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Nucleic Acids Research Advance Access published online on October 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn810
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

HMDB: a knowledgebase for the human metabolome

David S. Wishart1,2,3,*, Craig Knox1, An Chi Guo1, Roman Eisner1, Nelson Young1, Bijaya Gautam1, David D. Hau1, Nick Psychogios1, Edison Dong1, Souhaila Bouatra1, Rupasri Mandal1, Igor Sinelnikov1, Jianguo Xia2, Leslie Jia1, Joseph A. Cruz1, Emilia Lim1, Constance A. Sobsey1, Savita Shrivastava1, Paul Huang4, Philip Liu1, Lydia Fang1, Jun Peng4, Ryan Fradette4, Dean Cheng1, Dan Tzur1, Melisa Clements4, Avalyn Lewis4, Andrea De Souza4, Azaret Zuniga4, Margot Dawe4, Yeping Xiong4, Derrick Clive4, Russ Greiner1, Alsu Nazyrova5, Rustem Shaykhutdinov5, Liang Li4, Hans J. Vogel5 and Ian Forsythe1

1Department of Computing Science, 2Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8, 3National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, AB, Canada T6G 2M9, 4Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2 and 5Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4

*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart{at}ualberta.ca

Received September 15, 2008. Revised October 9, 2008. Accepted October 10, 2008.

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.


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