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

TitleBiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
Publication TypeJournal Article
Year of Publication2010
AuthorsSchellenberger J, Park JO, Conrad TM, Palsson BØ
JournalBMC bioinformatics
Volume11
Pagination213
PubMed Date2010
ISSN1471-2105
KeywordsGenome, Genomics, Knowledge Bases, Metabolic Networks and Pathways, Software
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.

Alternate JournalBMC Bioinformatics
PubMed ID20426874

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