HMDB 3.0 - The Human Metabolome Database in 2013
- David S. Wishart, Departments of Computing Science and Biology, University of Alberta
- Timothy Jewison
- An Chi Guo
- Michael Wilson
- Craig Knox
- Yifeng Liu
- Yannick Djoumbou Feunang
- Rupasri Mandal
- Farid Aziat
- Edison Dong
- Souhaila Bouatra
- Igor Sinelnikov
- David Arndt
- Jianguo Xia
- Philip Liu
- Faizath Yallou
- Trent Bjorndahl
- Rolando Perez-Pineiro
- Roman Eisner
- Felicity Allen
- Vanessa Neveu
- Russ Greiner, Dept of Computing Science; PI of AICML
- Augustin Scalbert
The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40 000 (a 600% increase). This enormous expansion is a result of the inclusion of both detected metabolites (those with measured concentrations or experimental confirmation of their existence) and expected metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue.
Citation
D. Wishart, T. Jewison, A. Guo, M. Wilson, C. Knox, Y. Liu, Y. Djoumbou Feunang, R. Mandal, F. Aziat, E. Dong, S. Bouatra, I. Sinelnikov, D. Arndt, J. Xia, P. Liu, F. Yallou, T. Bjorndahl, R. Perez-Pineiro, R. Eisner, F. Allen, V. Neveu, R. Greiner, A. Scalbert. "HMDB 3.0 - The Human Metabolome Database in 2013". Nucleic Acids Research (NAR), 41(Database), pp D801–D807, November 2012.| Keywords: | metabolomics, medical informatics, bioinformatics |
| Category: | In Journal |
| Web Links: | URL |
| DOI |
BibTeX
@article{Wishart+al:NAR12,
author = {David S. Wishart and Timothy Jewison and An Chi Guo and Michael
Wilson and Craig Knox and Yifeng Liu and Yannick Djoumbou Feunang and
Rupasri Mandal and Farid Aziat and Edison Dong and Souhaila Bouatra and
Igor Sinelnikov and David Arndt and Jianguo Xia and Philip Liu and Faizath
Yallou and Trent Bjorndahl and Rolando Perez-Pineiro and Roman Eisner and
Felicity Allen and Vanessa Neveu and Russ Greiner and Augustin Scalbert},
title = {HMDB 3.0 - The Human Metabolome Database in 2013},
Volume = "41",
Number = "Database",
Pages = {D801–D807},
journal = {Nucleic Acids Research (NAR)},
year = 2012,
}Last Updated: February 10, 2020Submitted by Sabina P
