title: BKM-react, an integrated biochemical reaction database.
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.
authors.affiliation: Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany.
authors.forename: Maren
authors.initials: M
authors.lastname: Lang
authors.forename: Michael
authors.initials: M
authors.lastname: Stelzer
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
mesh_terms: D001671:Biochemistry; D016208:Databases, Factual; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D004798:Enzymes