SRI International and a group of collaborators propose to further develop the EcoCyc database (DB). EcoCyc is a freely and openly available model-organism DB for the bacterium Escherichia coll K-12 that is accessible to scientists through theWorldWideWeb, and may be downloaded for local installation. The project will create descriptions of the functions of all E. coli genes, and of its metabolic pathways, with information derived from the biomedical literature, thus creating a comprehensive knowledge base of E. coli. The project will begin a new effort to create DB descriptions of all types of gene regulation in E. coli, and to create a comprehensive collection of enzyme kinetics data for E. coli enzymes to facilitate systems biology. The project will also expand the Pathway Tools software used to query EcoCyc. EcoCyc serves as a general reference source on E. coli for experimental biologists, and is particularly useful for the analysis of functional-genomics experiments. The database also serves computational biologists who undertake global studies of E. coli, metabolic engineers who seek to make purposeful alterations to the metabolic network of E. coli, and bioinformaticists who use EcoCyc as a gold-standard dataset to develop new computational methods. Relevance. E. coli is the best studied bacterium on earth, therefore an electronic knowledge base that integrates experimental findings on E. coli from thousands of literature articles is a valuable resource not only for E. coli biologists, but for the many biologists who routinely learn about other bacteria by analogy to E. coli. For 1 example, scientists who study drug-resistant bacteria, and bacteria that are the subjects of bioterrorism research, frequently turn to the comprehensive collection of information in EcoCyc to accelerate their research.
| Caspi, Ron; Billington, Richard; Fulcher, Carol A et al. (2018) The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res 46:D633-D639 |
| Karp, Peter D; Billington, Richard; Caspi, Ron et al. (2017) The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform : |
| Keseler, Ingrid M; Mackie, Amanda; Santos-Zavaleta, Alberto et al. (2017) The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res 45:D543-D550 |
| Karp, Peter D; Latendresse, Mario; Paley, Suzanne M et al. (2016) Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform 17:877-90 |
| Karp, Peter D (2016) Crowd-sourcing and author submission as alternatives to professional curation. Database (Oxford) 2016: |
| Karp, Peter D (2016) How much does curation cost? Database (Oxford) 2016: |
| Gama-Castro, Socorro; Salgado, Heladia; Santos-Zavaleta, Alberto et al. (2016) RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res 44:D133-43 |
| Caspi, Ron; Billington, Richard; Ferrer, Luciana et al. (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44:D471-80 |
| Karp, Peter D (2016) Can we replace curation with information extraction software? Database (Oxford) 2016: |
| Weaver, Daniel S; Keseler, Ingrid M; Mackie, Amanda et al. (2014) A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst Biol 8:79 |
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