Managers 19Dec07

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GO Managers, Weds. Dec. 19 8a.m. PST, 9a.m. MST, 10a.m. CST, 11a.m. EST, 4p.m. GMT,

Agenda/chair: Jen

Minutes: David

Present:

Review Action Items from previous meeting

Summary of action items:

  • Chris will write up a formal proposal regarding the removal of GO slims from the public file, and send it to the manager's list in the first instance. This will be done.
  • Pascale will contact the various groups with wiki-related annotation tool technology to discuss how they can work together on this. [in progress]. We talked at the biocurator meeting and this is getting coordinated. There are still questions about outside vs. inside GO wiki. Suzi says that this coordination is in the plan for one of the releases, but there are some things that we will want to keep on some wikis and not others.
  • Jennifer to initiate conference call on gohelp technical topics. Resolving issue 1 at a time on e-mail. [in progress]
  • Jennifer will call an annotation-outreach meeting in a couple of weeks to discuss the changes in the annotation-outreach effort. They will stop having meetings for now. [done]
  • Pascale will take the Annotation SOPs to the reference genome group and web presence group for improvement. Mike is interested in getting some general annotation calls happening. We are very interested in this and resolving issues at 'virtual' meetings rather than having e-mails. Will be one of the first topics of the annotation group conference call.[in progress]
  • Jennifer is to include work of the web presence group in the advocacy monthly reports. She will contact Ben, Rama and Amelia to ask them to contribute information to the report. Amelia is sending reports to Jen. [not yet done]
  • Judy to get back to Midori about Current Protocols paper. [done]
  • Judy will contact the new Sea Urchin database to see whether/how/who will do GO annotations and how to help them.[in progress]
  • Jen will start collecting information for the annual report from all groups using GO: collect talks, posters, tutorials, etc. Judy still needs to add her part.[in progress]
  • Pascale: [annotation documentation] add literature annotation decision tree on the web (seen at consortium meeting). Amelia did it.[done]


Current Topics and Concerns

  • (Pascale): Tanya and Eva (TAIR) had the following suggestion: "We thought it would be good to propose to either GO or GMOD (or both) that GO/GMOD develop a generic GO (or, more generally, OBO-compliant controlled vocabulary) submission module that could be plugged into many/any online journal submission workflows. From a GO perspective, if we (GO) developed the module, we could control exactly what information we'd be getting from the authors. If our collaboration with Plant Phys takes off and goes well, it should be easy to convince other journals to go the same way, especially if they don't have to engineer their own software. " [action item] We should keep track of this.

Individual Manager reports

Ontology Development

Regulates is almost done. Tanya and David have resolved almost all of the regulates orphans and we will finalize the product while David is in CA in January. At that point, we will put to gether a plan to go live with this project.
Sensu is almost done. Jen and David have been working with experts to resolve the Sensu terms. After the ribosomal terms are taken care of tomorrow, there will be less that 10 left.
Electron transport:A large rearrangement is being undertaken by David, Jen, Pascale, Jim, Michele, and Debbie Siegle
Transport work will start again in January with groups from the UK, America and Australia.

Outreach / User Advocacy

MGED Should we send representatives to MGED 2008? It is in Italy in September 1-5. Gavin Sherlock wanted to know as he is considering it just now. We don't know, but it depends on how much it will focus on GO.

Please see these monthly reports:

outreach http://gocwiki.geneontology.org/index.php/November_2007_Monthly_Report advocacy http://gocwiki.geneontology.org/index.php/November_2007


Software

AMIGO is up on the development server. There has been an obo-edit release through Naomi. There have been a few issues with sequence loading. Ben and Stan are working on that. The GP2protein reports are a bit out of date, we need to work on this as they become more prominent. A new person has started at dicty and will work on the reference genome tracker.

Reference Genomes

We are ready to start the orthology analysis. Kara would like to run the analysis over the holiday.

Meetings

Larry Hunter will meet with us on the 11th to look at GO consistency (Suzi, Chris, David, TAIR folks). We will check to see if we can stream this meeting off site.

Collaborations and Interactions, active and new

Operations and Procedures

Webex VOIP, probably not.

Staffing and Personnel

New Dictybase programmer started at the beginning of the month. Still looking for John's replacement.

Budget issues

Publications

Agenda item from Emily Dimmer:

'Practical Proteomics' journal has asked for a paper reviewing the GO resource. This publication will focus on applied use of the GO, particularly on the annotation resources, examples will have a cardiovascular slant (as per the British Heart Foundation grant that Ruth is now working on). This has come about due to Ruth's contact with Mike Dunn (Editor) who is co-chair on the HUPO Cardiovascular Initiative. Ruth and I will be the main authors of this paper.

There will also be an editorial in proteomics.