Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Langer Kamp 19 B, 38106 Braunschweig, Germany.
BMC Biochem. 2011 Aug 8;12:42. doi: 10.1186/1471-2091-12-42.
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.
系统、完整和正确地重建基因组规模的代谢网络或代谢途径是系统生物学研究中最具挑战性的任务之一。一个基本的要求是获得完整的生化知识——特别是生化反应方面的知识。这些知识是从科学文献中提取出来的，并收集在生物数据库中。由于现有的数据库在生化反应的数量和反应的注释上存在差异，因此集成的知识库将具有巨大的价值。
我们开发了一个综合的非冗余反应数据库，其中包含已知的酶催化和自发反应。目前，它包含 18172 个独特的生化反应。作为源数据库，使用了生化数据库 BRENDA、KEGG 和 MetaCyc。通过对齐底物和产物对这些数据库中的反应进行匹配和整合。对于后者，通过使用它们的结构（通过 InChIs）和名称进行了两步比较。数据库中包含了至少在一个数据库中出现的作为反应方程给出的每个生化反应。
已经开发了一个综合的非冗余反应数据库，并提供给用户使用。该数据库可以显著促进和加速准确生化模型的构建。
