Managers 25Apr07

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GO Managers, Weds. April 25 8 AM PDT / 10 AM CDT / 11 AM EDT / 4 PM BST

Agenda/chair: Eurie Minutes: Chris

Present: all -m, -j

    • The usual topics:

1. Review Action Items from previous meeting

a. Chris and the biochemists involved in making links between function and process to set up WebEx with folks working on this project to set the stage and get a scope of the project.

ACTION: remaining

b. Evelyn Camon, Judy Blake, Chris Mungall, Jennifer Clark to explore possible cancer grant proposal.

Had a conference call. Going in for grant together. Funding for GOA. Basic GO annotation of cancer-related genes.

(Jen will send extra details for minutes)

c. PIs: should we send someone to MGED?

ACTION: still to discuss (10am)

MGED is in Brisbane this year

Mike did discuss this - does not think it is a good use of money. Jen will talk to Fiona. Fiona may be there, does not know. If Fiona was going there anyway she could give a talk.

d. Jane to set up a conference call with the folks at ChEBI to begin working with them so ChEBI can align better with GO.

Ball is rolling

e. Chris to write up a summary of the issues and reasons in order to incorporate an ontology versioning system to present at an upcoming manager's call.

ACTION: remaining

2. Individual Manager reports

   a. Ontology Development
  1. Inner ear development
  2. Sensu - set up a webex for tomorrow
  3. Spindles, mitotic and meiotic
  4. Transport
  5. Summary of MIT work has been sent round

ACTION: David circulate to wider group

David going to Milwaukee for cardio physiologist meetings. Focus ontology development meetings.

Erika has 5 muscle experts + postdocs learned to use oboedit

Erika has written Italian tutorial

(Judy joins in)

Jane: mapping IMG to GO is well underway, first pass. Prokaryotic enzymes

   b. Outreach

* Jen: should I sign up to be on the chicken committee?

Emily and Jen asked by Dave Burt + AGBase, international committee. Should both join?

Mike: gotop has no problem

* should I put a different outreach group member in charge while I am away in May?

ACTION: Eurie will talk to Rama

3 groups, ISS IEA and literature. Meet on skype instead of phone.

   c. Software

- ID mapping

- refgenomes

- amigo

- func-process enrichment

- new docs for SQL DDL

- oe 1.1 released last week

   d. Reference Genomes

* documentation of reference genome methodology

Mary Dolan new refgenomes graphs. See which organisms are annotated. todo integrate with AmiGO.

assignment of orthology: at most basic level, go into YOGY, nothing there, claim there is no orthology. Other people root around on their own. People identify things that look like orthologs, full length, recprical best hits, not just a domain. Idiosyncratic. Some people uncomfortable with sequence based approach, but in some cases it's the best we can do.

Suzi: stresses importance of writing this down

Rex: groups have different algorirthms

Chris: both protocols and evidence/source must be recorded

Sohel has created a prototype. Spreadsheets aren't working.

Judy: Mary using homologene

Judy: refgenome meeting

Rex: looking for location in Chicago, late summer?

Judy: GOC meeting already there in September

Suzi: write stuff down, must be reconstructable

Suzi: has looked at treefam code, combine w software from Paul Thomas

Judy: vertebrate set has a lot of work down, more complex adding in other groups

ACTION: Rex will get group to document process, unfiied approach down the road

ACTION: Rex will set up meeting

   f. User Advocacy

gohelp, central entry point on gmail, recruiting other people on gohelp.

webex to demo

amigo-wg, seth sent out for testing

may newsletter is being put together

3. Meetings

David: Wisconsin (see above)

David: devbio poster

Judy: ISMB, Bio-Ontology SIGs. Due May 1

Chris: Chado paper

Karen: RNA meeting @ Madison, protein feature people & Janet thornton, merging efforts

Suzi: honeybee @ CSHL

Judy: applied tutorial for international mouse genome meeting

4. Collaborations and Interactions, active and new

ACTION: Suzi will send out details on SO + PharmGKB meeting, poss meeting on sequence variations

Midori: biosapiens protein annotation ontology, will talk to Gaby Reeves

Suzi: need to coordinate on this

5. Operations and Procedures


6. Staffing and Personnel

Midori: in May GO Editors will be away

Evelyn is moving to Ireland. Will still be GOA for 6 months

new MGI curator

7. Budget issues


8. Publications


9. Other Current Topics and Concerns