Manager Call 2017-05-17

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Agenda & Minutes

GOC meeting

  • Times for discussions will be 2 full days on Thursday and Friday and half a day on Saturday.
  • Add an item for GO help report. This will be brief. There isn’t a Help desk rotation anymore, and the number of questions and requests is lower than in the past, with users submitting more refined and detail questions and requests.
  • Criteria for proposed discussion items (by to S. Lewis):
    • whether it is a status report
    • whether it is a specific proposal to address a particular issue
  • Adding items to the agenda:
    • Dealing with applying qualifiers to legacy annotations.
      • Do we change GAF 2.0 to allow additional qualifiers?
      • The easiest and most consistent application would be to use involved_in or causally_upstream_of. The longer we wait, the longer it will take us to change.
      • We should issue an announcement along the lines of “We are creating a relationship term, everything is getting the parent qualifier term and we believe it is accurate. All annotations have a relationship between the entity and the GO and the default one is *this* and we are applying it to everything. Some suggestions to applying a more specific one are “x, y, and z”. Here are some examples when using experiments of “a” kind and here when annotating experiments of “b” kind”.
      • Concern about having some guidelines for approach on how we are making other annotations more precise. Explain clearly what causally_upstream_of means. involved_in is very precise, and should not be the default relation.
      • Let’s make the annotation guidelines Noctua-centric, with the expectation that people will be primarily using Noctua to add these qualifiers.
  • Suzi: if you have specific questions you want the PIs to ask regarding immediate future plans and overall goals of the current GOC efforts, please send them to us.
    • David: it would be good to have concrete goals for the end of the year. e.g. all groups should be using Noctua by the end of the year.
  • Breakouts: should there be breakouts at GOC meeting? If so, please propose the topic on the agenda. Also, Suzi suggests to mark current items on the agenda as potential for breakout sessions.
    • PAINT update does not need a breakout
    • TermGenie replacement warrants a breakout
  • Huaiyu brought up the work of a graduate student who has created taxon constraints. Regardless of where the taxon constrains come from, let’s discuss how to implement them. And to do this please create a ticket with that request.

Ontology Developer Training

Follow up on idea of doing an advanced Ontology Developer Training workshop this summer

  • Who will participate David H, Kimberly, David OS, Moni, Chris, Pascale, Karen, Huaiyu, Barbara, Paul T, ....
  • Where will it be: Berkeley
  • When will it be: Tues Aug 15- Friday Aug 19
  • *Potential Topics*
    • Equivalence axioms - editors would like more guidelines on how to construct these.
    • OWL GCIs- Where do they live and how do they work?
    • Advanced Querying?
    • Pipelines and how they run. Starting jobs with ROBOT.
    • Build failures
      • Document the various fail messages and how to correct the issues.
    • Problematic GitHub tickets

In Attendance

David, Kimberly, Chris, Suzanna, Huaiyu, Pascale, Moni

Agenda & Minutes: Pascale & Moni.