GO-CAM August 9th, 2017

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

• https://github.com/geneontology/noctua/issues/461
• Work is ongoing, progress has been made, but nothing is live yet

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