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EcoCyc: a comprehensive database resource for Escherichia coli
Open accessAbstract
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.
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Cited by
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Self-citationFaith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050008 · Cited by 1,563
Sublethal Antibiotic Treatment Leads to Multidrug Resistance via Radical-Induced Mutagenesis
Kohanski, M. A., DePristo, M. A., & Collins, J. J. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.01.003 · Cited by 985
Rolfe, M. D., Rice, C. J., Lucchini, S., Pin, C., Thompson, A., Cameron, A. D. S., Alston, M., Stringer, M. F., Betts, R. P., Baranyi, J., et al. (2012) · Journal of Bacteriology · doi:10.1128/jb.06112-11 · Cited by 711
Minimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622
Metadata
- Authors
- Keseler, I. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-12-17
- Volume
- 33
- Issue
- Database issue
- Pages
- D334-D337
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2108078368
- Cited by
- 733
- References
- 0
- FWCI
- 27.55
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Keseler, I. M. (2004). EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research. https://doi.org/10.1093/nar/gki108
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
