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Article  July 1, 2021

The EcoCyc Database in 2021

SRI Authors Peter Karp

Citation

COPY

Ingrid M. Keseler, Socorro Gama-Castro, Amanda Mackie, Richard Billington, César Bonavides-Martínez, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Luis Muñiz-Rascado, Wai Kit Ong, Suzanne Paley, Alberto Santos-Zavaleta, Pallavi Subhraveti, Víctor H. Tierrafría, Alan J. Wolfe, Julio Collado-Vides, Ian T. Paulsen, Peter. D. Karp. Frontiers in Microbiology, Vol. 12, July 2021, Article 711077.

Abstract

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

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