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HMDB 5.0:2022 年人类代谢组数据库。

HMDB 5.0: the Human Metabolome Database for 2022.

机构信息

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.

出版信息

Nucleic Acids Res. 2022 Jan 7;50(D1):D622-D631. doi: 10.1093/nar/gkab1062.

Abstract

The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.

摘要

人类代谢物数据库(HMDB)(https://hmdb.ca)自 2007 年以来一直提供有关人类代谢物及其相关生物学、生理学和化学特性的综合参考信息。在过去的 15 年中,HMDB 经历了显著的发展和演变,以满足代谢组学社区的需求,并应对互联网和计算技术的持续变化。今年的更新版本 HMDB 5.0 为数据库带来了许多重要的改进和升级。这些改进应该使 HMDB 对更多的用户更加有用和更具吸引力。特别是,这些改进包括:(i)代谢物条目数量的大幅增加(从 114100 个增加到 217920 个化合物);(ii)代谢物描述的质量和深度的增强;(iii)添加新的结构、光谱和途径可视化工具;(iv)包含许多新的和更准确预测的光谱数据集,包括预测 NMR 光谱、更准确预测的 MS 光谱、预测保留指数和预测碰撞截面数据;(v)HMDB 搜索功能的增强,以方便更好的化合物鉴定。HMDB 网站的内容、界面和一般性能也进行了许多其他较小的改进和更新。总体而言,我们相信这些升级和更新将大大提高 HMDB 的易用性及其在人类代谢组学以及暴露组学、脂质组学、营养科学、生物化学和临床化学等领域的潜在应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9724/8728138/e8308054b115/gkab1062fig1.jpg

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