Skip to main content
SpringerLink
Log in

Systems Biology Resources Arising from the Human Metabolome Project

  • Chapter
  • First Online:
Book cover Genetics Meets Metabolomics

Abstract

This chapter provides an overview of a number of the on-line, open-access databases that have arisen from the Human Metabolome Project (HMP). It is primarily intended to show how these resources can be used to easily link genetic, proteomic or physiological data to human metabolomic data. The HMP was started in 2005 and continues to this day. It was mandated to use advanced experimental methods along with literature/data mining to quantitatively characterize and describe as many human metabolites in common biofluids and tissues as possible. The HMP was also tasked with linking this metabolomic information to diseases, mechanisms, genes/proteins and pathways. These data sets have been made public through a variety of on-line, continuously updated databases including the Human Metabolome Database (HMDB), DrugBank, the Toxin, Toxin-Target Database (T3DB), FooDB and the Small Molecule Pathway Database (SMPDB). The integration of such a large quantity of proteomic, genomic and metabolomic data on humans has made these resources particular valuable for wide ranging applications from systems biology to medicine.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Jakobs C, Schweitzer S, Dorland B (1995) Galactitol in galactosemia. Eur J Pediatr 154:S50–S52

    Article  PubMed  CAS  Google Scholar 

  2. Bory C, Boulieu R, Chantin C, Mathieu M (1990) Diagnosis of alcaptonuria: rapid analysis of homogentisic acid by HPLC. Clin Chim Acta 189:7–11

    Article  PubMed  CAS  Google Scholar 

  3. Kornberg H (2000) Krebs and his trinity of cycles. Nat Rev Mol Cell Biol 1:225–228

    Article  PubMed  CAS  Google Scholar 

  4. Kohler R (1982) From medical chemistry to biochemistry: the making of a biomedical discipline. Cambridge University Press, Cambridge

    Book  Google Scholar 

  5. German JB, Hammock BD, Watkins SM (2005) Metabolomics: building on a century of biochemistry to guide human health. Metabolomics 1:3–9

    Article  PubMed  CAS  Google Scholar 

  6. Tietz NW (1995) Clinical guide to laboratory tests, 3rd edn. WB Saunders Press, Philadelphia

    Google Scholar 

  7. Wishart DS (2008) Metabolomics: applications to food science and nutrition research. Trends Food Sci Technol 19:482–493

    Article  CAS  Google Scholar 

  8. Mahido C, Ruchirawat S, Prawat H et al (1998) Pure Appl Chem 70:2065–2072

    Article  Google Scholar 

  9. Hamosh A, Scott AF, Amberger J et al (2002) Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 30:52–55

    Article  PubMed  CAS  Google Scholar 

  10. Katzmarzyk PT, Janssen I (2004) The economic costs associated with physical inactivity and obesity. Can J Appl Physiol 29:90–115

    Article  PubMed  Google Scholar 

  11. Johnson JA, Pohar SL, Majumdar SR (2006) Health care use and costs in the decade after identification of type 1 and type 2 diabetes: a population-based study. Diabetes Care 29:2403–2408

    Article  PubMed  Google Scholar 

  12. Lazarou J, Pomeranz BH, Corey PN (1998) Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA 279:1200–1205

    Article  PubMed  CAS  Google Scholar 

  13. Koren G (1993) Preconceptional folate and neural tube defects: time for rethinking. Can J Public Health 84:207–208

    PubMed  CAS  Google Scholar 

  14. French AE, Grant R, Weitzman S et al (2003) Folic acid food fortification is associated with a decline in neuroblastoma. Clin Pharmacol Ther 74:288–294

    Article  PubMed  CAS  Google Scholar 

  15. Verster A (2004) Food fortification: good to have or need to have? East Mediterr Health J 10:771–777

    PubMed  CAS  Google Scholar 

  16. Venter JC, Adams MD, Meyers EW et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  PubMed  CAS  Google Scholar 

  17. HUPO (2010) A gene-centric human proteome project: HUPO–the Human Proteome organization. Mol Cell Proteomics 9:427–429

    Article  Google Scholar 

  18. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500–544

    PubMed  CAS  Google Scholar 

  19. Wishart DS (2007) Proteomics and the human metabolome project. Expert Rev Proteomics 4:333–335

    Article  PubMed  CAS  Google Scholar 

  20. Wishart DS, Knox C, Guo AC et al (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37:D603–D610

    Article  PubMed  CAS  Google Scholar 

  21. Knox C, Law V, Jewison T et al (2011) DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs. Nucleic Acids Res 39:D1035–D1041

    Article  PubMed  Google Scholar 

  22. Lim E, Pon A, Djoumbou Y et al (2010) T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res 38:D781–D786

    Article  PubMed  CAS  Google Scholar 

  23. Scalbert A, Andres-Lacueva C, Arita M et al (2011) Databases on food phytochemicals and their health-promoting effects. J Agric Food Chem 59:4331–4348

    Google Scholar 

  24. Wishart DS, Lewis MJ, Morrissey JA et al (2008) The human cerebrospinal fluid metabolome. J Chromatogr B Analyt Technol Biomed Life Sci 871:164–173

    Article  PubMed  CAS  Google Scholar 

  25. Guo K, Bamforth F, Li L (2011) Qualitative metabolome analysis of human cerebrospinal fluid by (13)c-/(12)c-isotope dansylation labeling combined with liquid chromatography fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 22:339–347

    Article  PubMed  CAS  Google Scholar 

  26. Psychogios N, Hau DD, Peng J et al (2011) The human serum metabolome. PLoS One 6:e16957

    Article  PubMed  CAS  Google Scholar 

  27. Guo K, Li L (2009) Differential 12 C-/13 C-isotope dansylation labeling and fast liquid chromatography/mass spectrometry for absolute and relative quantification of the metabolome. Anal Chem 81:3919–3932

    Article  PubMed  CAS  Google Scholar 

  28. Eckburg PB, Bik EM, Bernstein CN et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638

    Article  PubMed  Google Scholar 

  29. Holmes E, Wilson ID, Nicholson JK (2008) Metabolic phenotyping in health and disease. Cell 134:714–717

    Article  PubMed  CAS  Google Scholar 

  30. Slupsky CM, Rankin KN, Wagner J et al (2007) Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles. Anal Chem 79:6995–7004

    Article  PubMed  CAS  Google Scholar 

  31. Bou Khalil M, Hou W, Zhou H et al (2010) Lipidomics era: accomplishments and challenges. Mass Spectrom Rev 29:877–929

    Article  PubMed  Google Scholar 

  32. Smith CA, O’Maille G, Want EJ et al (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27:747–751

    Article  PubMed  CAS  Google Scholar 

  33. Wishart DS (2009) Computational strategies for metabolite identification in metabolomics. Bioanalysis 1:1579–1596

    Article  PubMed  CAS  Google Scholar 

  34. Kanehisa M, Goto S, Hattori M et al (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357

    Article  PubMed  CAS  Google Scholar 

  35. Krummenacker M, Paley S, Mueller L et al (2005) Querying and computing with BioCyc databases. Bioinformatics 21:3454–3455

    Article  PubMed  CAS  Google Scholar 

  36. Wang Y, Xiao J, Suzek TO et al (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37:W623–W633

    Article  PubMed  CAS  Google Scholar 

  37. Degtyarenko K, de Matos P, Ennis M et al (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36:D344–D350

    Article  PubMed  CAS  Google Scholar 

  38. Westbrook J, Feng Z, Jain S et al (2002) The protein data bank: unifying the archive. Nucleic Acids Res 30:245–248

    Article  PubMed  CAS  Google Scholar 

  39. Boutet E, Lieberherr D, Tognolli M et al (2007) UniProtKB/Swiss-Prot. Methods Mol Biol 406:89–112

    PubMed  CAS  Google Scholar 

  40. Benson DA, Karsch-Mizrachi I, Lipman DJ et al (2010) GenBank. Nucleic Acids Res 38:D46–D51

    Article  PubMed  CAS  Google Scholar 

  41. Wishart DS (2008) Applications of metabolomics in drug discovery and development. Drugs R&D 9:307–322

    Article  CAS  Google Scholar 

  42. Wishart DS, Knox C, Guo AC et al (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36:D901–D906

    Article  PubMed  CAS  Google Scholar 

  43. Sumner L, Amberg A, Barrett D et al (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3:211–221

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computing Science and Biological Sciences, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB, T6G 2E8, Canada

    David Wishart Ph.D.

Authors
  1. David Wishart Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David Wishart Ph.D. .

Editor information

Editors and Affiliations

  1. Qatar Foundation-Education City, Weill Cornell Medical College in Qatar, Education City – Qatar Foundation, Doha, 24144, Qatar

    Karsten Suhre

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Wishart, D. (2012). Systems Biology Resources Arising from the Human Metabolome Project. In: Suhre, K. (eds) Genetics Meets Metabolomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1689-0_11

Download citation

Publish with us

Policies and ethics

Search

Navigation