Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D334-7.
doi: 10.1093/nar/gki108.

EcoCyc: a comprehensive database resource for Escherichia coli

Ingrid M Keseler  1 , Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne Paley, Ian T Paulsen, Martín Peralta-Gil, Peter D Karp
Affiliations

EcoCyc: a comprehensive database resource for Escherichia coli

Ingrid M Keseler et al. Nucleic Acids Res. .

Abstract

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein-ligand interactions.

PubMed Disclaimer

References

    1. Paley S.M. and Karp,P.D. (2002) Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics, 18, 715–724. - PubMed
    1. Krieger C.J., Zhang,P., Mueller,L.A., Wang,A., Paley,S., Arnaud,M., Pick,J., Rhee,S.Y. and Karp,P.D. (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 32, D438–D442. - PMC - PubMed
    1. Karp P.D., Arnaud,M., Collado-Vides,J., Ingraham,J., Paulsen,I.T. and Saier,M.H.,Jr (2004) The E. coli EcoCyc database: no longer just a metabolic pathway database. ASM News, 70, 25–30.
    1. Karp P.D., Paley,S., Krieger,C.J. and Zhang,P. (2004) An evidence ontology for use in pathway/genome databases. In Altman,R.B., Dunker,A.K., Hunter,L., Jung,T. and Klein,T.E. (eds), Pacific Symposium on Biocomputing 2004. World Scientific Press, Singapore, pp. 190–201. - PubMed
    1. Blattner F.R., Plunkett,G.,III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453–1462. - PubMed

Publication types

Substances