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

TITLE=The EcoCyc Database in 2021

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.711077

DOI=10.3389/fmicb.2021.711077

ISSN=1664-302X

ABSTRACT=<p>The EcoCyc model-organism database collects and summarizes experimental data for <italic>Escherichia coli</italic> 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.</p>