Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D608-D617.
doi: 10.1093/nar/gkx1089.

HMDB 4.0: The Human Metabolome Database for 2018

Free PMC article

HMDB 4.0: The Human Metabolome Database for 2018

David S Wishart et al. Nucleic Acids Res. .
Free PMC article


The Human Metabolome Database or HMDB ( 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.


Figure 1.
Figure 1.
An illustration of how the lipid structures looked like in HMDB 3.0 (A) and how they now appear in HMDB 4.0 (B) for the compound Cardiolipin(16:0/16:1/16:1/22:6).
Figure 2.
Figure 2.
A schematic diagram of the ontology structure in HMDB 4.0 for the first three ontological levels.

Similar articles

  • HMDB: a knowledgebase for the human metabolome.
    Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I. Wishart DS, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25. Nucleic Acids Res. 2009. PMID: 18953024 Free PMC article.
  • HMDB 3.0--The Human Metabolome Database in 2013.
    Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A. Wishart DS, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D801-7. doi: 10.1093/nar/gks1065. Epub 2012 Nov 17. Nucleic Acids Res. 2013. PMID: 23161693 Free PMC article.
  • HMDB: the Human Metabolome Database.
    Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L. Wishart DS, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. doi: 10.1093/nar/gkl923. Nucleic Acids Res. 2007. PMID: 17202168 Free PMC article.
  • The role of the Human Metabolome Database in inborn errors of metabolism.
    Mandal R, Chamot D, Wishart DS. Mandal R, et al. J Inherit Metab Dis. 2018 May;41(3):329-336. doi: 10.1007/s10545-018-0137-8. Epub 2018 Apr 16. J Inherit Metab Dis. 2018. PMID: 29663269 Review.
  • Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.
    Wolahan SM, Hirt D, Glenn TC. Wolahan SM, et al. In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. 2015. PMID: 26269925 Free Books & Documents. Review.
See all similar articles

Cited by 335 articles

See all "Cited by" articles


    1. Wishart D.S. Metabolomics: applications to food science and nutrition research. Trends Food Sci. Technol. 2008; 19:482–493.
    1. Wishart D.S. Current progress in computational metabolomics. Brief. Bioinf. 2007; 8:279–293. - PubMed
    1. Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2017; 45:D37–D42. - PMC - PubMed
    1. The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017; 45:D158–D169. - PMC - PubMed
    1. Kanehisa M., Furumichi M., Tanabe M., Sato Y., Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017; 45:D353–D361. - PMC - PubMed

Publication types

Grant support