Nucleic Acids Research, 2007, Vol. 35, Database issue D521-D526
© 2006 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.
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HMDB: the Human Metabolome Database
1 Department of Computing Science, University of Alberta Edmonton, AB, Canada T6G 2E8 2 Department of Biochemistry, University of Alberta Edmonton, AB, Canada T6G 2E8 3 Department of Chemistry, University of Alberta Edmonton, AB, Canada T6G 2E8 4 Department of Medicine, University of Alberta Edmonton, AB, Canada T6G 2E8 5 Department of Biological Sciences, University of Alberta Edmonton, AB, Canada T6G 2E8 6 Department of Biological Sciences, University of Calgary Calgary, AB, Canada T2N 1N4 7 National Institute for Nanotechnology, 11421 Saskatchewan Drive Edmonton, AB, Canada T6G 2M9
*To whom correspondence should be addressed. Tel: +780 492 0383; Fax: +780 492 1071; Email: david.wishart{at}ualberta.ca
Received August 16, 2006. Revised October 15, 2006. Accepted October 17, 2006.
The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca
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