HMDB 3.0—The Human Metabolome Database in 2013

By David S. Wishart, Timothy Jewison, Anchi Guo, Michael Wilson, Craig Knox, Yifeng Liu, Yannick Djoumbou, R. Mandal, Farid Aziat, Edison Dong and 13 more. 2012

2,793 citations recorded by the source corpus.

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.).

Subfields: Molecular Biology, Physiology

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Citations in the corpus

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra (2014, background): “The Human Metabalome Database (14), Metlin (4) and MassBank (16) all have search functionality that query these databases for likely molecules matching an input MS / MS spectrum.”
Computational approaches in target identification and drug discovery (2016, methodology): “Tools such as the humanmetabolome database [22] andMetaboAnalyst [23] support integrative omics pathway analysis.”
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease (2018, background): “From each map entity, users can access the corresponding entry in the VMH database and obtain further information from external resources, such as the HMDB24, KEGG25, and CHEBI.”
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy (2016, methodology): “A test set was built by randomly selecting 800 unique structures from DrugBank, the LIPID MAPS Lipidomics Gateway, HMDB [32], and T3DB [44].”