November 2006 Monthly Report

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Community feedback and annotation efforts

WormBase are planning a web form to let users submit GO annotatons and requests to have their favourite gene prioritized for annotation. (Ranjana Kishore)

Immunology Wiki - Alex Diehl, Jamie Lee, Evelyn Camon, Ruth Lovering, Judy Blake, and Richard Scheuermann: Developing wiki pages to let users contribute information that will help improve GO annotation of their favourite immunology genes. To be live by january.

AgBase - Accepting community annotations into a “community gene association” file (publically available). Annotations are checked by AgBase GO curators, and then MGI annotation mentor (Harold Drabkin), before being submitted to the GO repository via GOA's protein2go tool.

Eurofung Aspergillus Annotation Jamboree - Copenhagen Nov 28th - Dec 1st, 2006. Jennifer Clark attended this meeting along with a TIGR representative (Jennifer Wortman). TIGR had manatee set up with the Aspergillus nidulans genome. Attendees spent two days checking sequences and adding GO annotations. The plan is for further annotations to be applied in the coming months. 500 manual GO annotations were made during the conference. I (J. Clark) am planning to write up this meeting in more detail for the annotation documentation.


Conference outreach

AgBase

Plant and Animal Genome XIV Conference 2006

New contacts:

Dr Larry Cogburn (University of Delaware)

- Requested assistance with matching GO annotations for chicken gene products with a University of Delaware EST array.

Ron Shigeta (Affymetrix Inc.) Venu Valmeekam (Affymetrix Inc.).

- Indicated that they provide GO annotations for their array products but would like to see targeted annotations for those gene products represented on arrays. Discussions focused on chicken annotations but they indicated that the same was true for all of their arrays.

May 2006

Shane Burgess attended the Cold Spring Harbor Chicken Genomics and Development Workshop. Shane presented an introduction about the GO. Many attendees at this conference expressed an interest in chicken GO annotation and standardized nomenclature. The group at Roslin Institute, headed by Dave Burt, is pursuing funding to do GO annotation. Representatives from AgBase will attend the 2007 Chicken Genomics and Development Workshop.


October 2006

Queensland Biosciences Precinct Special Seminar Series October 11, Brisbane, Australia

A general introduction to GO and some of the tools for analyzing datasets using the GO was presented. After this AgBase were contacted by groups at the Queensland Department of Primary Industries who wish to use the GO to analyze Chiton, Lobster and Prawn. They requested more information about the GO and were referred to the educational resources at the GO Homepage.


In addition to conference and workshop presentations AgBase have also written review articles describing the utility of GO to the agricultural community. These are listed below:

• McCarthy F.M., Bridges S.M. and Burgess S.C. (2006). "GOing from Functional Genomics to Biological Significance." Cytogen. Gen. Res. In Press. • Nanduri* B., McCarthy* F.M., Bridges S.M., Corzo A., Koter M.D., Buza J.J., van den Berg B., Wang N. and Burgess S.C. (2005). “Proteomics Applied to Disease in Poultry”. Invited Review. Future outreach plans:

- Conference of Research Workers in Animal Diseases (December 3- 5, 2006, Chicago)

- PAG 2007 - AgBase and PAMGO will have a joint booth at this conference.

- Mississippi Academy of Sciences Annual Meeting (February 21-23 2007, Mississippi State University)

AgBase will give presentations highlighting how GO can facilitate functional analysis for livestock species.


New AgBase Contacts

Several groups who may be interested in making some annotations:

Dawn Luthe Formerly MSU, now Penn State (maize; in contact with MaizeDB and Gramene).

Cetin Yuceer Department of Forestry, MSU (poplar)

Chipper Swiderski College of Veterinary Medicine, MSU (equine)

Erdogan Memilli Animal & Dairy Sciences, MSU (bovine & porcine)

Attila Karsi College of Veterinary Medicine, MSU (Edwardsiella ictaluri & channel catfish)

Larry Cogburn University of Delaware (chicken)

Abigail Elizur Queensland Department of Primary Industries (crustaceans, pearl oysters, chiton)

Chris Bidwell Purdue University (sheep & cattle)