • involved_in_negative_regulation_of
      • Regulation terms will thus need to be instantiated in the ontology, if wanted for GPAD output

Minutes

  • On call: David H., Harold, Jim, Kevin, Kimberly, Moni, Pascale, Paul T., Rob, Sabrina, Sage, Seth, Stacia, Suzi, Terry

Update on Proposal for a Tabular Editing Interface

Discussion of Models, Inferred Annotations, and GPAD Output

  • Missing inferred annotations
    • Complex members will all receive contributes_to annotation to the Molecular Function
    • Subfunctions that are part of compound Molecular Functions will also get 'enables' relations in the GPAD output
  • Remove relations from GPAD qualifiers list
    • This ticket specifically refers to qualifiers that we will use for GPAD output
    • Need test models to examine the behavior of acts_upstream_of vs regulation outputs
    • Need to check that all property chains exist to give expected output

Priorities

  • GPAD output is still the highest priority for development as this will allow curators to get the output files they currently need
  • Still some tool optimization needed
    • Tabular editing interface is high priority
    • Other issues have been listed in the Noctua tracker