Managers 7Nov07

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GO Managers, Weds. Nov. 07 8a.m. PST, 9a.m. MST, 10a.m. CST, 11a.m. EST, 4p.m. GMT,

Agenda/chair: Jen

Minutes: Pascale

Present: Jen, David, Judy, Pascale, Mike, Michael

Review Action Items from previous meeting

Summary of action items:

  • Chris will write up a formal proposal regarding the removal of GO slims from the public file, and send it to the manager's list in the first instance.
  • Pascale will contact the various groups with wiki-related annotation tool technology to discuss how they can work together on this. [DONE] We talked at the biocurator meeting and this is getting coordinated.
  • Jennifer to initiate conference call on gohelp technical topics. [in progress]
  • Jennifer will call an annotation-outreach meeting in a couple of weeks to discuss the changes in the annotation-outreach effort. [next week]
  • Pascale will take the Annotation SOPs to the reference genome group and web presence group for improvement. [next week at conference call]
  • Jennifer is to include work of the web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. [not yet done]
  • Judy to get back to Midori about Current Protocols paper. [Judy says it's due Nov 15 now, and Midori has sent her part]

Current Topics and Concerns

Individual Manager reports

Ontology Development

  • Cardio and muscle stuff is live. Will go in the next newsletter.
  • Pushing community annotation - will write a paper
  • Tanya and David are still working on 'regulates'; 2/3 done
  • Lung development: in the scratch directory. There is a contents meeting Dec 5 in Boston.
  • Jen, Suzi, Chris, David, Amelia, Midori and Jen had a conference call to make the Function-process links, will mine the reactome data to find possible F-P links that can be reviewed by experts

Outreach / User Advocacy

  • transport annotation and mapping grant proposal being written by Tsai-Tien Tseng at Virginia Tech; Judy: how do we make sure the annotations are high quality? Jen: maybe through our usual mentoring system? Judy: like who? this will be discussed at the GO tops meeting. Might make sense that it would be Jen since she's done a lot of the ontology, maybe with Michelle.
  • David: there is the Sea urchin database hiring; have we contacted them? Judy will.
  • Susan Tweedie, Emily Dimmer: contacted Kira Anthony from NNCI-Nature Pathway Interaction Database; she is curating human pathways and we will see if she can contribute annotations to the GO. One of the issues is that they use part of the GO evidence codes but made up some others, liek IAE (inferred from array experiment). We need to sort that out.


nothing reported

Reference Genomes

November gene list is out (done by TAIR)


  • Judy: mouse meeting in Kyoto: gave a GO workshop
  • Biocurators meeting: David, Judy: excellent meeting, great overview of GO and tools; Judy gave a great overview of GO (slides available on biocurator site) also David,Pascale and Chris (Alex remotely)attended the cell ontology meeting, looks like the rearrangements they are making will not eliminate cell types and therefore we can move ahead with GO plans that are in place to incorporate CL info into GO.
  • European Science Foundation Comparative Genomics of Eukaryotic Microorganisms', 20-25 October 2007, St Feliu de Guixols, Spain: (Michael): GO talk.
  • Bari, Italy: Midori, Emily Dimmer, and Erika Feltrin went to teach GO

Collaborations and Interactions, active and new

Larry Hunter's group is doing ontology metrics that will hopefully complement the metrics we're already doing. Meeting planned in January in California.

Operations and Procedures

Staffing and Personnel

Budget issues


  • NAR paper out
  • 'What is a GO annotation' paper accepted, special BMC bioinformatics for papers from BioOntology SIG in Vienna(Judy, David, Barry)
  • Mary's visualization paper accepted in applied ontologies
  • writing up papers about cardio and muscle, to include experts involved in ontology development (submitting cardio to physiological genomics)Simon, David leading the cardio paper. Jen and Erika will work on the muscle one.
  • SGD paper in NAR database issue is all about GO
  • Judy and Midori working on Current Protocols update

New action items

  • Judy will contact the new Sea Urchin database to see whether/how/who will do GO annotations and how to help them.
  • Jen will start collecting information for the annual report from all groups using GO: collect talks, posters, tutorials, etc
  • Pascale: [annotation documentation] add literature annotation decision tree on the web (seen at consortium meeting).