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      HMDB 3.0—The Human Metabolome Database in 2013

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          The Human Metabolome Database (HMDB) ( 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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          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 and 4IARC Biomarkers Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
          Author notes
          *To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart@
          Nucleic Acids Res
          Nucleic Acids Res
          Nucleic Acids Research
          Oxford University Press
          January 2013
          17 November 2012
          17 November 2012
          : 41
          : Database issue , Database issue
          : D801-D807
          23161693 3531200 10.1093/nar/gks1065 gks1065
          © The Author(s) 2012. Published by Oxford University Press.

          This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

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