D602 Nucleic Acids Research, 2007, Vol. 35, Database issue COMMUNITY REQUESTS FOR GO ANNOTATIONS There are numerous tools available for functional analysis of datasets (27–32) but these tools assume that a signiﬁcant number of the gene products of interest have GO annotation available. Since this is not the case for agriculturally impor- tant organisms we designed the GOanna tool so that a user can leverage data from closely related organisms to add GO annotations to their experimental dataset. However, even highly homologous genes may have different functions in different organisms and direct experimental evidence is the best data for assigning function to a particular gene product. Typically (but not always) individual groups within the GO Consortium are responsible for annotating particular species. In species where there is a dedicated GO annotation effort, researchers can contact the responsible database directly to request further annotations but there is currently no mechani- sm for requesting annotations in the many other species that researchers may be studying. At AgBase we have developed a Community Requests and Submission form to meet the GO annotation needs of researchers interested in agriculturally important species. The type of data that a user must complete to make a request is scalable, allowing both users new to GO and users who have had GO biocuration training to enter requests. The basic request for GO annotations requires that the researcher identify the gene product of interest using a unique database accession identiﬁer, the species the gene product comes from and nominate functional literature about the gene product (using PubMed ID). Researchers with expert knowledge about particular gene products have the option of supplying additional information about the types of experimental data available and the GO terms associated with the gene product. Users with biocuration training can upload their data as a gene association directly to be sanity checked and assimilated into GO databases. Researchers who submit their own gene association ﬁles will be provided with a unique AgBase anno- tator ID so that their annotations can be acknowledged. All users are asked to register and provide a valid email address so that they may be notiﬁed about the progress of their requests and submissions. Requests are prioritized based on the number of commu- nity requests for each gene product and when the request was received. Gene product priority lists are species speciﬁc (i.e. chicken and cow gene products will not compete) and time spent on annotating each species is split proportionally based on the number of requests for each species. Annota- tions that have been submitted as a gene association ﬁle receive the highest priority as they are quality checked and submitted to the GO Consortium. Requests are acknowledged with a return email stating their rank in the request queue and researchers are notiﬁed by email when their request has been processed and the GO annotation added to the AgBase database; they are also notiﬁed if there is no functional data available for GO annotation. AVAILABILITY OF AGBASE DATA AND TOOLS Access to the AgBase databases is via http://www.agbase. msstate.edu and access to data is unrestricted. The tools we have developed are either freely available online at AgBase or by contacting us at agbase@cse.msstate.edu. OBTAINING HELP FROM AgBase Extensive online help, including worked examples, is avail- able at AgBase by clicking on the help link in the top right corner of the site. All of our computational tools are freely available via AgBase, and technical support can be obtained by contacting us. Our biocurators make every effort to main- tain data integrity by linking data with researchers, references and methods. However, similar to all databases, AgBase is an on-going project and interaction with the user community is vital for its success. We encourage the submission of data, correction of errors and suggestions for making AgBase of greater use including ideas for new computational tools (email: agbase@cse.msstate.edu). FUTURE DIRECTIONS The primary focus of the AgBase databases is to provide a resource that facilitates functional analysis in agriculturally important species. We will continue to work with GO Con- sortium members (particularly EBI-GOA), other agricultural based groups [including the Roslin Institute and Gramene (33)] and community groups to provide improved functional annotations for agricultural organisms. We are also using experimental-based approaches for improving genomic struc- tural annotation and future work will focus on improving the proteogenomic pipeline, visualizing ePST data and integra- ting this structural annotation data with functional data. ACKNOWLEDGEMENTS We would like to thank MGI and EBI-GOA for their continued help and support with the Gene Ontology aspects of this manuscript. Financial support for our projects has come from the USDA NRI, MSU Office of Research (MAFES contribution number J11020), MSU Bagley College of Engineering, MSU College of Veterinary Medicine and the MSU Life Science and Biotechnology institute. Funding to pay the Open Access publication charges for this article was provided by the Office of Research and Graduate Studies, College of Veterinary Medicine, MSU. Conflict of interest statement. None declared. REFERENCES 1. Goff,S.A., Ricke,D., Lan,T.H., Presting,G., Wang,R., Dunn,M., Glazebrook,J., Sessions,A., Oeller,P., Varma,H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100. 2. Hillier,L.W., Miller,W., Birney,E., Warren,W., Hardison,R.C., Ponting,C.P., Bork,P., Burt,D.W., Groenen,M.A., Delany,M.E. et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716. 3. Yu,J., Hu,S., Wang,J., Wong,G.K., Li,S., Liu,B., Deng,Y., Dai,L., Zhou,Y., Zhang,X. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92. 4. Spencer,G. and Tomlin,R. (2006) NIH News Advisory. 5. Messing,J. and Dooner,H.K. 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