Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jan;40(Database issue):D815-20.
doi: 10.1093/nar/gkr916. Epub 2011 Nov 7.

YMDB: The Yeast Metabolome Database

Affiliations
Free PMC article

YMDB: The Yeast Metabolome Database

Timothy Jewison et al. Nucleic Acids Res. .
Free PMC article

Abstract

The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry.

Figures

Figure 1.
Figure 1.
A screenshot montage of the YMDB showing several of the YMDB's search and data display tools describing the metabolite l-Glutamine. Not all fields are shown.

Similar articles

  • ECMDB: the E. coli Metabolome Database.
    Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Guo AC, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D625-30. doi: 10.1093/nar/gks992. Epub 2012 Oct 29. Nucleic Acids Res. 2013. PMID: 23109553 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.
  • PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.
    Huang W, Brewer LK, Jones JW, Nguyen AT, Marcu A, Wishart DS, Oglesby-Sherrouse AG, Kane MA, Wilks A. Huang W, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D575-D580. doi: 10.1093/nar/gkx1061. Nucleic Acids Res. 2018. PMID: 29106626 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.
  • A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database.
    Karu N, Deng L, Slae M, Guo AC, Sajed T, Huynh H, Wine E, Wishart DS. Karu N, et al. Anal Chim Acta. 2018 Nov 7;1030:1-24. doi: 10.1016/j.aca.2018.05.031. Epub 2018 May 12. Anal Chim Acta. 2018. PMID: 30032758 Review.
See all similar articles

Cited by 52 articles

See all "Cited by" articles

References

    1. Weckwerth W. Metabolomics: an integral technique in systems biology. Bioanalysis. 2010;2:829–836. - PubMed
    1. Wishart DS. Current progress in computational metabolomics. Brief. Bioinform. 2007;8:279–293. - PubMed
    1. Wohlgemuth G, Haldiya PK, Willighagen E, Kind T, Fiehn O. The Chemical Translation Service–a web-based tool to improve standardization of metabolomic reports. Bioinformatics. 2010;26:2647–2648. - PMC - PubMed
    1. Xia J, Psychogios N, Young N, Wishart DS. MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 2009;37:W652–W660. - PMC - PubMed
    1. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009;37:D603–D610. - PMC - PubMed

Publication types

Substances

Feedback