Managers 20Dec06

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GO Managers Meeting Minutes 20th December 2006

Present: Michael Ashburner, Suzanna Lewis, Judy Blake, Midori Harris, Jane Lomax, Jennifer Clark, Eurie Hong, David Hill, Chris Mungall, Karen Eilbeck.
Absent: Rex Chisholm and Mike Cherry.

1. Review Action Items from previous meeting

· Midori will email abstract link (go/doc/GO.references in CVS, ftp). [done]

· Chris will explore introduction of a contributions field.

The idea of this field is to provide a way for outside contributors to the ontology structure will be able to be properly acknowledged. Ideally we would like to have something that can be referenced in their cv.

We considered just having an entry in the definition dbxref. However that is really just a place to acknowledge sources of definitions.

Alternative suggestions is to have an entry in the references file. We could add a new 'contributes' field to the obo format once it goes to obo 1.3. The contributes field would point from each relevant term to a reference. The reference would describe the content meeting and list the experts who were present.

Until obo 1.3 we could do this by having a structured comment to contain the information.


action: Jane: to work out syntax for comments. Add comments.
Midori: will add go refs are required.
Alex: to make ref for immunology meeting.


The possibility was discussed that we could have an annotation tool with oboedit backend that submits direct to sourceforge. The submitter would get back a url for the sourceforge id that they could use temporarily for annotation until the go term exists.


Ongoing tasks discussed:


* Jane to merge go/scratch/IsaComplete.obo with live GO. [on hold while obo edit merge is implemented] done
* David and Suzi to work on list of experts for heart dev content meeting- [DH: some people contacted. Looking to Wisconsin group to identify a partner to work with David in the same way Doug Howe did for the CNS development content group]

This meeting is morphing topic. It is now more cardiovascular physiology rather than development. Note: Bruce can't come but can be involved long distance. He does the genmap software. We can hopefully later have a cardiovascular development meeting, but it seems like just now we are having a lot of development meetings so this one is more physiology. Meeting will be mid to late May or June. No date yet.

David is going to wisconsin early may to talk it over and to prepare the ground in the same way that he did with Doug and Cindy for the cns meeting. There is not yet a mailing list for this meeting.



* Michael to look at sex determination terms and questions about them from is_a complete work (David to remind him). (6 Dec - no comments added)
* Suzi & Chris to send new definition of "flagellum" (SF item).-[pending] (6 Dec - no comments added)
* Jane & Eurie to go ahead with including public wiki in AmiGO/web presence wg remit. [In process.] (6 Dec - no comments added)
* Conference call with ChEBI; also including Chris. [CM: chatted with someone a ChEBI regarding REX, but currently awaiting a web enabled tool.] (6 Dec - no comments added)
* Chris to look at J. Liu/MIT material.-[defered to ontology development group] (6 Dec - no comments added)
* The advocacy group will look into some type of calendar to keep track of which meetings are being attended by GOC members. [EH: found something to put on the wiki that would track these activities, but needs time to implement]

Eurie has added a calendar extenstion to wiki. It is not totally satisfactory because you cannot view more than a week at a time.


2. Individual Manager reports

a. Ontology Development Isacomplete is done and waiting to commit.
Merge done.
Mailed round for people to look.
Comments from a few people. Now being addressed. Keeping track on google spreadsheet.
Want to commit and then carry on editing live file.
Chris still finding missing isa links.
In each case we found the best isa parent but it is not exhaustive. Still needs a clean up.
We have found that it is impossible not to have isa diamonds.
Chris will put in implied links with logical defs.
After it has gone live we will do regulation terms.
Wiki has been rearranged to be better.

David is in communication with Jonathon Liu on engineering.
There will perhaps be a meeting to see if some changes can be implemented based on the work he has done.

b. Outreach Jen attended the Aspergillus annotation jamboree. It was a good meeting with 45 biologist annotating GO with their genome. This was mainly set up by EuroFung and Jennifer Wortman of TIGR.
They got about 500 annotation. The biologsts really liked AmiGO but were unwilling to read def and mainly just annotated to term names. They need a new ref for a generic ISS. They were mostly making ISS and IDA annotations. This meeting was a good model for further meetings.

c. Software Amigo 1 released.
Chris is doing term enrichment in perl api.
obol 1.2 syntax is being clarified.
SGD looking at speeding up database loading.
New code is being written for loading GO.xrf_abbs file into database.
b14 of oboedit available now.
Metadata for all obol ontologies is being put together. This is now parseable.
Now can automatically generate html or xml format.

d. Reference Genomes Rex absent


action: Can Rex tell us when the next reference genome list is coming out. (Before or after consortium meeting.)


e. User Advocacy Working on AmiGO 1, now released.
Working on new AmiGO and how it will work.
Set of workflows produced:
http://gocwiki.geneontology.org/index.php/AmiGO_workflows

AmiGO working group are thinking about how the whole website and AmiGO can work together.


3. Meetings

* Consortium meeting in Jan.

PIs are working on the agenda by round robin. Sending to us when done.
Now 7 pages long. Not being done on wiki.


action: Can Mike find out how to upload a doc or pdf file to the wiki? Suzi was unable to do it.

oboedit demo after consortium meeting.
Teach:
merging
cvs clash resolution
jen
action: book a room.
We will have practise, and then actual editing.

4. Collaborations and Interactions, active and new
5. Operations and Procedures.
6. Staffing and Personnel.
7. Budget issues.
8. Publications.

Instance paper cut down yet again to be submitted elsewhere.
Now 6.5 pages. Sent to 'Bioinformatics'.
The stuff cut out is now supplimental data.

9. Other Current Topics and Concerns.

a. public GO wiki scope. Eurie and Jane.

Various suggestions from earlier have included the following suggestions:


1. a page for each GO term that's linked from AmiGO?

2. a page for each gene that's linked from AmiGO?

3. a page for each of the tools that are listed so developers and users can have a forum for discussion?

Progress in meeting:

Need input from group on how this should be used.

Do we want comments on individual gene products and genes or terms or just a discussion forum? chris: exisiting wiki software is not ideal for this as there would be too many pages. Maybe just add wiki style stuff to AmiGO so people can comment?

What do we use exisiting pulic wiki for? We could use this for our own stuff that is not firm enough for real docs but that we want to expose to general public. We could say: 'we are working on this: what do you think?' We don't want the wiki to evolve organically as it might get out of control.

Alex is putting community annotation pages for immunology on there. Annotating individual genes. Oboedit wiki is on the public go wiki. Maybe have a page for each of the tools that are listed. (Resounding 'Yes!') Community annotation pages?

Physiology: will we have wiki pages like the immunology ones? David hasn't thought about community annotation. He has concernes about quality. Jen requests page for biologists to submit ideas for general ontology content revamp. She has a contact with big ideas for transport who might use this.


c. On-the-Fly Species Gene Annotation. Jennifer. Would have been useful for the annotation jamboree if we could have got a complete download easily of just the aspergillus annotation (IEA and manual) from the GO website. In the St Croix meeting it was agreed that Mike would write a script that would allow users to type in a taxon id and be given a file (filtered from the Uniprot or GOA file) that would just contain all the annotation from that taxon. Has their been any progress on this and is there a date for expected completion? This would be very helpful for the outreach effort.
action: Mike please get back to Jen with an expected date for completion of this.

d. Creating a mailing list so non-consortium members can sign up for curator requests emails. Jane. Michelle suggests a mailing list that people can sign up to to get the sourceforge digest. Agreed.


action: mike: create mailing list midori: add address to sourceforge script. Put on everyone who has been in a content meeting?

Remind people that subject line of sourceforge requests is very important. 'New term and definition' is not good.


Action items

Jane: to work out syntax for comments that will temporarily capture references for all expert input. Add comments.
Midori: will add go refs for contenet meetings and expert input as required.
Alex: to make ref for immunology meeting.

Rex: tell us when the next reference genome list is coming out. (Before or after consortium meeting.)

Mike: find out how to upload a doc or pdf file to the wiki. Suzi was unable to do it.

Jen: book a room for oboedit demo.

Mike: please get back to Jen with an expected date for completion of the script that will allow people to download just the annotations from a single taxon from the UniProt file.
To go on the GO website.

Midori: create mailing list for people to get sourceforge item listing.
Midori: add address to sourceforge script.

who?: Remind people that subject line of sourceforge requests is very important. 'New term and definition' is not good.


Next meeting 8 am Pacific, 11 noon Eastern, 10 am Central, 4 pm UK. 3rd January.