Manager Call 2017-03-01

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Updates on ACTION items from last meeting

  • GOC meeting:
    • ACTION: Suzi will contact Pankaj to get more details about the Reactome workshop, and will distribute these details to consortium.
  • After the annotation call:
    • Pascale will look at IMP rules and Val’s matrices, paying close attention at ambiguities.
    • Chris and David will work on enrichment analysis with and without IMPs included.
      • I have done this with three gene sets using Joel's VLAD tool. One set is a cancer set, one set is a skeletal muscle development set and one set is as hair follicle/stem cell set. I have the results in spreadsheet form. We need to decide how we are going to proceed in their analysis. I also looked at phenoptype enrichment for these. From just eyeballing the results, it looks like the complete annotations sets might be the most informative. We should plan to look at the data together, maybe at the GOC meeting.--david
    • Kimberly will look at GO and phenotype enrichment.

GO Help Rotation

  • Currently, only six volunteers to cover rotation for the year. If continuing with same model until now, this means at least 8 weeks of Help rotation for each volunteer over the next 12 months.
    • Is there an update from GO-directors on the proposed plans to move away from current GO Help rotation model?
      • The first step would be to have the documentation jamboree and see what kinds of resources we have. What will be the rota schedule for go-help? Week before biocurator or in April. Do we have any dedicated people? What are the faqs that we need the most? Moni will put together an idea about the best way to communicate.
  • JIRA service is going (went) away on February 28th. This is an update on the steps taken to replace JIRA system for go-help. Seth Carbon, Tanya Berardini, Moni Munoz-Torres, Stuart Miyasato, and Chris Mungall have been working on this.

Report on Ontology/Protege Workshop

  • Berkeley Feb. 22 - 24th, 2017
  • Attendees: Chris, David H., Eric, Harold, Jeremy, Karen, Kimberly, Pascale, Paul T., Seth
  • Basic Protege, git, and github training for ontology editing
    • We have now moved to using github as the official repository for the ontology files. The ontology editors at the meeting were all trained in how to retrieve, commit and troubleshoot files. A number of us have done this post-meeting and it looks like it will be a relatively smooth transition (I hope).
  • Managing tickets going forward
    • We have decided move forward using a different approach to assigning tickets. Rather than have a weekly rota, we will assign tickets as they come in. If possible, we will assign them in accordance with an ontology editor's biological expertise. If there is no one with specific expertise, they will be assigned on a rotating basis.

Proposal for Documentation Jamboree

  • Discussed as a possible working group meeting at Berkeley Ontology/Protege workshop
  • Agree that we need a uniform system for documentation that integrates well with github, the GO web site
  • Can we schedule a working group meeting? When? Where? Who?