Managers 20Jun07

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Participants: Judy Blake, Eurie Hong, Suzi Lewis, Chris Mungall, Jane Lomax, Jen Deegan (nee Clark), Rex Chisholm
Agenda/Chair: Chris Mungall
Minutes: Midori Harris

Review Action Items from previous meeting

Suzi: Forward John's versioning write-up to the group

Done.

Reference Genomes group: Review meeting agenda that Rex sent out. Rex: Forward reviewed agenda to managers.

See Ref Gen report below; agenda on its way to managers.

Mike: Check with Kara at Princeton about venue for Ref Gen meeting.

Phone call on Friday to sort this out (Mike, Judy, Kara).

Chris: Check with John about OBO-Edit bugs (for GO-Cell cross-products).

Point was to get next beta (i.e. OBO-Edit 2.0) up and running; first couple beta(s) are out but still rather buggy.

David & Chris: Discuss writing a paper on the GO-Cell cross-products.

Carried over.

Amelia (via Midori): Link GO database documentation to main web page.

Done.

Eurie, Chris, & Jane: Continue to follow up on GO Tools compilation & contact with Stefan Goetz.

Followed up briefly; Stefan's not interested in maintaining his own list; his was a one-off for a paper. Only thing to do is check back when paper is published to make sure we have everything he has.

Rex: Find out if Ref Gen annotators are conscientiously submitting new term requests.

Email sent; a few responses came, and said no problems with request sub per se. Rex asked Pascale to graph request activity; it revealed an early burst and then a decline. Rex is forwarding the data to managers.

Chris mentioned XML tools to do this sort of mining (but I didn't catch all details).

Jane: Put RSS feed information from Colin Batchelor on the wiki. (Note: the action item in the minutes says "Put screenshots on the wiki" but Jane recalled the discussion mentioning Colin's email, not screenshots.)

Colin's email is now on the wiki.

Also got clarification from Suzi: "Screenshots" refers to material to go in slides. New action item for Jane.

Action: Jane to take screenshots of RSC markup and RSS feeds and 
        put on wiki for people to use in slides.

Everyone: mention RSC's GO markup and RSS feeds in GO talks.

Assume that people will do so.

Jane: Look into using an RSS feed to post daily ontology changes to the outside world.

GO website tracker item created.

Ben & Jane: Prepare GO workshop for Interactome meeting; Ben will attend.

Jen will do this, because Jane will be on maternity leave. Jen has talked with Ewan Birney, and the workshop will be joint with Reactome. Dates: Aug 29-Sept 1.

EBI staff: take GO flyers and GO newsletter to distribute at ISMB/ECCB.

All in hand.

Judy: Launch a web-based journal club to review relevant publications about GO.

Not done yet, but demo of alternative to Webex at jax coming up on 29th. Still interested!

Individual Manager reports

Ontology Development

  • Incremental progress on things reported before:
    • David has the cardio meeting in hand.
    • Transporter changes to go live July 4.
    • Work on RNA processing almost done.
  • Plan to resume work on cross-products, starting with GO-cell when David is back next week; Pascale will also get involved; Chris has beeen doing preparatory work.

Outreach

Judy - lots of politics; don't know whether we should send someone. Gramene?

Action: Jen to ask Pankaj whether anyone from Gramene is going.
  • Working on SOP flowcharts. Top-level chart (manual vs. ISS, IEA) proving challenging.
Jane - lots of groups have ESTs.
Action: Annotation outreach group to include EST annotation in flowchart.

Software

  • Improving Obol (relevant to cross-products, above)
  • Also see User Advocacy and Reference Genomes

Reference Genomes

  • Phone conf last week very good. Reviewed meeting draft agenda; topics include
    • How to identify orthologs
    • Metrics and how to use them
    • Software to supersede Google spreadsheets
Sohel has prototypes
    • choosing new genes
Midori - EBI Industry Programme may get involved in "druggable genome" effort proposed by some pharmas; resulting gene list may be good Ref Gen fodder. Will keep the managers informed of developments (not much expected before Sept.).
  • More meeting details in agenda (in email and on wiki)
  • Rex sent some metrics on how various groups are doing; there are 209 genes as of June; 1/3 - 1/2 of groups have completed the list.
  • Ref Gen will have monthly phone confs; alternate times so UK & US west coast equally inconvenienced.

User Advocacy

  • AmiGO 1 development coming on apace; release on target for July.
    • Seth has added the map2slim CGI, and it's being tested

Meetings

  • SGD curators going to CSH Yeast Cell Biology meeting; Eurie trying for talk slot on GO.
  • Jane - GO talk at Wellcome Trust Advanced Course on functional genomics on Monday.

Collaborations and Interactions, active and new

Operations and Procedures

Staffing and Personnel

Budget issues

Publications

  • Current protocols article update: opted for actual deadline of October 15th (tho it will say Nov. 1 in publisher's sysetm. Judy and Midori will be in touch for content contributions!
  • NAR database issue: we definitely want to do an update. Limit is 4 pages. Ideas:
    • AmiGO new features
    • Suzi: look at newsletters for ideas
Judy: good idea -- that will focus on what's new, and give us 4 pages
  • OBO-Edit applications note published.
  • Ideas for standalone papers:
    • Ontology content changes (including cross-products).
    • Reference Genomes effort.

Other Current Topics and Concerns

Next call

July 18 (the 4th is a holinday in the U.S.), usual time. Agenda: Midori; Minutes: Chris.

Summary of Action items

  • Jane: Take screenshots of RSC markup and RSS feeds and put on wiki for people to use in slides.
  • Jen: Ask Pankaj whether anyone from Gramene is going to rice meeting.
  • Annotation outreach group: Include EST annotation in flowchart.

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