Managers 11Mar09

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Agenda/chair: Midori
Minutes: Jen

Present: Suzi, Judy, David, Midori, Jen, Chris.

Action items from Feb 25

  • Jen: continue working with Doug (and occasionally Judy) to set up phone and video for the Oregon GOC meeting.

In progress

  • Pascale: Organize conference call on usage of tricky GO terms; include ontology editors and annotators (both ref gen and broader annotation list).

carried over

  • Jane: Wikipedia Gene Ontology page on Web Presence agenda.

Who is going to update wikipedia page?
Chris will talk with Amelia and Jane.

  • Judy: Send annotation column 16 & 17 documentation to managers for approval.

Hangup is getting the docs written and up.
There is a wiki page for each column and docs should be consolidated on the wiki.
Chris feels there is a lack of engagement and wonders is this is because people don't completely understand the scheme?
People in charge of annotation should produce a test annotation file and send to Chris, and he will look over the files and help them with the files.
Maybe send a request to the list for these test files? (Reference genome group list.)
Action item for Chris: write to list to ask for these files.

  • Pascale, Chris: Finish and circulate gp2protein file documentation.

In progress.

Discussion items

Oregon GOC meeting

Confirm decision to use Stanford WebEx account
Yes, to be run by Mike.

Participant list now has as many people offsite as onsite.
Meeting will be very different from usual.
We should consider how to accommodate this.
All groups are represented one way or another.
About 30 people in total.
Biggest concern is that Pascale isn't there for reference genome project.

Timing:

Tuesday morning needs to be ontology development to get Midori and Tanya both present.
Maybe have OBO-Edit breakout session on Monday morning early?
Action item: Jen to ask Amina if she will be there Monday morning.

David:For the talks that we have been asked to give we need to know how much time is allotted so the talks can be adjusted.

Plan for meeting timing:

Tuesday am: Ontology development

Order:
David
Midori
discussion
chris software + discussion

Tuesday pm:

outreach report

How much of each section should we use for reporting and how much for discussion?
Judy: maybe one or two slides on progress reports
then questions to be addressed by the group.

Maybe put organization and management first in each session:
highlights of progress, then lead into work in progress.
more or less detail can be included depending on the time available.

Monday pm: annotation

Action item: Judy will put that first pass agenda on the wiki.
Action item: Suzi do same for reference genome agenda?


Wiki

At the moment, the progress report links at the bottom of the Consortium Meetings page are a mishmash. Problem is we need a page to collect all progress reports; then the meetings page can link just to reports prepared for meetings.

Judy wants progress reports -- and list of publications, talks, etc. -- to be much easier to find. (General agreement.)

Action item: Midori will create new progress reports page, organize progress report links, and have Mike C add links to the left-hand navigation bar.


Book chapter

Invitation to contribute book chapter on ontologies for "Knowledge-Based Bioinformatics: From Analysis to Interpretation" (Marco Ramoni and Gil Alterovitz, eds)
David suggested that he, Tanya, and Chris might do something on the regulates and/or QC work they've been doing.
Action item: To be considered amonst these volunteers further.

Topics?

talk about knowledge driven + annotation driven + logic driven ontology development.
Action item: block out a morning with Judy and David to get a draft to send to the managers.

Midori will write to book editors with update.

Discussion of priorities in ontology development:

We should track metrics on which general processes are missing. David checked with molecular biology of the cell and we are doing pretty well by chapters and subject headings.
How do we prioritize? Do these headings help?
How about we rerun Gil's analysis to see if the fitness of the terms has improved, with all the ontology changes and the annotation that has been done. We have added thousands of relationships.
This could produce another paper on evaluating ontology with information theory.
Chris: it is easy to do this with today's GO but it is hard to compare with older ones. This is a thing we can do on todays GO with goose. Would be good to do once a year and store.


Jen - funding probem discussed

Action item: PIs will discuss and get back to Jen almost immediately.
Ideal thing would be to get funding for Jen to concentrate on OBO-Edit programming, but with some ontology editing.
Action item: To take into account 9 year rule at EBI Jen will find out about options for paying bench fees to remain at EBI after 9 years.

Jen - New collaborator

A computer scientist called Satnam Singh (Microsoft Research, Cambridge) is possibly interested to collaborate on speeding up incremental reasoning in OBO-Edit. If we could get incremental reasoning fast enough that we could have it turned on during ontology editing, then this would be a huge advantage. Would you be happy for me to go ahead and explain the problem to him, to see if he is interested to pursue this further? Clearly there would have to be very solid agreements about the work remaining open source, and in the public domain, but I could discuss this aspect with him and report back.

Action Item: Jen - Yes, follow this up with Satnam.

Action items

  • Jen: continue working with Doug (and occasionally Judy) to set up phone and video for the Oregon GOC meeting.
  • Pascale: Organize conference call on usage of tricky GO terms; include ontology editors and annotators (both ref gen and broader annotation list).
  • Jane: Wikipedia Gene Ontology page on Web Presence agenda. Who is going to update wikipedia page?
  • Chris will talk with Amelia and Jane about Wikipedia's Gene Ontology page.
  • Chris: write to reference genome list to ask for test annotation files for column 16 & 17.
  • Pascale, Chris: Finish and circulate gp2protein file documentation.
  • Mike to run Stanford webex for Eugene meetings.
  • Judy will put first pass Consortium meeting agenda on the wiki.
  • Suzi do same for reference genome agenda (with Pascale).
  • Midori create new progress reports page, organize progress report links, and have Mike C add links to the left-hand navigation bar. DONE
  • Book chapter to be considered by Tanya, Chris and David, with Judy and David meeting to put first pass draft together.
  • Midori to respond to book editors. DONE
  • PIs will discuss Jen's funding situation and get back to Jen immediately.
  • Jen to find out situation with paying bench fees to remain at EBI after 9 year period, and forward to PIs.
  • Jen to follow up with Satnam Singh on reasoner optimization.