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. 2013 Jan;41(Database issue):D801-7.
doi: 10.1093/nar/gks1065. Epub 2012 Nov 17.

HMDB 3.0--The Human Metabolome Database in 2013

David S Wishart  1 , Timothy Jewison, An Chi Guo, Michael Wilson, Craig Knox, Yifeng Liu, Yannick Djoumbou, 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, Augustin Scalbert
Affiliations

HMDB 3.0--The Human Metabolome Database in 2013

David S Wishart et al. Nucleic Acids Res. 2013 Jan.

Abstract

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. (Note to referees, HMDB 3.0 will go live on 18 September 2012.).

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Figures

Figure 1.
Figure 1.
A screenshot montage of the different HMDB views showing the new layout of the MetaboCards and the new structure search tool.
See this image and copyright information in PMC

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