Managers 15Aug07

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Participants: Michael Ashburner, Judy Blake, Jane Lomax, Jen Deegan (nee Clark), Pascale Gaudet, David Hill, Midori Harris
Agenda/Chair: Jane
Minutes: Midori
Cameo Appearance: John Day-Richter

Review Action Items from previous meeting

Chris: Add replaced_by & consider tags to database

Chris: Write abstract for Biocurator meeting

Chris not present

Eurie: Send the document [tool standards] round to GO list for further development

Sent, so done.

Individual Manager reports

Ontology Development

  • Jen: May Waclaw have access to the internal wiki to help with the taxon-go proposal?
    • General consensus that internal wiki is only for GOC members.
Action: Jen to email taxon proposal draft to Waclaw.
  • Some discussion of the taxon proposal; see http://gocwiki.geneontology.org/index.php/Taxon_Main_Page. Judy thinks this low priority since terms used by given taxa can be generated by anyone, but some others on the April 27 conf call thought it high priority to have available somewhere in GO directory. What needs to be done is simply to decide on details of files that can be generated using the ontology and gene_association files and whether we will commit to updating these files on some regular basis and where we would make these files available.
  • David, Jen, Midori have resumed work on 'sensu' terms; hope to finish by GOC meeting
    • Judy: was there a problem with the microbial terms?
    • David: yes, lots of remaining ones are prokaryotic; problem is lck of expertise
    • Judy suggests Jim Hu may be able to help.
Action: Sensu team to ask Jim Hu to help with sensu terms for prokaryotes.
Action: Pascale to find distinguishing characteristic(s) for Dicty fruiting body development.
  • Cardiovascular physiology: David has almost finished post-meeting to-do items; the ontology file is go/scratch/gene_ontology_cardio.obo.
    • Interesting thing: this area is a tangled web of relationships -- but cardiologists confirm that the biology really is like that.
  • Muscle development: Jen has started on post-meeting work.

Outreach

  • Jennifer: Should I write a letter of support for text2go or should it come from a PI?
    • Michael A has sent one on behalf of FB.
    • Judy is writing one on behalf of MGI
    • Judy suggests Mike Cherry to write on behalf of GOC because running annotation camps is relevant.
Action: Jen to forward text2go support letter request to Mike Cherry.

Software

Chris not present

Reference Genomes

  • RefGen meeting draft agenda is on wiki.

User Advocacy

  • AmiGO release: still testing and revising interface.
  • August newsletter will be out any day now.
  • Core slide collection: sent sets to manager groups, who are reviewing/updating/revising
  • Tool standards: draft document on wiki; revision under way
  • This is Jane's last meeting for six months! Jen to take over user advocacy duties whilst Jane on maternity leave (until Feb 08). Eurie to take more of a back seat, although still involved.
  • Item from Harold Drabkin:

I'd like to suggest a new effort, which I think might be very important; this concerns the appearance of several papers that claim to analyze the efficiency and/or "correctness" of GO, etc. It is clear from reading these that the purpose, scope, and functioning of the GO are being grossly misunderstood. I think we should contact the journal editorial boards to require a member of the GOC to be a reviewer on any such manuscript. This may be a massive letter writing campaign best done by GO-Tops; My two pence anyways.

  • General agreement that it's not realistic.
  • Judy: The "how to review" wiki page will help at least for GOC reviewers.

Meetings

  • SAB: Judy is working on documents, and will send a draft around to managers to be fleshed out.
    • TBD whether individual managers will give talks at SAB, or just PIs.
Action: Individual managers to fill in progress report for SAB.
  • GOC meeting: program will probably be similar to the Jan. '07 meeting, starting with ~30 min, talks from managers followed by action item review.
  • RefGen meeting: afternoon devoted to orthology/homology; may bring in outside speakers.

Collaborations and Interactions, active and new

Operations and Procedures

Staffing and Personnel

  • Jane on leave starting Aug. 20; back in Feb '08. We'll miss her!!!

Budget issues

Publications

  • NAR database issue: David and Midori propose to organize the manuscript roughly around management areas (tho we won't actually describe the management structure itself).
    • Each manager should choose highlights from the past two years for inclusion, and write a short summary. We really mean SHORT -- anything from a sentence to one paragraph (maybe two if there's that much to report, and we have room). Limit for the whole thing, including any figures, is four pages.
    • Suggestion to use one of Mary's RefGen graphs as a figure was well received.
    • Small points from Judy: include URLs for downloads etc.; make sure distinction between ontology development and annotation is clear.
Action: Each individual manager to summarize the most important developments in their area
over the past two years, distilled down to a single paragraph. Please have these ready by
the next call!
 * David to write ontology development text.
 * Jen - annotation outreach
 * Jen & Eurie - user advocacy
 * Chris - software
 * Pascale - reference genomes
Action: Midori to collect managers' summaries, assemble into a first draft, and circulate
to managers and then rest of GOC.
Action: Midori to get the manuscript (once edited to our satisfaction) through the
submission process. 
  • Judy has been invited to submit a full-length paper to BMC Bioinformatics based on her Bio-Ontologies SIG talk.

Other Current Topics and Concerns

  • David gives a heads-up about protein complexes -- more discussion at the GOC meeting.

Next call

August 29, usual time. Agenda: Eurie; Minutes: David.

Summary of Action items

Carried over from Aug. 1:

  • Chris: Add replaced_by & consider tags to database
  • Chris: Write abstract for Biocurator meeting

New Aug. 15:

  • Jen: Email taxon proposal draft to Waclaw.
  • Pascale: Find distinguishing characteristic(s) for Dicty fruiting body development.
  • Sensu team: Ask Jim Hu to help with sensu terms for prokaryotes.
  • Jen: Forward text2go support letter request to Mike Cherry.
  • Individual managers: Fill in progress report for SAB.
  • Individual managers: Contribute paragraphs for NAR manuscript.
  • Midori: Get the manuscript (once edited to our satisfaction) through the submission process.
  • Midori: Collect managers' summaries, assemble into a first draft, and circulate to managers and then rest of GOC.


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