Managers 24Oct07

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GO Managers, Weds. Nov. 07 8 AM PDT / 10 AM CDT / 11 AM EDT / 4 PM BST

Agenda/chair: Pascale

Minutes: Jennifer

Present: Suzanna Lewis, David Hill, Midori Harris, Pascale Gaudet, Chris Mungall, Jennifer Deegan.

Review Action Items from previous meeting

  • Midori was to create a new category in the Feature requests SF tracker for OBO edit called 'documentation'

DONE

  • Chris was to write a proposal for how to deal with annotations of alternate spliceforms (including adding a new column?). Also, we need to document which SO terms are allowed (all?) in the Object Type Column (column 12).

In progress


Current Topics and Concerns

  • slims removed from the .OBO file? (Chris, Judy)

This item was mainly coming from Judy Blake and she was not present at the meeting. However, we had a discussion of the subject to try to make some headway.

Judy's initial request was that the GO slims should not be presented to the users as part of the OBO file.

On the manager's mailing list Chris had suggested the following approach:

"Note that if [...] we focus on moving towards having a true editors version distinct from public version we solve the problem. The slims can be extracted from the editors version when generating the public version and split into a separate file. This makes it easier for the editor's to maintain consistency and synchrony with splits, merges and obsoletions. "

During the manager's call nobody felt strongly for or against the idea of removing the slims from the OBO file. However people said that if Judy would prefer the slims to be removed then they would be happy with that, as long as there was an easy way of keeping the slims synchronous with the ontology. Chris's proposal seemed to best accommodate everyone's requirements.

Chris pointed out that while we have a pseudo-editor's version of the file in gene_ontology_edit.obo, it is not working well at all, as the users are downloading and using this file. He would like to try to do this again and this time make an editor's version that is only used internally.

[later...Judy: I appreciate this. I think it will result in the slims being used in better context.]

ACTION: Chris will write up a formal proposal and send it to the manager's list in the first instance.

Individual Manager reports

Ontology Development

Enzyme activity:

Midori has been making enzyme activity terms and synonyms with help from from Colin Batchelor of the Royal Society of Chemistry.

Muscle and cardiovascular physiology

Jen, Erika and David have been working on cardiovascular physiology and muscle meeting edits. These edits were made in a single branch file and the file is to be commited on Monday.

Alex Diehl is going to set up an annotation wiki for muscle as the muscle meeting participants were very keen that annotation would follow their content development work.

Wiki annotation system

We discussed the advantages of Jim Hu's wiki system and Alex Diehl's wiki system and considered whether these might be brought together in some way.

Jim Hu has made a wiki with a page for every GO term and at the bottom of each page is an annotation form that people can use to fill in annotation fields. The form then sends the annotation information on, to be checked and included in the GO annotation set. There was discussion of whether this system could be brought together with Alex's system. It makes a page for each gene product and allows users to edit in information about GO terms that are appropriate for each gene prodcut. There was concern about conflicting territory, but Chris Mungall felt strongly that Jim would be very happy to collaborate on wiki development to make one excellent tool rather than several good ones. It was also mentioned that the AmiGO/Web presence group were working on this kind of thing and that it would be good to get all three parties together to discuss how best to combine the technologies.

ACTION: As working group leader in the reference genome group (which is now resonsible for all annotation issues) Pascale will contact the various groups to discuss how they can work together on this.

Lung development

Judy has some funds left over from previous content meetings that she can use to run a further content meeting, as long as it happens before the end of the year. It has been decided to hold a lung development content meeting at Harvard on the 5th December. Many of the big players in the field have been signed up and they already have a starter graph as David had a summer student this yearmaking lung anatomical development terms. He is continuning to work on the graph, and as soon as the cardiovascular/muscle graph is committed, a new branch will be taken from the live file and the lung development graph integrated. The new branch will be in go/scratch.

Plant processes

A contact from Syngenta, UK has been in touch with Jennifer to figure out when she could visit to make some biological process terms. These terms are to describe processes that are inhibited by herbicides.

Regulates

David and Tanya are working together to fix the regulates terms. They are working on the live graph, but it is not going as fast as they had hoped. For each small thing that they try to fix they are finding that there is another 10 or so things that need to be fixed round about it. This makes the work quite slow, but means that it will have a big positive effect on the graph when it is done.

Outreach / User Advocacy

Advocacy

There have been a few technical questions about GOhelp. We should figure out how to address some of the issues and have a conference call about it. Jennifer is trying to figure out some answers to the questions before calling everyone together to discuss it.

The questions include:
How exactly is gohelp archived, and how does spam avoid being archived?
How best can we work out statistics on our success rate at answering?
How active are people at updating the FAQ?

ACTION: Jennifer to initiate conference call on gohelp technical topics.

Outreach

Giorgio Valle of the Franco-Italian Grape Genome Sequencing Project has committed to carrying out GO annotation for the grape genome. Erika Feltrin is to head up the annotation effort after she finishes her PhD, which is likely to be in January 2008. The group is located in Padua (Padova) in Italy and Erika is very experienced with GO, having carried out content and annotation efforts in neurobiology, and run a content meeting on muscle development.

ACTION: Jennifer will call an annotation-outreach meeting in a couple of weeks to discuss the changes in the annotation-outreach effort.

Pascale suggests that more work should be done on the annotation SOPs, and she will take this work to the reference genome group meeting as that group is now dealing with all annotation issues.
Someone in the reference genome group will talk to Amelia and the web presence group to figure out how best to make improvements.
ACTION: Pascale will take Annotation SOPs to reference genome group and web presence group for improvement.


Software

On the database side, Ben has set up bulk loading so that the database load is now much quicker and so they have a tighter update cycle.

A number of scripts are ready to go into production to pre-populate the database with gene products, so that the counts are by species source rather than by annotating database. The taxonomy tree stuff is also ready to go into production and this will enable users to filter by phylum and kingdom and so on. This is better than just being able to filter by annotating database, especially where there are multi-species annotation groups.

The group is also working with Trudy on how to enable multiple taxon ids to by included in an annotation for 'multi-organism process' terms.

Trudy is having a problem as PAMGO sometimes would like to fill in strain ids as well as just species ids, and if there is no NCBI strain id this makes things very difficult. They could use internal ids but as a first pass it might make sense to map up to the existing NCBI taxon parent before submitting to the main GO database. If they want this data in the public repository we need to find a way to be sure about ids and how to map internal ids to external ids.

PAMGO are also keen to use the new annotation properties column where there is a process of regulation of a gene product in another species.

Seth has been improving the graph display that Mary produced so that you can now see terms highlighted on on. He is about ready to show that to the working group. He is mostly just getting map2slim and term enrichment sorted out.

ACTION: 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.

Reference Genomes

The reference genome group is switching to a rotation system for assigning genes. TAIR are starting the rotation by doing the genes for November.


Meetings

The Biocurator meeting starts tomorrow night.
Chris, Suzi, Petra, Pascale and others are going and there will be 120 people in total.

Midori, Emily Dimmer, and Erika Feltrin are going to teach GO at a meeting Bari in Italy next month.

Judy is going to a mouse meeting in Kyoto.


Collaborations and Interactions, active and new

Operations and Procedures

Staffing and Personnel

Pascale has a date for her new programmer to start now. He will start on the 12th November.

Budget issues

Publications

AmiGO publications - Pascale has sent some comments on it. Seth is working on it now.

NAR paper is not out yet. Midori has sent an improved version of the figure.

Pascale is working on a Dicty paper just now but will be more free to work on other things once that is finished.

Judy and Midori are meant to have the Current protocols paper back the published in a week. Judy has been very busy and unable to respond, but Suzi is going to ask if she will have time soon when she talks to her in the GO-Top conference call.

ACTION: Suzi to ask Judy if she can contact Midori about the Current Protocols paper.
ACTION: Judy to get back to Midori about Current Protocols paper. [Judy asked Midori to get extension and that's been done. Revised paper now due Nov. 15. Thanks Midori]

Summary of action items

ACTION: 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.
ACTION: Pascale will contact the various groups with wiki-related annotation tool technology to discuss how they can work together on this.
ACTION: Jennifer to initiate conference call on gohelp technical topics.
ACTION: Jennifer will call an annotation-outreach meeting in a couple of weeks to discuss the changes in the annotation-outreach effort.
ACTION: Pascale will take the Annotation SOPs to the reference genome group and web presence group for improvement.
ACTION: 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.
ACTION: Suzi to ask Judy if she can contact Midori about the Current Protocols paper.
ACTION: Judy to get back to Midori about Current Protocols paper.