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Open Access Highly Accessed Research article

BKM-react, an integrated biochemical reaction database

Maren Lang, Michael Stelzer and Dietmar Schomburg*

Author Affiliations

Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany

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BMC Biochemistry 2011, 12:42  doi:10.1186/1471-2091-12-42

Published: 8 August 2011

Abstract

Background

The systematic, complete and correct reconstruction of genome-scale metabolic networks or metabolic pathways is one of the most challenging tasks in systems biology research. An essential requirement is the access to the complete biochemical knowledge - especially on the biochemical reactions. This knowledge is extracted from the scientific literature and collected in biological databases. Since the available databases differ in the number of biochemical reactions and the annotation of the reactions, an integrated knowledge resource would be of great value.

Results

We developed a comprehensive non-redundant reaction database containing known enzyme-catalyzed and spontaneous reactions. Currently, it comprises 18,172 unique biochemical reactions. As source databases the biochemical databases BRENDA, KEGG, and MetaCyc were used. Reactions of these databases were matched and integrated by aligning substrates and products. For the latter a two-step comparison using their structures (via InChIs) and names was performed. Each biochemical reaction given as a reaction equation occurring in at least one of the databases was included.

Conclusions

An integrated non-redundant reaction database has been developed and is made available to users. The database can significantly facilitate and accelerate the construction of accurate biochemical models.