December 2006 - January 2007 Report

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Plant and Animal Genome Conference XV, 2007

GO effort organized by Rama Balakrishnan.
Teaching by Rama Balakrishnan, Trudy Torto-Alalibo, Fiona McCarthy, Candace Collmer, Michelle Gwinn-Giglio, Sandra Orchard.

Collective report from the group submitted by Rama:

The GO workshop at the 2007 PAG meeting was well attended and received. Michelle(TIGR) gave an introductory talk on GO and about 60 people attended this talk. The rest of the talks had somewhere between 20-40 people. Overall I felt that we kept the audience engaged and they asked many questions (ranging from difference between ISS and RCA, benchmarks for evaluating annotations, creating GO slims, is it better to use GOst over NCBI BLAST, can you add a download button on AmiGO etc).

The PAMGO workshop and Fiona's talk about how they came to GO and what they are doing with GO was really helpful and I believe that gave the audience a real application of GO. In the future, we should always try to include presentations from biologists on how they use GO (for example, at a Neuroscience meeting we should have neurobiologists talk about their experience with GO). That is the best way to connect to the audience.

I put up a sign-up sheet and requested the audience to put their Name/ Email if they wanted GO to contact them. This has now been attended to with an invitation to join GO-Friends.

The PAMGO/AgBase booth was well attended and very successful. Overall I will say there were about 50 people at the booth and we have contact information for 25 of them. Many people expressed interest in getting involved in the PAMGO effort. These included folks who were interested in terms describing host processes during the interaction and others who were interested in knowing whether the proposed terms can be used to annotate gene products from microbes involved in interactions with animals as well.

Some questions:

1) One user who is working on the Salmon genome asked me about setting up community annotation system. I told her that AgBase has a system and the ECOLI Hub has set up a community WIKI to do this. I think she doesn't have the resources to put a wiki or an interface together. Does the annotation outreach group address this issue?

2) The PAMGO folks mentioned that while they are annotating genes from the pathogens they capture information on the host genes as well, but they only submit the annotations for the genes from the pathogen. We should have a mechanism to get the annotations for the host genes.

(These two questions have been sent to the GO Managers meeting.)

Please let me know if you need more information.



Donghui Li of TAIR also reports that people were asking about community annotation at the TAIR booth at this conference.

Chicken and Cow Meeting - 22nd January in Cambridge, UK (Jennifer Clark and Evelyn Camon)
- Attended to encourage more GO annotatation.
- Talks on latest GO improvements and GO annotation respectively.
- The meeting next year will also include horse, dog, cat. Passed outreach contacts on.

Visit to CRIBI at the University of Padua - 26th-27th January, Padua, Italy. (Jennifer Clark)
Visit organized by Erika Feltrin (GO annotator and content developer) and funded by Giorgio Valle (Her PI).
Departmental lecture well received, included information about how the community can annotate.
Discussed plans for future muscle content meeting and also possible development of terms for grape secondary metablism.
Received final confirmation that the funding is available for muscle meeting.

Royal Society of Chemistry training - 19th January at RSc in Cambridge, UK. (Jennifer Clark and Jane Lomax)
- Training technical editors to highlight GO terms in papers.
- This marked up text will hopefully go live on 1st February.

Other events

TreeGenes database located at: wrote to say they are annotating. I write to ask if they would like to be mentored by TAIR.

Future opportunities investigated:

Cold Spring Harbor Meeetings general investigation. (Jennifer Clark and PIs)
Honey Bee Meeting - Cold Spring Harbor Honey Bee meeting speaker opportunity found via Chris Elsik, Suzanna Lewis has volunteered to speak.

TACBAC meeting (Therapeutic Applications of Computational Biology and Chemistry) at Hinxton in March, Jennifer Clark signed up to take poster along.

Wellcome Trust Advanced Courses - Enquiries made about potential opportunities. (Jennifer Clark)