Manager Call 2018-02-21

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Call in info

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

Agenda

GO outreach role

Agenda for GOC meeting and SAB meeting

  • People are starting to make their travel arrangements and would like more information about the exact dates, workshops, etc.

Annotation transfer across species (more generally, common annotation practices across groups)

https://github.com/geneontology/go-annotation/issues/1807

Can we come up with a plan for annotation propagation across species moving forward? We have 3 main pipelines at the moment, PAINT, interpro2go, Ensembl (plus various groups may be using their own). Are all using the same rules? Are these clear? Do we need extra rules for blocking certain branches across certain levels? Are we all implementing the do-not-annotate subsets consistently? Do these need expanded, better strategy for response-to terms? - Chris

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For example, in addition to PAINT, MGI brings in rat and human experimental annotations via ISO using MGI orthology assertions.

We do not use InterPro2GO for cross-species annotations.

The task first is, as you say, to gather status of major groups in this regard. This comes under AGR thinking too.

- Judy

USC developers hackaton jamboree report

Feb 7-8

Noctua V1 status report

GH ontology ticket marathon report

Feb 12-16, Denver


Outstanding from the docathon: What is a GO contributor, GO collaborator, and a GO resource?

see also website http://geneontology.org/page/contributors (Pascale) I want to double check this correctly represents people working on the project.

References in GAF/GPAD/OWL

  • I (Kimberly) would like to propose that we move towards a single identifier for any given reference in our annotation files.
  • This would simplify their representation.
  • The proposed hierarchy for reference identifiers would be:
    • PMID
    • doi
    • Internal MOD or GO_REF
  • Any drawbacks?
  • Noctua issue with imported annotations

Minutes

  • On call: Chris, Huaiyu, Judy, Kimberly, Mike, Pascale, Paul T., Stacia, Suzanna, Suzi A.

GO outreach role

  • Chris and Paul T. have a doc that discusses what tasks are not assigned to someone in GO, could be done by an outreach coordinator
  • What should the role of the outreach coordinator be?
  • Who should be targeted?
    • Authors
    • Students
    • Bioinformaticians
    • Biologists
    • Clinicians
  • What should the tasks be?
    • Slides
    • Videos
    • Monitor Q/A forum, e.g. StackOverflow, BioStar
  • Need to have documentation for who will be point-of-contact for various issues
    • Each working group will need a point-of-contact (name, contact, github handle, brief description)
    • PIs will discuss allocation of resources
  • AI: Kimberly, Pascale, Suzi A. to discuss GO annotator welcome kit
  • AI: Chris, Seth will look into mechanism to allow easier GO helpdesk contact

May GOC Meeting

  • Consortium members should plan for full days on the 12th and 13th, 1/2 day on the 14th
  • SAB is on the 15th
    • Attendance TBD
    • AI: Paul T. will check with Peter D. about room size
  • AI: Start looking at milestones to assess progress
    • For each tracker, look at tickets with May meeting milestone

Annotation Practices

  • Need to assess what different groups do wrt different annotation pipelines
    • Orthology-based methods (e.g. PAINT, ISO pipeline at MGD)
    • Other sequence-based methods (e.g. InterPro2GO)
    • IEA-based methods (e.g. UniProtKB keywords, subcellular localization, EC2GO)
    • Manual methods

AI: Flesh out the survey, get feedback on questions, send out to consortium members

USC Software Hackathon

  • Solidify working relationship between Berkeley and USC
  • Work on enhancements, bug fixes for SAE
    • Still needs some final testing