Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Database

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Jan Schellenberger1, Junyoung O Park2, Tom M Conrad3 and Bernhard Ø Palsson2*

Author affiliations

1 Bioinformatics Program, University of California San Diego, 9500 Gilman Dr, La Jolla, California, 92093-0419, USA

2 Bioengineering Department, University of California San Diego, 9500 Gilman Dr, La Jolla, California, 92093-0412, USA

3 Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, California, 92093-0332, USA

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2010, 11:213  doi:10.1186/1471-2105-11-213

Published: 29 April 2010

Abstract

Background

Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use.

Description

We describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

Conclusions

BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu webcite.