Quarterly Report August 2006

Annotation Outreach Working Group Quarterly Report - August 2006

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Progress by month

April

Initial report/plan submitted to GO-top - 13th April (Jennifer)

Evelyn Camon working with Dave Burt (Roslin Institute) on finalising chicken
grant proposal.

Evelyn Camon working with Alex Evans (University College Dublin)
on finalising cow grant proposal.

Mailing list for outreach group set up, people signed up. (Jennifer, Mike)

Communication with Medaka fish group that are already doing manual annotation.
(Jennifer)

Annotation meeting invitations sent to full list of outreach contacts
(Jennifer). (See below for more information about annotation camp.)


May

Discussions start on mailing list.

Group members briefed on history and current status of outreach work. (Jennifer,
Evelyn)

Policy discussion begins.

Visit to GlaxoSmithCline (Jennifer, Erika Feltrin). They are interested but are waiting
to see the results of Erika's work on Neurogenesis terms before proceeding.

Response to drug discussion. The discussion was successfully resolved and Erika
Feltrin is taking this forward from her office in Italy.

June

Outreach IRC meeting.

The initial outreach plan was written by me in isolation due to shortage of
time, so on getting everyone together we started from scratch and asked what
everyone felt should be a priority.

The group were keen to look into getting an annotation tool written, and some
clearer criteria made up on the nature of associate and member status in the
consortium. I took these points to the management group for discussion.

There was a long delay in getting feedback during which Alex made a great deal
of headway into discussing what could be done to make a really useful tool. All
of the discussion is archived in case it is useful in future.

When feedback was received, the PIs said that that there are insufficient
resources to look at making an annotation tool just now so we abandoned that
route as requested.

With respect to the associate question they said that there was nothing more
that they could write on the website about associate status. They suggested that
any questions on associate status should be passed to the GO-top list, so we are
adopting that policy. Some members of the outreach group still have considerable
concerns about this question but we are hoping that these will be resolved as we
send specific questions to GO-top and hear their responses.

The PIs requested a new priority list for 2006. The working group had a
conference call and compiled a new list. The list was sent to the management
group but no comments have come back so far (August).

Work from the outreach group is largely on hold until we get feedback on
priorities, partly because people are on vacation, and partly because we don't
want to use valuable time working on things that may not be a priority from the
point of view of the PIs.

Raymond Lee outreached at Society of Nematologists held in Hawaii, June 2006
He distributed Ranjana Kishore's custom designed flier and got a moderate amount of interest.
This was the first exposure for GO at a Society of Nematologists annual meeting.


July

Fiona McCarthy has done a lot of outreach work. I (Jennifer) discussed with her
the idea of her joining the outreach working group but we decided that at this
stage it might be better for her to devote time to getting her annotation to the
stage where she is able to train other annotators. This would be a very useful
thing for the future of AgBase so is currently a priority. Fiona will continue
to send information about her outreach contacts to the outreach group.

Communication with PseudoCAP (by Jennifer) about ongoing annotation submission.
They have agreed to send annotation in a fully compiled gene_association file
format at least once a year but more often if they can manage.

August

Update on Grants from Evelyn at GOA:

GOA/Roslin BBSRC Grant application for 2 Chicken GO annotators received three
very positive reviews and one slightly negative.
Prof. Dave Burt has responded to the comments and they are now awaiting
the BBSRC decision.

GOA/UCD Irish Dept. of Agriculture Grant submission to support 1 bovine GO
annotator and 1 PhD student has been temporarily halted as they thought they had
not enough research element to it. It was agreed to submit it in 2007 instead.

GOA/MGI/UCL Grant Application to be submitted to Wellcome Trust mid September
2007 to support 3 Human and 1 Mouse GO annotator. Ruth Lovering and Evelyn Camon
are writing the grant. This grant does not expand the Human GO annotation effort
it would merely keep it at current levels.

GOA BBSRC Grant application being made by Nicky Mulder to develop QuickGO tool
for batch services and to resolve users multiple identifier problem.

General

Outreach at Conferences Planned for the future

GOA considering whether to send curator to HUPO 2006 as EBI has a stand(Nov 2006)

Evelyn (GOA) and Jennifer (Ed Office) to attend
ARK-Genomics 6th Farm Animal Functional Genomics Workshop, 27th & 28th
September. Cambridge, UK.

PAG - I am wondering if it would be better to ask curators in the US to handle
PAG this year and I (Jennifer) can outreach at an equivalent meeting in Europe. This would
save a lot of travel time and travel funds.

Database access issues

The outreach group are keen to get access to the outreach database but I
have not yet been able to find a way to give them this.

I have done some more work on the database schema and the database is now fully
functional. All information on collaboration between groups has been removed
from the database and is held in an ontology file instead. I am currently
working through the text file moving the information to the ontology and
database.

I am in communication with Mike Cherry to try to find a way to make the database
and ontology available to the outreach group. I am also in communication with
Rex about whether the ontology and database might be of use to the reference genomes group.

I will start outreaching to new groups by e-mail again once I have all the
information about current contacts entered into the database.

Annotation Camp

Throughout the last three month period a great deal of work was done at SGD
in setting up the annotation camp and this was a huge contribution to annotation
outreach. Karen, Eurie, and Rama were the main organisers.

My allocated role (jennifer) after the annotation camp is to keep in touch with
the people who attended and ask if they need further help and whether they are
ready to contribute annotations. The attendees were briefed to expect my mails,
as last year when I tried to follow up with groups that were trained they seemed
to feel very under pressure and unwilling to communicate.