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


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.


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


6. Staffing and Personnel


7. Budget issues


8. Publications


9. Other Current Topics and Concerns