ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli.
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli.
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DOI：
10.1093/nar/gkv1060
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Wishart DS
中科院分区：
文献类型：
--
作者：
Sajed T;Marcu A;Ramirez M;Pon A;Guo AC;Knox C;Wilson M;Grant JR;Djoumbou Y;Wishart DS
ECMDB或大肠杆菌代谢组数据库（http：www.ecmdb.ca）是一个包含大肠杆菌基因组和代谢组详细信息的综合性数据库。coli（K-12）。ECMDB于2012年首次发布，在过去4年中经历了大幅扩展和多次修改。本手稿描述了ECMDB的最新版本（ECMDB 2.0）。特别是，它提供了以前在2013年NAR数据库问题中描述的数据库的全面更新，并详细介绍了在此期间对ECMDB进行的许多添加和改进。一些最重要或最显著的增强包括代谢途径图的数量增加了13倍（从125到1650），与途径相关的化合物数量增加了3倍（从1058到3280），增加了几十个操纵子/代谢物信号通路，数据库中的化合物数量增加了44%（从2610到3760），具有NMR或MS谱的化合物数量增加了7倍（从412到3261），与其他E.大肠杆菌或化学资源。这些增加，沿着许多其他增强，旨在提高查询，搜索和查看ECMDB中的数据的易用性或速度，应大大促进理解不仅是E.大肠杆菌，而且还允许深入探索其广泛的代谢网络，其许多信号通路和其基本的生物化学。
ECMDB or the Escherichia coli Metabolome Database (http://www.ecmdb.ca) is a comprehensive database containing detailed information about the genome and metabolome of E. coli (K-12). First released in 2012, the ECMDB has undergone substantial expansion and many modifications over the past 4 years. This manuscript describes the most recent version of ECMDB (ECMDB 2.0). In particular, it provides a comprehensive update of the database that was previously described in the 2013 NAR Database Issue and details many of the additions and improvements made to the ECMDB over that time. Some of the most important or significant enhancements include a 13-fold increase in the number of metabolic pathway diagrams (from 125 to 1650), a 3-fold increase in the number of compounds linked to pathways (from 1058 to 3280), the addition of dozens of operon/metabolite signalling pathways, a 44% increase in the number of compounds in the database (from 2610 to 3760), a 7-fold increase in the number of compounds with NMR or MS spectra (from 412 to 3261) and a massive increase in the number of external links to other E. coli or chemical resources. These additions, along with many other enhancements aimed at improving the ease or speed of querying, searching and viewing the data within ECMDB should greatly facilitate the understanding of not only the metabolism of E. coli, but also allow the in-depth exploration of its extensive metabolic networks, its many signalling pathways and its essential biochemistry.