title: HMDB 3.0--The Human Metabolome Database in 2013.
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.).
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8. david.wishart@ualberta.ca
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
authors.forename: Timothy
authors.initials: T
authors.lastname: Jewison
authors.forename: An Chi
authors.initials: AC
authors.lastname: Guo
authors.forename: Michael
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authors.lastname: Wilson
authors.forename: Craig
authors.initials: C
authors.lastname: Knox
authors.forename: Yifeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Yannick
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authors.lastname: Djoumbou
authors.forename: Rupasri
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authors.lastname: Mandal
authors.forename: Farid
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authors.lastname: Aziat
authors.forename: Edison
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authors.lastname: Dong
authors.forename: Souhaila
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authors.lastname: Bouatra
authors.forename: Igor
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authors.lastname: Sinelnikov
authors.forename: David
authors.initials: D
authors.lastname: Arndt
authors.forename: Jianguo
authors.initials: J
authors.lastname: Xia
authors.forename: Philip
authors.initials: P
authors.lastname: Liu
authors.forename: Faizath
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authors.lastname: Yallou
authors.forename: Trent
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authors.lastname: Bjorndahl
authors.forename: Rolando
authors.initials: R
authors.lastname: Perez-Pineiro
authors.forename: Roman
authors.initials: R
authors.lastname: Eisner
authors.forename: Felicity
authors.initials: F
authors.lastname: Allen
authors.forename: Vanessa
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authors.lastname: Neveu
authors.forename: Russ
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authors.lastname: Greiner
authors.forename: Augustin
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authors.lastname: Scalbert
mesh_terms: D062126:Databases, Chemical; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry; D055442:Metabolome; D055432:Metabolomics; D019906:Nuclear Magnetic Resonance, Biomolecular; D014584:User-Computer Interface