Manager Call 2018-04-19

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Agenda

NYC Meeting Agenda

ACTION POINT Please everyone make slides for your part by Friday April 27 Slides should be added here: https://drive.google.com/drive/u/0/folders/1iOGHjKc9FN_ShrlNEW0CvOmJANzXqep-


Working Groups/Projects

HTP Codes

RCA Evidence Code

  • Need to work with several groups to review their annotations:
    • Gramene (35815 annotations)
    • As an example, 2929 RCA Molecular Function annotations
      • Date: 20060831
      • Reference: GR_REF:8030
      • Manual review of mappings; can we suggest ISM?
    • GeneDB
      • Some annotations from reviews, but some to papers that describe a systems analysis that is probably more in line with the original intent of RCA
      • RCA -> CCA (combined computational analysis)??
    • EcoCyc
    • AgBase
    • AspGD
    • PAMGO_MGG
  • If we decide to keep RCA, then we'd need to remove the one-year limit; it doesn't make sense.

Documentation

GO Site- Can we explicitly identify which tools/file formats are compatible with which relations/extensions (curator facing)

  • SGD wants list of Noctua relations via category- BP to MF, to BP, to CC, MF to BP...

Protein2GO- GO RELS are not in RO. Eliminate some?

  • Long term plans? including identifying/removing least common annotation extensions after re-annotation

Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928

Working Group Meetings

  • Quarterly?
    • Rotate between ontology and annotation (small, focused groups)
    • Test virtual meetings, but still focused on the task

Noctua

1.0 Rollout

  • Merge Tremayne's fork with Noctua-dev for further testing
  • Some outstanding issues on SAE
  • Single source file for MODs to consume

Reactome Imports

  • David, Kimberly have looked at some imports/translations
  • Ben's work looks to be potentially very useful and promising for seeding templates, models
  • Will probably require significant manual input, refinement, testing

End User Tools

GO Helpdesk

Discuss this ticket: https://github.com/geneontology/go-site/issues/584

This is up for discussion at next Manager meeting. Seems like an outreach task. There is some documentation on GO for curators- 1st step is to contact GO. No guidelines on what GO should do (how to train, submit, who is responsible for maintaining...)

Email forwarded to Suzi A.

Ontology

Announcing changes to the wider user community

  • This was brought up by Birgit in the protein complex merge ticket - she was suggesting we make an announcement. However we never made annoucements before (except for obsoletions); should we start? What would be the guidelines? For example when a merge affects more than 100, 1000 annotations ? EXP only ?
  • Pascale: changes to definitions of root terms: https://github.com/geneontology/go-ontology/issues/14899; isn't this a big change ? How should we notify people?
    • Should we create a label in GH 'Major change', so we can easily pull out the tickets and show them at Ontology and Annotation calls ? (perhaps in annual reports as well)
  • Pascale: suggestion: create a new label 'major change' and announce them either on twitter and/or on the website as user stories (or whatever it's called).


Minutes