Exploring Human Metabolites Using the Human Metabolome Database

Ian J. Forsythe1, David S. Wishart2

1 Genome Alberta, Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada, 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 Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.8
DOI:  10.1002/0471250953.bi1408s25
Online Posting Date:  March, 2009
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Abstract

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.

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

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Navigating the Human Metabolome Database Web Site
  • Basic Protocol 2: Chemical Structure Similarity Searching
  • Basic Protocol 3: Metabolite Identification via Spectral Matching
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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Internet Resources
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  Human Metabolome Database.
  http://www.genome.jp/dbget‐bin/www_bfind?compound
  KEGG Ligand Database for Chemical Compounds.
  http://biocyc.org/META/server.html
  BioCyc.
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  WebMol Web site.
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  PDB.
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  BMRB.
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  PubMed.
  http://www.ncbi.nlm.nih.gov/omim/
  OMIM.
  http://www.metagene.de/programm/tdb.prg?esp=index
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  http://www.genome.jp/dbget‐bin/www_bfind?pathway
  KEGG Pathway Database.
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  GenBank.
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  Gene Ontology.
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  KEGG Ligand Database for Enzyme Nomenclature.
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  GeneCards.
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  Genatlas.
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  HUGO Gene Nomenclature Committee (HGNC).
  http://www.ncbi.nlm.nih.gov/projects/SNP/
  dbSNP.
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  NMRShiftDB.
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  NIST Spectral Database.
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  Spectral Database for Organic Compounds.
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  Golm Metabolome Database.
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