UNIT 14.8 Exploring Human Metabolites Using the Human Metabolome Database

  1. Ian J. Forsythe1,
  2. David S. Wishart2

Published Online: 1 MAR 2009

DOI: 10.1002/0471250953.bi1408s25

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Forsythe, I. J. and Wishart, D. S. 2009. Exploring Human Metabolites Using the Human Metabolome Database. Current Protocols in Bioinformatics. 25:14.8:14.8.1–14.8.45.

Author Information

  1. 1

    Genome Alberta, Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada

  2. 2

    Departments of Computing Science and Biological Sciences, University of Alberta, and The National Institute of Nanotechnology (NINT), National Research Council, Edmonton, Alberta, Canada

Publication History

  1. Published Online: 1 MAR 2009
  2. Published Print: MAR 2009


The Human Metabolome Database (HMDB) is a Web-based bioinformatic/cheminformatic resource with detailed information about human metabolites and metabolic enzymes. It can be used for fields of study including metabolomics, biochemistry, clinical chemistry, biomarker discovery, medicine, nutrition, and general education. In addition to its comprehensive literature-derived data, the HMDB contains an extensive collection of experimental metabolite concentration data for plasma, urine, CSF, and/or other biofluids The HMDB is fully searchable, with many tools for viewing, sorting and extracting metabolite names, chemical structures, biofluid concentrations, enzymes, genes, NMR or MS spectra, and disease information. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, chemical structure information, physico-chemical data, reference NMR and MS spectra, normal and abnormal biofluid concentrations, tissue locations, disease associations, pathway information, enzyme data, gene sequence data, and SNP and mutation data, as well as extensive links to images, references and other public databases. Curr. Protoc. Bioinform. 25:14.8.1-14.8.45. © 2009 by John Wiley & Sons, Inc.


  • Database;
  • metabolomics;
  • bioinformatics;
  • cheminformatics;
  • biochemistry;
  • genomics;
  • proteomics;
  • systems biology;
  • pathways;
  • spectra