What is ECMDB?

ECMDB Version 2.0


The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. ECMDB currently contains 3755 small molecules with 1402 associated enzymes and 387 associated transporters. It also has 1542 metabolic pathways that are linked to 3011 metabolites. A total of 19,294 NMR and MS spectra (experimental and predicted) for 3098 different E. coli metabolites are also contained in the database. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.

ECMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (ECMDB) and the original publication (see below). We ask that users who download significant portions of the database cite the ECMDB paper in any resulting publications.

Citing ECMDB :

  1. Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A., Knox, C., Wilson, M., Grant, J., Djoumbou, Y. and Wishart, D. (2015). ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res, p.gkv1060. 26481353 .
  2. 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. Nucleic Acids Res. 2012 Jan;41(Database issue):D625-30. 23109553 .