Managers 14Mar07

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GO Managers Phone Conference

March 14, 2007

Participants: David Hill, Judy Blake, Chris Mungall, Jane Lomax, Midori Harris, Jen Clark, Eurie Hong, Suzi Lewis, Mike Cherry


1. Specific items:

Crediting contributors: how to reference individuals (Ontology Development, User Advocacy)

--Action Item: Chris and Jane will make a proposal on how best to do this. – Ongoing.

Standards for including tools on GO Tools page (User Advocacy, Software)

--Action Item: Jane will circulate to GO list for comments then to GO-friends after revision.

GOC meeting minutes: has everyone commented?

--Action Item: everyone should take a final look. FINALIZED.


2. The usual topics:

Review Action Items from previous meeting:

Webex - complete purchase, issue passwords.

--Action Item: contract and need to finalize in the next day or two – DONE

Outreach report circulated—DONE.

--Action Item: Chris will try to automatically mine biochemical pathways from Reactome, IMG, etc .

CM:set up mailing list

CM: Nice way of linking GO terms and other resources.

DH: Liked tool Chris pointed everyone to. Perhaps use Webex to discuss further and demo tool.

Individual Manager reports

Ontology Development

MH: meeting at MIT for GO engineering starts Thursday. There was a conference call to do preplanning. Wiki page on Ontology development. One goal to develop metrics for ontology development.

DH: Sensu revamp. Met twice since last meeting. Used WEBEX effectively, now down to a couple hundred terms, The next batch are hard, such as oogenesis, behavioral terms, perhaps don’t need sensu. Should add specific terms instead.

CM: Should we bring in other people interested in behavior ontologies.

DH: Yes. Should it be in GO or in a separate aligned ontology? GO could hold high level terms.

DH: Often there single genes responsible, so use for annotation seems reasonable

JB: A single gene involved is not sufficient. Needs much more discussion. Useful for GO to think critically about the role of behavior in GO.

RC: needs to be discussed at the next GOC but might also want a working group

JB: supported a working group to prepare

MH: sourceforge assignment of entries is moving forward.

DH: concerned that ref genome annotators are not making more requests.

RC: need to address this with ref genome group.

MH: especially need to do this if there are roadblocks

MH: Jen, Val, Michelle working on transporters

JC: reviewed by expert and liked what they saw


Outreach.

JC: monthly report. Possible collaboration with Cancer Bioinformatics group. Evelyn putting in a cancer annotation grant.

CM: what would the topics be? Is there overlap with Disease Ontology?

RC: group of evelyn, jb, cm, jen clark to explore

JC: GO lacking process that would be affected by herbacides

DH: means plant metabolism must be lacking

JB: need to focus on plants more this way. Definitely worth following up.

DH: Contact TAIR.


Software

CM: working Michael A. to get GO to CHEbi process. Also working with REACTOME to develop a GO to Reactome mapping. Still lacking fair amount of specificity. Probably need a working group

CM: First software group meeting in 30 minutes.


Reference Genomes.

RC: new Dolan graphs were loaded onto a GO site Mar 1.

JB: need more thought about interfaces to display


User Advocacy:

JL: set priorities for June amigo 1.0 release. Include term term enrichment tool, download options, sort search results, more sophisticated search tools; filtering by species. Reorganizing GO home page to merge with Amigo page

JL: GOdatabase help queries should now go to GO help

EH: newsletter could be longer, keep the PDF 1 page but allow the web version to be long.

3. Meetings

JB:Interoperability of ontologies in march

JB: ISMB abstracts due april 6 do we want to be coordinated

JB: New program soliciting new sessions/speakers based on papers published in 2006.

MH: good idea to coordinate. Could ontology development be worth of a poster such as describing is_a completeness

JB: may be impacted by budget issues

JL/MH: GO posters will generate randome go questions is it is good outreach

EH: Fungal genetics meeting 1.5 hr workshop

JL: JGI users meeting looks like not worth a GO rep going

JL: Ontogenesis meeting next week

4. Collaborations and Interactions, active and new

JL: IMG people in touch with JL who will work on IMG to GO mapping

CM: Reported a paper on naming conventions is in the works.


5. Operations and Procedures

Nothing

6. Staffing and Personnel

Nothing

7. Budget issues

Nothing

8. Publications

Nothing

9. Other Current Topics and Concerns

Nothing