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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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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Literature Cited

   Ausloos, P., Clifton, C.L., Lias, S.G., Mikaya, A.I., Stein, S.E., Tchekhovskoi, D.V., Sparkman, O.D., Zaikin, V., and Zhu, D. 1999. The critical evaluation of a comprehensive mass spectral library. J. Am. Soc. Mass Spectrom. 10:287‐299 [Published erratum appears in J. Am. Soc. Mass Spectrom. 10:565].
   Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O'Donovan, C., Redaschi, N., and Yeh, L.S. 2005. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33:D154‐D159.
   Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths‐Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., Studholme, D.J., Yeats, C., and Eddy, S.R. 2004. The Pfam protein families database. Nucleic Acids Res. 32:D138‐D141.
   Brooksbank, C., Cameron, G., and Thornton, J. 2005. The European Bioinformatics Institute's data resources: Towards systems biology. Nucleic Acids Res. 33:D46‐D53.
   Frézal, J. 1998. Genatlas database, genes and development defects. C. R. Acad. Sci. III. 321:805‐817.
   Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A., and McKusick, V.A. 2005. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33:D514‐D517.
   Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277‐D280.
   Kopka, J., Schauer, N., Krueger, S., Birkemeyer, C., Usadel, B., Bergmüller, E., Dörmann, P., Weckwerth, W., Gibon, Y., Stitt, M., Willmitzer, L., Fernie, A.R., and Steinhauser, D. 2005. GMD@CSB.DB: The Golm Metabolome Database. Bioinformatics 21:1635‐1638.
   Krummenacker, M., Paley, S., Mueller, L., Yan, T., and Karp, P.D. 2005. Querying and computing with BioCyc databases. Bioinformatics 21:3454‐3455.
   Manber, U. and Bigot, P. 1997. USENIX Symposium on Internet Technologies and Systems (NSITS'97), Monterey, Calif., pp.231‐239. USENIX, Berkeley, Calif.
   Rebhan, M., Chalifa‐Caspi, V., Prilusky, J., and Lancet, D. 1998. GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics 14:656‐664.
   Sadowski, J. and Gasteiger, J. 1993. From atoms to bonds to three‐dimensional atomic coordinates: Automatic model builders. Chem. Rev. 93:2567‐2581.
   Smith, C.A., O'Maille, G., Want, E.J., Qin, C., Trauger, S.A., Brandon, T.R., Custodio, D.E., Abagyan, R., and Siuzdak, G. 2005. METLIN: A metabolite mass spectral database. Ther. Drug Monit. 27:747‐751.
   Steinbeck, C., Krause, S., and Kuhn, S. 2003. NMRShiftDB‐constructing a free chemical information system with open‐source components. J. Chem. Inf. Comput. Sci. 43:1733‐1739.
   Wain, H.M., Lush, M., Ducluzeau, F., and Povey, S. 2002. Genew: The human gene nomenclature database. Nucleic Acids Res. 30:169‐171.
   Walther, D. 1997. WebMol—a Java‐based PDB viewer. Trends Biochem. Sci. 22:274‐275.
   Weininger, D. 1988. SMILES 1. Introduction and encoding rules. J. Chem. Inf. Comput. Sci. 28:31‐38.
   Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Helmberg, W., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Pontius, J.U., Pruitt, K.D., Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A., Wagner, L., and Yaschenko, E. 2005. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33:D39‐D45.
   Wishart, D.S. 2007. Current progress in computational metabolomics. Brief. Bioinform. 8:279‐293.
   Wishart, D.S., Yang, R., Arndt, D., Tang, P., and Cruz, J. 2005. Dynamic cellular automata: An alternative approach to cellular simulation. In Silico Biol. 5:139‐161.
   Wishart, D.S., Knox, C., Guo, A., Shrivastava, S., Hassanali, M., Stothard, P., and Woolsey, J. 2006. DrugBank: A comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34:D668‐D672.
   Wishart, D.S., Tzur, D., Knox, C., Eisner, R., Guo, A.C., Young, N., Cheng, D., Jewell, K., Arndt, D., Sawhney, S., Fung, C., Nikolai, L., Lewis, M., Coutouly, M.‐A., Forsythe, I., Tang, P., Shrivastava, S., Jeroncic, K., Stothard, P., Amegbey, G., Block, D., Hau, D.D., Wagner, J., Miniaci, J., Clements, M., Gebremedhin, M., Guo, N., Zhang, Y., Duggan, G.E., MacInnis, G.D., Weljie, A.M., Dowlatabadi, R., Bamforth, F., Clive, D., Greiner, R., Li, L., Marrie, T., Sykes, B.D., Vogel, H.J., and Querengesser, L. 2007. HMDB: The Human Metabolome Database. Nucleic Acids Res. 35:D521‐D526.
Internet Resources
  Human Metabolome Database.
  KEGG Ligand Database for Chemical Compounds.
  BiGG Database.
  ACD/Structure Drawing Applet.
  WebMol Web site.
  KEGG Pathway Database.
  Gene Ontology.
  KEGG Ligand Database for Enzyme Nomenclature.
  HUGO Gene Nomenclature Committee (HGNC).
  NIST Spectral Database.
  Spectral Database for Organic Compounds.
  Golm Metabolome Database.
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