Advocacy & Outreach Progress Report for December 2008

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User Advocacy

Staff

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

GO helpdesk

  • Central email address (gohelp@geneontology.org) for 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

Helpdesk queries 2008.jpg

Response time.jpg

Query topics.jpg

Newsletter

  • May and August editions. The newsletter is now discontinued, and will be replaced by a news page with RSS feed early next year.

Training Meetings

AgBase Avian Training Meeting

Led by Fiona McCarthy and Harold Drabkin.
Mississippi Stat, May 2008.
This training aimed to give a good grounding in the use of GO ontologies and annotations for researchers analysing data. The training included a demonstration of the Onto-tools software suite by the tool developer P. Khatri

Content: http://www.agbase.msstate.edu/agcworkshop/
Feedback: http://wiki.geneontology.org/index.php/Outreach_May_2008_Report





Annotation Outreach

New annotation groups:

Sol Genomics Network

In February/March 2008 Naama Menda and Anuradha Pujar of the Sol Genomics Network worked with staff at TAIR and Gramene/Cornell to adapt their annotation system to accommodate GO annotation. They began formally submitting annotations to the GO central repository in March.

Swiss-Prot

The Swiss-Prot group in Geneva, headed by Amos Bairoch has committed to start contributing GO annotations from a large range of species 9 to 12 months from now. This is a major contribution, and will further help to fill in the annotation gap for those species that do not currently have MODs or funding for GO annotation.

Community annotation sets:

Drug Transporters

Paul Dobson of the University of Manchester (UK) contributed a very comprehensive and well researched set of GO-style annotations for drug transport gene products on rat, human and mouse. These have been passed on to the relevant MODs for conversion to actual GO annotations.

Annotation submission with publications

Tanya Berardini of TAIR worked with editors at Plant Physiology journal (http://www.plantphysiol.org/) to enable authors to submit GO annotation information at the time of research data publication.
A web front end has been designed to take the data: http://wiki.geneontology.org/index.php/Image:PlantPhysiol.png

Annotation training in the community:

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

PAG

Donghui Li reports that TAIR organised a workshop on community annotation at the Plant and Animal Genome XVI Conference on 13 January 2008, San Diego, CA.
Representatives from three MODs talked about the current status and future plans in regard to community annotation. The groups were TAIR, SGN (SOL Genomics Network) and WormBase.

ISAFG Conference

Fiona McCarthy, Training in how to get and use annotations, for farm animal researchers.
April 2008
http://www.ark-genomics.org/events/workshops/3rdISAFG.php

Plant-Associated Microbe Gene Ontology (PAMGO) Training Workshop

By Trudy Torto-Alalibo, Michelle Gwinn-Giglio, Candace Collmer.
Virginia Bioinformatics Institute
July 14-16, 2008
http://www.cpe.vt.edu/vbi-genome/index.html

ASPB (American Society of Plant Biologists) Plant Biology Meeting,

TAIR Training Workshops, By Donghui Li and Tanya Berardini. June 29 2008, Merida Mexico

19th International Conference on Arabidopsis Research

TAIR Training Workshops, By Donghui Li and Tanya Berardini. July 23 2008, Montreal Canada

Dictyostelium meeting in Japan

In September, Petra Fey of dictyBase presented a talk that included some GO at a Dictyostelium meeting in Japan, prompting a student to inquire about GO in dictyBase and all GO tools, AmiGO, OBO-Edit.

European Muscle Congress

Paolo Lavader of CRIBI presented a GO annotation poster.
13-16 September 2008 at Keble College, Oxford, UK.

PAMGO

Virginia Bioinformatics Institute’s Plant-Associated Microbe Gene Ontology (PAMGO) Training Workshop took place at Blacksburg, VA, July 14-16, 2008
Candace Collmer of PAMGO visited four universities in the People’s Republic of China during May-June, 2008. She presented a talk entitled, “Comparative genomics of plant pathogens: How new Gene Ontology (GO) terms facilitate the study of microbe-host interactions” at Nanjing Agricultural University, Hangzhou University, and Shang Jiaotong University in Shanghai.

Candace Collmer of PAMGO presented a Poster, and “Flash and Dash” presentation entitled “Using the universal language of Gene Ontology (GO) to annotate gene products involved in the interactions between microbes and their hosts” at the annual (Centennial) meeting of the American Phytopathological Society, Minneapolis, MN, July 26-30, 2008. Authors on the poster were: Collmer, C. W.,Torto-Alalibo, T.,Lindeberg, M.,Chibucos, M., Gwinn-Giglio, M., Biehl, B., Ireland, A., Lomax, J., Bird, D., Collmer, A., Dean, R., Glasner, J., Hannick, L.., Mitchell, T., Perna, N., Setubal, J., White, O., Tyler, B. M. (Candace Collmer)

GOA

Rachael Huntley presented a talk "The Gene Ontology Annotation (GOA) Database: central resource for multi-species GO annotation" at the Eurofungbase meeting "Fungal Biology and Biotechnology in the Genomic Era" held in Feliu de Guixols, Spain. 22-24 October 2008. The Eurofungbase group have previously made COmmunity GO annotations and are considering how to follow this up.

Rachael Huntley also gave 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.

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.