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; Pallavi Subhraveti; Víctor H. Tierrafría; Alan J. Wolfe; Julio Collado-Vides; Ian T. Paulsen; Peter D. Karp

doi:10.3389/fmicb.2021.711077

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, Pallavi Subhraveti, Víctor H. Tierrafría, Alan J. Wolfe, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

173 Citations (Scopus)

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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.

Original language	English
Article number	711077
Pages (from-to)	1-10
Number of pages	10
Journal	Frontiers in Microbiology
Volume	12
DOIs	https://doi.org/10.3389/fmicb.2021.711077
Publication status	Published - Jul 2021

Bibliographical note

Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

Escherichia coli
EcoCyc
drug efflux transporters
metabolism
model-organism database
gene regulation

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10.3389/fmicb.2021.711077

Publisher version (open access)Final published version, 3.86 MBLicence: CC BY

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Keseler, I. M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., Muñiz-Rascado, L., Ong, W. K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V. H., Wolfe, A. J., Collado-Vides, J., Paulsen, I. T., & Karp, P. D. (2021). The EcoCyc Database in 2021. Frontiers in Microbiology, 12, 1-10. Article 711077. https://doi.org/10.3389/fmicb.2021.711077

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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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note = "Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher. ",

year = "2021",

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doi = "10.3389/fmicb.2021.711077",

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Keseler, IM, Gama-Castro, S, Mackie, A, Billington, R, Bonavides-Martínez, C, Caspi, R, Kothari, A, Krummenacker, M, Midford, PE, Muñiz-Rascado, L, Ong, WK, Paley, S, Santos-Zavaleta, A, Subhraveti, P, Tierrafría, VH, Wolfe, AJ, Collado-Vides, J, Paulsen, IT & Karp, PD 2021, 'The EcoCyc Database in 2021', Frontiers in Microbiology, vol. 12, 711077, pp. 1-10. https://doi.org/10.3389/fmicb.2021.711077

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AU - Keseler, Ingrid M.

AU - Gama-Castro, Socorro

AU - Mackie, Amanda

AU - Billington, Richard

AU - Bonavides-Martínez, César

AU - Caspi, Ron

AU - Kothari, Anamika

AU - Krummenacker, Markus

AU - Midford, Peter E.

AU - Muñiz-Rascado, Luis

AU - Ong, Wai Kit

AU - Paley, Suzanne

AU - Santos-Zavaleta, Alberto

AU - Subhraveti, Pallavi

AU - Tierrafría, Víctor H.

AU - Wolfe, Alan J.

AU - Collado-Vides, Julio

AU - Paulsen, Ian T.

AU - Karp, Peter D.

N1 - Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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N2 - 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.

AB - 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.

KW - Escherichia coli

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KW - drug efflux transporters

KW - metabolism

KW - model-organism database

KW - gene regulation

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SN - 1664-302X

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SP - 1

EP - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

M1 - 711077

ER -

The EcoCyc Database in 2021

Abstract

Bibliographical note

Keywords

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