The EcoCyc Database in 2021

Frontiers in Microbiology

卷:12

Markus Krummenacker¹  Pallavi Subhraveti¹  Suzanne Paley¹  Ron Caspi¹  Anamika Kothari¹  Wai Kit Ong¹  Ingrid M. Keseler¹  Peter D. Karp¹  Richard Billington¹  Peter E. Midford¹  Luis Muñiz-Rascado²  César Bonavides-Martínez²  Víctor H. Tierrafría²  Socorro Gama-Castro²  Julio Collado-Vides³  Alan J. Wolfe⁴  Ian T. Paulsen⁵  Amanda Mackie⁵  Alberto Santos-Zavaleta⁶ 

[1] Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States;

[2] Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México;

[3] Department of Biomedical Engineering, Boston University, Boston, MA, United States;

[4] Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States;

[5] Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia;

[6] Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, México;

关键词: Escherichia coli;    EcoCyc;    model-organism database;    drug efflux transporters;    metabolism;    gene regulation;   

DOI  :  10.3389/fmicb.2021.711077

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown