Managers 2Jan08

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GO Managers, Weds. Jan. 2, 2008 8a.m. PST, 9a.m. MST, 10a.m. CST, 11a.m. EST, 4p.m. GMT

Agenda/chair: David

Minutes: Midori

Present: Midori, David, Pascale, Suzi, Judy, Michael

Review Action Items from previous meeting

  • 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. [Chris absent, still jet-lagged]
  • Pascale will contact the various groups with wiki-related annotation tool technology to discuss how they can work together on this. [in progress]
Discussions are continuing following Biocurator meeting; Jim Hu and Alan Ruttenberg also involved. Combination of free text and controlled-vocabulary entries is feasible, and of interest.
  • Jennifer to initiate conference call on gohelp technical topics. Resolving issue 1 at a time on e-mail. [Jen away]
  • Pascale will take the Annotation SOPs to the reference genome group and web presence group for improvement. Mike is interested in getting some general annotation calls happening. We are very interested in this and resolving issues at 'virtual' meetings rather than having e-mails. Will be one of the first topics of the annotation group conference call. [in progress]
  • Jennifer is to include work of the web presence group in the advocacy monthly reports. [Jen away, but presumably next reports will follow this procedure]
  • Judy will contact the new Sea Urchin database to see whether/how/who will do GO annotations and how to help them. [in progress]
  • Jen will start collecting information for the annual report from all groups using GO: collect talks, posters, tutorials, etc. [in progress; wiki page created]

Current Topics and Concerns

  • GO/GMOD OBO submission item from last call should become new action item.
Discussion highlights:
  • Important considerations include volume, type of submissions that come in
  • A single route for capturing metadata is very desirable (no matter what it is); best done as part of publication process
  • We should test a few things, with aim of converging on one mechanism that works well
    • Options include wiki-based mechanism (e.g. GONUTS, immuno and cardio pages), ORB or similar tool, web form, etc.
      • Plant Physiology (TAIR), J. Reproduction and PLoS Genetics (senior editors at Jax) all good candidates for initial exploration
      • Pascale has a contact at Elsevier that we can follow up once we see what happens with the smaller-scale pilots
  • Tanya's presentation (given at Biocurator mtg and MGI) provided a good summary of considerations; invite her to present it to GO managers, probably via Webex + conf call.

Individual Manager reports

Ontology Development

  • Regulates: David and Tanya will work on regulates next week. Need a good definition of what the 'regulates' relationship means; might have to be more specific than the regulation term defs are at present. Will have 'regulates' rels between MF and BP, and between BP and biol quality, and other groups will want to use the relationship.
    • David & Tanya are keeping track of rules they're using as they correct violations; hope 'regulates' rel definition will fall out from those rules. Want to use 'regulates' consistently (another point to discuss next week, and maybe also at OBO REL meeting in May).
  • If time permits, have Chris run reasoner during Jan. 11 meeting to find missing relationships and clean up relationships generally.
  • Sensu is almost done; ribosome terms defined based on location rather than subunit composition; handle proteasomes similarly.

Changes in go/scratch/ directory; find out whether Jen made them live (when she returns next week).

Action: Midori to follow up on fungal terms with Val and Maria.
  • Work on electron transport is going on following conf call (David, Jen, Pascale, Jim, Michelle, and Debby Siegele)

Outreach / User Advocacy

Jen away

We had a very informal discussion of Google Mail spam threading and tricks for finding real messages in gohelp spam.


Chris away


  • focus on getting AmiGO release out
  • work continuing on ORB
  • making database release production cycle less painful
  • tool for ref genome annotation using TreeFam (joint proposal with Paul Thomas goes to council this month; fingers crossed!)

Reference Genomes

Have almost all sets for the orthology analysis; Kara will use whatever's available as of Jan. 31.


Meeting with Larry Hunter on Jan 11th to look at GO consistency (Suzi, Chris, David, TAIR folks), as noted at last call.

Relationships - meeting planned for May 19, 2008; Suzi will draft agenda today

discuss relationships to add, and how to implement them, and how ontologies interrelate
Larry Hunter very interested in adding lots of new relationships (of which many are quite specific)

Question to ponder: what is relationship between process and phenotype?

also possibly relevant: MA & Suzi have grant proposal in to fund further PATO development
GO curators trying to keep 'regulation biological quality' terms consistent with PATO (Suzi approves wholeheartedly)

Collaborations and Interactions, active and new

Operations and Procedures

Staffing and Personnel

Amina Abdulla is leading contender for OBO-Edit job. Midori, Jen and Melissa Haendel talked to her last month, and were generally favorably impressed.

Budget issues

NIH grant: Peter Good granted extension to Jan. 15 for Year 8 paperwork submissions; Judy thanks everyone who helped.


  • David working on cardio paper
  • Judy helping Erika with muscle paper
  • Pascale working on ref genome paper; will request contributions from various curators, etc. and send draft.

Next call

January 16, usual time. Agenda: Midori; Minutes: Pascale.

Summary of Action items

Carried over from Dec 19:

  • Chris: Draft proposal for GO slim maintenance.
  • Pascale, Jim et al.: Continue discussing wiki-based annotation tool.
  • Jen: Organize conf call on gohelp technology.
  • Pascale (and rest of annotators): Continue improving annotation SOPs
  • Judy: Contact sea urchin db.

New Jan 2:

  • Software group and annotators: Test various methods of accepting user submissions for annotation; converge on best solution, and seek journal buy-in.
  • Tanya and managers: Schedule Webex/call for Tanya to present her annotation-acquisition talk.
  • Midori: Follow up on fungal terms with Val and Maria for sensu work.

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