Figure 2: BKM-react. Complete menu for the MySQL query of the reaction table (A) and example query (B).

Mentions: The access to the integrated database is possible via the link to BKM-react [20], Figure 1A, or via the BRENDA website, making use of the BRENDA query engine. Figure 1B illustrates the access to the integrated non-redundant reaction database [21] → Reaction & Specificity → Biochemicals Reactions Aligned (see arrow). Parameters for doing queries are presented in Figure 2A for the reaction table. Figure 2B shows an example for a query result. The downloadable content of the database consists of three tables, containing the compared reactions, the according compounds as well as a link table connecting both with each other.

Lang M, Stelzer M, Schomburg D - BMC Biochem. (2011)

Bottom Line: Reactions of these databases were matched and integrated by aligning substrates and products.Each biochemical reaction given as a reaction equation occurring in at least one of the databases was included.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.

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

Abstract: 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.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.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.