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
- This ticket specifically refers to:
- 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?
- Cellular Component
- 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
- The list of qualifiers that we will use for GPAD output:
- This ticket specifically refers to:
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