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AgBase: a functional genomics resource for agriculture

Fiona M McCarthy17*, Nan Wang27, G Bryce Magee27, Bindu Nanduri17, Mark L Lawrence1, Evelyn B Camon3, Daniel G Barrell3, David P Hill4, Mary E Dolan4, W Paul Williams5, Dawn S Luthe67, Susan M Bridges27 and Shane C Burgess17

Author Affiliations

1 Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA

2 Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, MS 39762, USA

3 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

4 Mouse Genome Informatics, The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA

5 USDA ARS Corn Host Plant Resistance Research Unit, Box 5367, Mississippi State University, MS 39762, USA

6 Department of Biochemistry and Molecular Biology, P.O. Box 9650, Mississippi State University, MS 39762, USA

7 Institute for Digital Biology, Mississippi State University, MS 39762, USA

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BMC Genomics 2006, 7:229  doi:10.1186/1471-2164-7-229

Published: 8 September 2006

Abstract

Background

Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities.

Description

To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu webcite for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data.

Conclusion

The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.