Database
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
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* Corresponding author: Bernhard Ø Palsson palsson@ucsd.edu
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
BMC Bioinformatics 2010, 11:213 doi:10.1186/1471-2105-11-213
Published: 29 April 2010Additional files
Additional file 1:
Table 1 - Contents of BiGG. BiGG currently contains 7 reconstructions including two versions of E. coli. There are a total of 7234 unique reactions and exchanges in the database. Exchange reactions carry metabolites from the extracellular 'compartment' across the system boundary and are not technically part of the metabolic reconstruction. Translocation reactions carry a metabolite between compartments (possibly performing other transformations). Reactions can be gene associated or not. Every reconstruction contains the 'cytosol' and 'extracellular' compartment. Human and yeast contain 'endoplasmic reticulum', 'mitochondria', 'peroxisome', 'nucleus'. The 'periplasm' in iAF1260, vacuole in yeast, and lysosome in human are unique to these reconstructions.
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Additional file 2:
Table 2 - Orphan reactions. 58 E. coli iJR904 orphan (non-gene associated) reactions are categorized by current status. 'Found in 1260' shows whether the reactions are found in reconstruction iAF1260. 'Y*' indicates that the reaction is found in iAF1260 in modified form (usually because of the addition of the periplasm compartment). Notes: spont. -spontaneous, lump - lumped reaction, virtual - virtual reaction, P - H. pylori, S - S. aureus, Y - S. cerevisiae, H - H. sapiens,
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