Managers 5May06

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GO Managers call 5 May 2006

Calling in:

  • David Hill
  • Midori Harris
  • Eurie Hong
  • Jen Clark
  • Mike Cherry
  • Rex Chisholm
  • Suzi Lewis
  • Chris Mungall
  • Michael Ashburner

Notes: Midori will collate

Agenda Items:

  • Working Group Documents
    • Overlap between David Hill’s and Midori’s Groups
Merge into a single group under joint leadership? How does it change things?
Decisions are not final until Midori and I agree.
Members of the groups right now are divergent. Will these merge? Yes.
Midori and David will come up with a revised document. Channels of communication will be written out.
Still need to run by Judy
    • Community advocacy
Does Eurie have time to take this on?
Jane will co-lead this group with Eurie; they will revise the group document
    • Annotation Team
Rex will revise the document to address annotation consistency
We should think about this
  • Outreach
Chris will look at Jen’s database in May
What about teaching resources
Jen’s target will be for groups who want to annotate etc.
Eurie’s group will be for people who use the GO
We need to address the IEA issues and methods that can be used. Don’t worry too much about it yet. But, we have to decide on at least minimal standards for IEA annotation
Should we have an IEA competition? We certainly don’t want to develop tools ourselves.
We should have a meeting focusing on IEAs, similar to the first annotation camp. Mike Cherry is responsible for making sure this meeting happens.
Start with a small internal meeting. There are 2 maybe 3 meetings this year on automated functional annotation. We need to know what we are doing before we go outside. Do we want to be the IEA police?
  • Annotation Camp
John McMullen-work on annotation consistency during the internal part. His proposal will be sent to Rex.
Should internal session of camp include a discussion of the approach to reference genomes (consistency)
How do we get people to annotate papers for the human? How do we track this? This will be in the first 2 days.
Move forward with the ortholog visualization tool. This would be one way to address consistency.
SGD is not trying to take over annotation camp and welcomes suggestions.
Eurie asked — should we encourage specific people (e.g. reference genome group) to attend?
Chris/Suzi to ensure that someone from software group attends internal days (June 10–11)

This phone number can be used for any conference call.

  • Wiki page
We have none now. It should be a priority to have an in-house wiki.
Chris will set up a preliminary one.
It should be at Stanford
It will be open, but not advertised.
Chris, Mike, Amelia will work for this

NCBio one is at Stanford. Suzi will send out for perusal

  • Next GO managers conference call
June 2
Agenda: David will compile
Further details to follow
  • Newsletter: Gene Ontology Newsletter
Blood pressure
OBO file format
Is_a complete cellular component announcement
Upcoming meetings
Is this enough info?
The newsletter will go out within the next two weeks for the grant update.
Put GO-help email address on this.
  • St Croix minutes
Look good
Could we itemize action items from internal spots and at the end.
Can we link minutes with slides?
  • Should we have an e-mail to GO help? This way people won’t have to find the right person. Who will get this?
The people on this call will get it because we can either answer this ourselves, or should know who can.
We can rotate this responsibility.
Offloads responsibility from just Midori
Will force people to learn who does what in the project
If it goes to lots of people, who is supposed to answer?
We need to think formally about this. How do we make sure that people get answers?
Maybe we could rotate responsibility of responding
Frequency of rotation?
Keep track of what questions come in.
David will check MGI help, but keep it simple first.
Just a file or a wiki might work for now.
People don’t know what e-mail list to join, so we want to make it obvious where to write.
Maybe GO-in should be replaced.
Midori says it hardly ever gets “private” requests.
  • We need an e-mail list for the GO managers.
  • What about the April report from the GO office to GO-top? Don’t really know what this item was about.
Start to put group reports on Wiki pages.
  • Dates for change to OBO format
Newsletter dependent- at least 1 month after newsletter, newsletter people will make the decision
We need to come up with a standard for releases.
Content changes – two weeks (no new software required)
Format changes – two months? 6 weeks minimum. We want people to feel we are being reasonable.
There was a question about internal OBO version vs. external. At St. Croix we discussed having an internal version that included cross-products.

Action Items:

  • David and Midori will revise their reports into 1.
  • Jane will join Eurie as a co-leader of the advocacy group.
  • Chris will look at Jen’s database to keep track of groups that have approached us.
  • Mike will look into planning a meeting revolving around IEA annotations.
  • Mike or Eurie will send John McMullen’s proposal for annotation consistency checks to Rex.
  • Chris, Amelia and Mike will set up a Wiki page for our use.
  • Next conference call will be June 2. David will prepare the agenda
  • Eurie will oversee the newsletter going out in 2 weeks.
  • Mike will set up an e-mail list for GO managers.

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