Reconciliation of metabolites and biochemical reactions for metabolic networks
Reconciliation of metabolites and biochemical reactions for metabolic networks
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DOI：
10.1093/bib/bbs058
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发表时间：
2014-01-01
影响因子：
9.5
通讯作者：
Pagni, Marco
中科院分区：
文献类型：
--
作者：
Bernard, Thomas;Bridge, Alan;Pagni, Marco
基因组尺度的代谢网络重建现在通常用于代谢途径及其进化和设计的研究。这种重建的发展涉及到来自科学文献、公共数据库和现有基因组尺度代谢模型的反应和代谢物信息的整合。来自这些来源的数据之间的差异调和通常需要大量的人工管理，这构成了开发和应用基因组尺度代谢网络重建的主要障碍。在这项工作中，我们讨论了在代谢资源的绘制和调节中遇到的一些主要困难，并回顾了旨在加速这一过程的三个最新举措，即BKM-react， MetRxn和MNXref（在本文中提出）。这些资源中的每一个都提供了许多最常用的代谢资源的预编译调和。通过减少人工管理代谢物和反应差异所需的时间，这些资源旨在加速高质量基因组尺度代谢网络重建和模型的开发和应用。
Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.