Quarterly Report August 2006
Annotation Outreach Working Group Quarterly Report - August 2006
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.