GO Advisors Meeting
Aim of the meeting
The main focus of this meeting is to obtain our advisors views and perspectives on the work we have planned (i.e. the new proposal) and the approach we are taking to accomplish our aims.
Please add items below that you think need to be presented. When possible, please put your request in priority rank order:
Utility for Biologists
The highest priority for the GOC identified by grant reviewers and others is to enhance the ability of non-informatics biologists to access the GO resources as part of their data analysis efforts. Some of the participants in the GO Consortium provide access to GO data analysis tools as part of their MOD resource. But the GO site itself does not support data analysis directly from the site. We do provide listing of tools, but have not seen it as part of our 'mission' to support a general tool [such as GO TermFinder, for example] as part of the GOC. Should we do so? Wouldn't this be analogous to provide a BLAST server? While the individual MODs have a role to play here, the GOC is seen by some to be behind in supporting the work of the bench biologist.
- Who is the target audience for the annotation tool?
- How does the idea of an annual functional annotation tool bake-off sound to you? How would you approach it? Can it be used to keep orphaned genomes up-to-date?
- Almost everyone agrees that the GO Consortium should develop an annotation tool, [but not all people since most groups do annotation within the context of their genome annotation stream] Once we begin asking questions about what the tool should do, it becomes clear that every group has very different ideas about what such a tool should do. Groups within the GO tend to advocate for the development of a tool that satisfies their own research efforts at the moment, because that is the immediate need as they understand it. Could the advisors suggest a way of determining which of these special-purpose applications are best for the GO user community as a whole, so that we can decide how to focus our development efforts? What's the best way to encourage inter-group communication to foster collaboration on tools and minimize redundant development efforts? How can we decide whether specific, highly targeted annotation tools or general, lowest-common-denominator annotation tools would be most useful to our user community?
- This thread is
Encouraging community annotation
- How can we help community scientists to get credit for their GO work? Could we publish a short account of the work of individual content meetings with all experts having author credit? Could groups providing manual annotation of their own gene products of interest get a small publication giving an account of their contribution and of possible applications?
'Should GO capture the context of activity
Is there a facility to construct GO annotations which would capture the context in which a given gene product is associated with (e.g.) a given function? Thus, for example, instead of annotating protein X to oxygen transport [function] one might annotate:
<protein X in cell component Y> to oxygen transport [function']
At MGI we have this for cell types, anatomy and target molecules, but it is not a GO-wide policy. We capture this information in structured notes. So, for example we can make an annotation for gene product X having some function in oxygen transport in a lung epithelial cell. Our hope is that if X is also annotated to oxygen transporter activity in lung epithelial cell and plasma membrane of a lung epithelial cell, then we can draw a conclusion that X has the potential to execute a function of an oxygen transporter involved in oxygen transport in the plasma membrane of a lung epithelial cell. In the right spatio-temporal context, the function will be executed.
In order to meet our objectives, we need to present all of the material in the morning. The presentations will focus on the goals and progress of the Consortium and will reflect the new organization and management of the GOC developed through the process of writing the GO Consortium competitive renewal.
Morning presentations will be 30 minutes, plus 15 minutes for questions
The workshop will consist of these sessions:
- GO presentations: New initiatives in the renewal
- 8:00AM: Introductions (picture on display and circle everyone)
- 8:15AM: Ontology Developments (technical - Chris; biology - David & Midori)
- 9:00AM: Reference Genomes (Michael & Rex)
- 9:45AM: Outreach (Jen)
- 10:30AM: 15 minute Break
- 10:45AM: Advocacy (Eurie & Jane)
- 11:30AM: New management structure (Suzi)
- 12:15PM: Summary of issues we face: pink sheets and more (Judy)
- 1:00PM - 2:00PM, working lunch for advisors and GO-top
- 2:00PM - 3:30PM, advisors powwow
- 3:30PM - 5:00PM, feedback from advisors
- 6:00PM dinner with everyone
- GO representatives
- Michael Ashburner
- Judy Blake
- Eurie Hong
- Suzi Lewis
- Rex Chisholm
- Jen Clark
- Midori Harris
- David Hill
- Ben Hitz (representing production services)
- Jane Lomax
- Chris Mungall
- Simon Twigger
- Tanya Berardini
- GO Advisors
- Larry Hunter
- Lynette Hirschman
- Barry Smith
- David States
- Mike Tyers
- Craig Neville-Manning (unable to attend)
- Peter Tarczy-Harnach
- Ian Dix (Courtland Yockey attending)
- NIH Representative
- Peter Good
- Other possible attendees
- Monte Westerfield?
Accommodation: Silver Cloud Inns / Seattle-University Village
5036 25th Avenue NE Seattle, WA 98105 Phone: 206-526-5200