Outreach and Advocacy Progress Report December 2009

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Staff

  • Co-ordinated by Jane Lomax and Jennifer Deegan (EBI, Hinxton). Contributions from many members of GO consortium.

GO helpdesk

  • Central email address from all GO queries. Person on duty responsible for answering the email, or forwarding the email to appropriate person and ensuring it’s answered.

GO helpdesk staff

Rachael Huntley, Emily Dimmer, David Hill, Jane Lomax, Kimberly Van Auken, Midori Harris, Amelia Ireland, Tanya Berardini, Eurie Hong, Jennifer Deegan.

Statistics for past year

News

In May this year, the newsletter has been replaced by a a news page. Users can also follow news on this page via RSS feed and Twitter. The former newsletter working group now moderates the news feed. See the wiki pages for more information.

Website

The website has been undergoing an overhaul this year, with old documentation being rewritten - for example the [relations documentation - and the structure simplified.

Annotation training and user training in the community:

By its nature, annotation outreach and user training involves staff members giving a number of talks and training sessions in the community. Highlights in this period are shown below.

Fission Yeast Community curation

Valerie Wood ran a community curation pilot project for fission yeast, by sending forms to researchers to complete for a recent publication. The initial trial of 20 publications had a 95% response rate demonstrating that the fission yeast community is willing to participate actively in the curation process. See the pilot summary at http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml. Eight SF items were also raised for new biology, or ontology issues.

The pilot will be extended to 50 laboratories within one month. The hope is to get funding to develop a simple community curation interface as part of the fission yeast grant proposal. We believe that this initiative presents a significant cost-effective opportunity to enhance the efforts of core curation staff at low cost.

PathEpigen

In November Ana Barat and colleagues visited GOA and the GO Editorial Office at the EBI to discuss annotation systems. They are making manual literature annotations with genes involved in cancer.

GOA

  • Rachael Huntley presented a lecture and tutorial on "Gene Ontology - classifying your protein list" for the joint EMBL-EBI/Wellcome Trust workshop "Proteomics Bioinformatics" held at EBI, Hinxton, U.K. 8-12 December 2008.
  • Rachael Huntley gave a tutorial "Introduction to the Gene Ontology and GO annotation resources" for the EBI's Hands-on training course 'Transcriptomics' held at EBI on 19-22nd January 2009.
  • Emily Dimmer, Rachael Huntley and Michele McHale trained the first set of SIB curators in GO annotation on 28-29th January 2009 in Geneva.
  • Yasmin Alam-Faruque and Emily Dimmer were invited by the GUDMAP Team to Edinburgh in June 2009 to talk about GOA to the GUDMAP team. Emily talked with Graeme Grimes who was interested in discussing GO in relation to Wendy Bickmores Nuclear Protein Database, and Jeff Christiansen (EMAGE Gene Expression Database - http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html) - about general things regarding bringing GO into EMAGE.
  • Rachael Huntley trained the third set of SIB curators in GO annotation on 1st July 2009 in Geneva.
  • Rachael Huntley trained the penultimate set of SIB curators in GO annotation on 12th November 2009 in Geneva.

MGI

Alexander Diehl attended the first NIGMS Cell Behavior Ontology Workshop, May 4-6, 2009, as the invited representative of the GO Consortium, where he gave a talk "Introduction to the Gene Ontology" and provided advice on ontology development during the workshop sessions of the meeting.

E.Coli

  • Jim Hu gave a computer demo at the Plant and Animal Genome meeting in San Diego. This included using GONUTS to do community GO annotation.
  • Members of the EcoliWiki team presented posters about Gene Ontology and GONUTS at the annual symposium of the Program in the Biology of Filamentous Fungi at Texas A&M and at the Texas Protein Folders Conference.
  • Jim Hu and Debby Siegele attended the American Society for Microbiology Conference on Undergraduate Education (ASMCUE), where they discussed the importance of GO for microbiology, and using GONUTS in education.

WormBase

The sea urchin database staff are in touch with WormBase (they are on the same campus at Caltech). To begin with, they are interested in doing InterPro2GO mappings for their proteins, and intend later to submit a gene association file.

Pombe Database

Val Wood gave a talk and workshop on GO Tools for pombe researchers at a Wellcome Trust Advanced Course: Genome-Wide Approaches With Fission Yeast.

HGNC

Ruth Lovering presented a seminar to the Department of Medicine, UCL, entitled 'GO for it! Gene Ontology - an essential resource' on Friday 6th Feb.

GO Editorial Office

  • Jane Lomax gave a talk for the new European Bioinformatics Institute predocs on the 13th February called "Introduction to GO and other Biomedical Ontologies".
  • Jennifer Deegan took part in an EBI Roadshow at John Innes Centre, Norwich, UK. 18th February 2009.

She gave a 2 hour hands-on tutorial for 20 people, covering a general introduction to GO Project.

  • Jennifer Deegan taught general GO at a Master's students outreach day at the EBI.

Peach Genome

Bryon Sosinski (sosinski at ncsu.edu) wrote to say that he is coordinating the sequencing of the peach genome, and is writing a USDA-SCRI proposal to employ GO for the initial annotation of the sequence. He also wishes to offer workshops to the community on how to do the higher level annotations in their respective regions of interest. He has been put in contact with Tanya Berardini at TAIR and Fiona McCarthy as AgBase to follow this up.

University of Maryland

  • Michelle Gwinn-Giglio gave a GO workshop for 20 people at the University of Maryland.
  • July 28-31 IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus. Two more workshops are planned for September and November.

JCVI

Linda Hannick presented an hour-long Introduction to GO to the participants in the JCVI Eukaryotic Genome Annotation and Analysis Course, presented March 3-5, April 1-3, and June 10-12, 2009. Another course will be presented September 23-25, 2009.

RGD

Jennifer Smith at RGD produced and released an introductory video tutorial entitled "Introduction to Biomedical Ontologies #1: What is an Ontology?". It is the first in a planned series about Biomedical Ontologies and is available on both SciVee (http://www.scivee.tv/node/11759) and Vimeo (http://www.vimeo.com/5344028). The intended target audience is researchers and students who are largely, or completely, unfamiliar with ontologies, and the example that is used to illustrate ontologies, ontology annotations and ontology browsers (including AmiGO) is GO.