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. 2010 Apr 29:11:213.
doi: 10.1186/1471-2105-11-213.

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

Jan Schellenberger  1 , Junyoung O Park, Tom M Conrad, Bernhard Ø Palsson
Affiliations

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

Jan Schellenberger et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
Gene Protein Reaction interactions. Gene Protein Reactions formulas for two Human Recon1 reactions. Each graph indicates the relationship between genes (purple), transcripts (magenta), protein (green), and reaction (teal). A) Sphingosine kinase 2 (SPHK21c) is associated with only one gene. B) Platelet-activating factor acetylhydrolase (PAFH) can be transcribed by either gene PAFAH2 or in combination of genes PAFAH1B1, PAFAH1B2, and PAFAH1B3. The GPR expression for this reaction is (5051.1) or (5049.1 and 5050.1) or (5049.1 and 5050.1 and 5048.1).
Figure 2
Figure 2
Database Schema. BiGG is hosted on a Simpheny™ server running an Oracle database. Starred columns indicate primary keys. Arrows indicate foreign key relationships. GPR_table stores the relationship between reactions, proteins, and genes. All tables and entries shown in black are directly viewable by the user. Grey entries are used internally only. GPRXML (marked by *) is a function which returns the XML formatted GPR string given a reaction ID.
Figure 3
Figure 3
The BiGG website. The BiGG knowledgebase can be accessed through a web browser. It has been tested with Mozilla Firefox, Microsoft Internet Explorer, Opera, and Safari. Three screenshots in Firefox show: (a) the content browser, (b) map viewer, and (c) the export tool.
Figure 4
Figure 4
Content of BiGG. The three largest reconstructions in BiGG are E. coli iAF1260, S. cerevisiae iND750, and H. sapiens Recon 1. Their shared content can be queried with BiGG: a) The shared reactions. Non-exchange reactions are shown in parenthesis. b) The number of shared metabolites. c) The distribution of reactions and metabolites across all seven reconstructions.
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