Frontiers in Microbiology (Jul 2021)
The EcoCyc Database in 2021
- 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,
- Alberto Santos-Zavaleta,
- Pallavi Subhraveti,
- Víctor H. Tierrafría,
- Alan J. Wolfe,
- Julio Collado-Vides,
- Julio Collado-Vides,
- Ian T. Paulsen,
- Peter D. Karp
Affiliations
- Ingrid M. Keseler
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Amanda Mackie
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Richard Billington
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- César Bonavides-Martínez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Ron Caspi
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Anamika Kothari
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Markus Krummenacker
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Peter E. Midford
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Luis Muñiz-Rascado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Wai Kit Ong
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Suzanne Paley
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Alberto Santos-Zavaleta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Alberto Santos-Zavaleta
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, México
- Pallavi Subhraveti
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- Víctor H. Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Julio Collado-Vides
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
- Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Peter D. Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
- DOI
- https://doi.org/10.3389/fmicb.2021.711077
- Journal volume & issue
-
Vol. 12
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.
Keywords
