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The EcoCyc Database in 2021.
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.
Affiliation
  • Keseler IM; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Gama-Castro S; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Mackie A; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
  • Billington R; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Bonavides-Martínez C; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Caspi R; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Kothari A; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Krummenacker M; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Midford PE; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Muñiz-Rascado L; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Ong WK; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Paley S; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Santos-Zavaleta A; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Subhraveti P; Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, México.
  • Tierrafría VH; Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
  • Wolfe AJ; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Collado-Vides J; Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States.
  • Paulsen IT; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
  • Karp PD; Department of Biomedical Engineering, Boston University, Boston, MA, United States.
Front Microbiol ; 12: 711077, 2021.
Article in En | MEDLINE | ID: mdl-34394059
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Front Microbiol Year: 2021 Document type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Front Microbiol Year: 2021 Document type: Article Affiliation country: United States