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Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617. doi: 10.1093/nar/gkx1089.

HMDB 4.0: the human metabolome database for 2018.

Author information

1
Department of Biological Sciences University of Alberta, Edmonton, AB T6G 2E9, Canada.
2
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
3
Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2N8, Canada.
4
International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.
5
OMx Personal Health Analytics, Inc., 301-10359 104 St NW, Edmonton, AB T5J 1B9, Canada.
6
Institut National de la Recherche Agronomique (INRA) - Human Nutrition Unit, Université Clermont Auvergne, F63000 Clermont-Ferrand, France.

Abstract

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

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