Manager Call 2018-04-19

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Call in info

https://stanford.zoom.us/j/754529609

Agenda

NYC Meeting Agenda

SAB agenda, plans

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

External Groups

  • At least three new groups are interested in submitting GO annotations
  • What's our plan for handling this:
  • Is there an SOP for bringing a new dedicated annotation group on board (as opposed to drive-by contributions)?
    • Minimally:
      • GOC-approved curator docs
      • joining appropriate mail lists (to hear of obsoletion announces etc)
      • A new yaml file in datasets/
      • Some kind of QC of the annotations so we can trust them

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

  • For the SAB, for people listed they should prepare slides for their 15 minute presentations.
    • The agenda is on a Google Doc
  • There is a concern about groups submitting annotations. Who owns them, who maintains them? What if they come from Noctua models?
    • How will annotations be checked initially, ongoing?
      • Are they an active group? They will take ownership and be able to support their QC.
      • Are they a one-time submission? How do we handle those?
        • What if a group can't sustain their annotation, their project ends etc?
          • For literature curation, they will either have a contact point or they will give ownership to the GOC. They need to be responsive.
    • We should go through our documentation with new curation groups and make sure that the documentation is suitable for training new groups.
      • Who is going to do this? New groups will be assigned a GO person to work with them. Presumably it will be someone with expertise in the field.
      • Should we make it so people can run their own QC checks, at least the automated stuff? We need to have a validator available.
      • Review their annotations too.
      • Seth, SuziA, Kimberly and Pascale will take this on for these new groups.
    • We won't have specific assigned groups as mentors any more, instead, it will be GO central. GOC will provide all the necessary tools.
  • Update on the pipeline
    • Will be presented on the annotation call next week?
    • Paint annotations? What is the source?
    • We will continue to inject the paint annotations into the pipeline, but we will revise them.