Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jan;41(Database issue):D625-30.
doi: 10.1093/nar/gks992. Epub 2012 Oct 29.

ECMDB: The E. Coli Metabolome Database

Affiliations
Free PMC article

ECMDB: The E. Coli Metabolome Database

An Chi Guo et al. Nucleic Acids Res. .
Free PMC article

Abstract

The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. 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 E. coli'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 molecular biologists, systems biologists and individuals in the biotechnology industry.

Figures

Figure 1.
Figure 1.
A screenshot montage of ECMDB showing several of the ECMDBs search and data display tools for various metabolites. Not all fields are shown.

Similar articles

  • YMDB: the Yeast Metabolome Database.
    Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P, Mandal R, Krishnamurthy R, Sinelnikov I, Wilson M, Wishart DS. Jewison T, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D815-20. doi: 10.1093/nar/gkr916. Epub 2011 Nov 7. Nucleic Acids Res. 2012. PMID: 22064855 Free PMC article.
  • ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli.
    Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS. Sajed T, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. Nucleic Acids Res. 2016. PMID: 26481353 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 EcoCyc Database.
    Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I. Karp PD, et al. EcoSal Plus. 2018 Nov;8(1):10.1128/ecosalplus.ESP-0006-2018. doi: 10.1128/ecosalplus.ESP-0006-2018. EcoSal Plus. 2018. PMID: 30406744 Free PMC article. 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 41 articles

See all "Cited by" articles

References

    1. Vinayavekhin N, Homan EA, Saghatelian A. Exploring disease through metabolomics. ACS Chem. Biol. 2010;15:91–103. - 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, Mandal R, Sinelnikov IV, Broadhurst D, Wishart DS. MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis. Nucleic Acids Res. 2012;40:W127–W133. - 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

MeSH terms

Substances

Feedback