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

TLDR

Genome‑scale metabolic reconstructions under the COBRA framework are valuable for analyzing organismal metabolic capabilities, but the growing number of reconstructions creates a need for uniform, easily distributed, high‑quality curated models. This work introduces BiGG, a knowledgebase that organizes genome‑scale metabolic network reconstructions biochemically, genetically, and genomically. BiGG integrates published reconstructions into a single resource with standardized nomenclature, enabling browsing, pathway visualization, SBML export, and links to external databases for genes, proteins, reactions, metabolites, and citations. BiGG is freely available for academic use at http://bigg.ucsd.edu.

Abstract

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.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.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.