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AgBase


NAR Molecular Biology Database Collection entry number 974
McCarthy F.M.1,2, Bridges S.M.2,3, Wang N.2,3, Magee G.B.2,3, Williams W.P.4, Luthe D.5, and Burgess S.C.1,3,6
1Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA
2Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA
3Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, Mississippi State, MS 39762, USA
4USDA ARS Corn Host Plant Resistance Research Unit, Box 5367, Mississippi State, MS 39762, USA
5Department of Crop and Soil Sciences, The Pennsylvania State University, University Park, PA 16802, USA
6Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762, USA

Database Description

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. We have developed a novel method for facilitating structural annotation of genomes, "expressed protein sequence tags" (ePSTs) and these ePSTs are provided through AgBase. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. We provide tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO.

Recent Developments

AgBase has recently provided a mechanism for researchers to add or request GO annotations for agriculturally important species.
Statistics for the GO annotations provided by AgBase and the AgBase Journal Database (JDB) used by AgBase biocurators for GO annotations are now available. The "expressed protein sequence tags" (ePSTs) database can now be searched using Blast queries.

Acknowledgements

We acknowledge the following groups for their help and support: The GO Consortium, especially DictyBase for providing the database schema and for technical assistance with implementation, MGI for providing training and continued support with manual curation issues and GOA for allowing us access to their tools and for their continued help, support and patience. AgBase has received financial support from the Mississippi State University Office of Research, Division of Agriculture and Forestry, College of Veterinary Medicine, Bagley College of Engineering and Life Sciences and Biotechnology Institute. AgBase is also supported by grants from the United States Department of Agriculture and the National Science Foundation.

References

1. McCarthy, F. M., N. Wang, G. B. Magee, B. Nanduri, M. L. Lawrence, E. B. Camon, D. G. Barrell, D. P. Hill, M. E. Dolan, W. P. Williams, D. S. Luthe, S. M. Bridges, and S. C. Burgess (2006). AgBase: a functional genomics resource for agriculture." BMC Genomics 7:229.

Category: Plant databases

Go to the abstract in the NAR 2007 Database Issue.
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