Reconciliation of metabolites and biochemical reactions for metabolic networks

被引:40
作者
Bernard, Thomas [1 ]
Bridge, Alan [2 ]
Morgat, Anne [1 ]
Moretti, Sebastien [1 ]
Xenarios, Ioannis [3 ,4 ,5 ]
Pagni, Marco [1 ]
机构
[1] SIB Swiss Inst Bioinformat, Lausanne, Switzerland
[2] SIB Swiss Inst Bioinformat, Swiss Prot Grp, Lausanne, Switzerland
[3] SIB Swiss Inst Bioinformat, Vital IT Grp Lausanne, Lausanne, Switzerland
[4] SIB Swiss Inst Bioinformat, Swiss Prot Grp Geneva, Lausanne, Switzerland
[5] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland
关键词
data integration; data interoperability; metabolic resources; metabolic networks; cheminformatics; ESCHERICHIA-COLI; ESSENTIAL GENES; RECONSTRUCTION; MODELS; OPTIMIZATION; SYSTEM;
D O I
10.1093/bib/bbs058
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:123 / 135
页数:13
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