Managers 28Feb07

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GO Managers, Weds. February 28 8 AM PST / 10 AM CST / 11 AM EST / 4 PM GMT

Agenda/chair: Midori Minutes: Rex

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

Specific items (with relevant management groups):

Public GO MySQL interface at EBI (Software, User Advocacy, maybe Operations)

CM: This will be a mirror with a port open for SQL queries. Chris suggested a simple password protection should be used to reduce hacking opportunities.

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

JL: go-refs would contain name and affiliations which the comment field would point to. When we switch to OBO 1.3 it will have its own field.

SL: could we just store the emails by having a url point to the email text?

CM: needs a tool to make it easier

MA: could this be solved with a field in database that points to a table that contains names, id and affiliation?

SL: that approach tracks credit, but not provide history of the term which email links would

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

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

JL: circulated draft. DH: problem with unknowns will go away over time, so maybe its not a big issue

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

Non-public CVS repository, e.g. for annotation outreach data (Annotation Outreach, Software, maybe Operations)

Obo files containing outreach data.

RC: Use wiki? MA: just save a new file each version and use the wiki

Should GO be represented at JGI users meeting? Rama has volunteered.

SL: should be in touch with them. Not clear how relevant GO would be, but would provide a way to maintain contact.

MA: Left up to Mike and Rama. If Rama goes she should be briefed. Jane to send an email to JGI as follow up.

GOC meeting minutes: has everyone commented?

MH: everyone should take a final look.

**The usual topics:

Review Action Items from previous meeting

New Feb. 14:

Associate a date (more precise than year) to GO_REFs,especially those for meetings

MA: agreed to a date

Judy will figure out which funding pot to use for the March MIT meeting

JB: done. Arrangements thru Jax.

At least a week before the GO-MIT meeting, look at documents from Jonathan Liu again. Schedule conference call. [March 8, 4pm GMT/8 am PST proposed]

JB: Internal wiki page. Good agenda.

JL can't make March 8; email to reschedule conf call.

David will book rooms at the MIT hotel. All participants, please email arrival and departure dates to David


Eurie to put list of meetings to consider on wiki


Jen, Jane, Eurie to confer about wiki pages, etc. to manage conference attendance


Carried over from earlier:

Google calendar - everyone to fill in their meetings.


Webex - complete purchase, issue passwords.

JB: contract and need to finalize in the next day or two

IMG mapping (Jane)

JL:MA: will meet on Friday.

Individual Manager reports

Ontology Development

update on sensu revamp (in progress;

DH: conference calls on sensu terms, about half done. Most insect related. They are being pursued with fly people. Also worked on cuticle terms and eye development. Behavior nodes are a difficult.

CM: major rearrangements resulting from removal of sensus have broken tools. DH: eye domain was indeed reorganized. Mostly definition changes though.

Cardiovascular conference underway. Already have comments from Ruth, Simon and colleages arrangeing meeting details. Using strategy used for neural development.

DH: Links to function and process. Tackle biochemical pathways first. Want to capture order of functions in a process. DH drafting emails to enlist participants and then will submit portions of the GO for revision

MA: how to capture order?

DH: need a process in the database perhaps using sequential entries and pipes?

SL: should use resources such as Reactome, kegg etc.

CM: Could we do that automatically to produce tab delimited file

Action Item: Chris will try to do this automatically from Reactome, IMG, etc

JL: how to deal with differences in the same pathway in different organisms?

DH: need a separate process for each one

JL: will be a lot of them

MH: discussed assigning SF entries to curators based on knowledge of relevant biology


JC: working on report


CM: software group will start having regular meetings in the next week or two. Ben working on database loading optimization, AMIGO query issues to improve SQL queries.

Reference Genomes

RC: March genome targets released. Users were reminded to maintain the organization of the “top” page at least as far out as the publication column to allow consolidation of data.

Based on suggestions from the group, the March targets include clustering of genes associated with a particular gene. This was a great suggestion that will allow us to assert a disease has been “completely” annotated.

Need input on database requirements. It is clear that the Googlespread sheet approach is not robust enough for a long term solution.

User Advocacy

JL: new newsletter came out.

SL: Need to better highlight the newsletter of the GO web page.

JL: starting to get more help queries, web form seems to have helped a lot


cardiovascular ontology development


honey bee genomics

SL: to contact honeybee folks

DH: sensu changes might impact honeybee so they should be encouraged to propose new terms

DH: should we consider a behavior ontology?

CM: if so it should be consistent with GO standards

JB: should be seriously considered

Collaborations and Interactions, active and new

Nothing new

Operations and Procedures

Nothing new

Staffing and Personnel

Nothing new

Budget issues




Other Current Topics and Concerns