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The EcoCyc Database

P. D. Karp
2002 Nucleic Acids Research  
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of E. coli, its enzymes, its transport proteins, and its mechanisms of transcriptional  ...  EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at URL http://ecocyc.org/.  ...  The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1093/nar/30.1.56 pmid:11752253 pmcid:PMC99147 fatcat:yohs2hxug5dujlgg6b5sbj3qqe

The EcoCyc Database

Peter D. Karp, Daniel Weaver, Suzanne Paley, Carol Fulcher, Aya Kubo, Anamika Kothari, Markus Krummenacker, Pallavi Subhraveti, Deepika Weerasinghe, Socorro Gama-Castro, Araceli M. Huerta, Luis Muñiz-Rascado (+10 others)
2014 EcoSal Plus  
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655.  ...  The database also includes information on E. coli gene essentiality, and on nutrient conditions that do or do not support the growth of E. coli.  ...  Acknowledgments Monica Riley led the curation of EcoCyc for many years, from its inception. Her efforts created the content for the first organism-scale metabolic database.  ... 
doi:10.1128/ecosalplus.esp-0009-2013 pmid:26442933 pmcid:PMC4243172 fatcat:7pymd2qgnfaw3bauwad5hox5l4

The EcoCyc and MetaCyc databases

P. D. Karp
2000 Nucleic Acids Research  
EcoCyc is an organism-speci c Pathway/Genome Database that describes the metabolic and signal-transduction pathways of E. coli, its enzymes, and | a new addition | its transport proteins.  ...  Both databases are queried using the Pathway T ools graphical user interface, which provides a wide variety of query operations and visualization tools.  ...  The contents of this article are solely the responsibility of the authors and do not necessarily represent the o cial views of the National Institutes of Health.  ... 
doi:10.1093/nar/28.1.56 pmid:10592180 pmcid:PMC102475 fatcat:c4vlajpphvdz3ln27dydoxs6vq

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 (+7 others)
2021 Frontiers in Microbiology  
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  ...  To leverage the EcoCyc curation effort and enhance the quality and usability of all E. coli databases within the BioCyc database collection (of which EcoCyc is a member database), curated gene and protein  ... 
doi:10.3389/fmicb.2021.711077 pmid:34394059 pmcid:PMC8357350 fatcat:zcjlf33bwbhk7dg3vqd7ch4wqq

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado (+9 others)
2016 Nucleic Acids Research  
EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the beststudied bacterial model organism.  ...  EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.  ...  Since our last publication on EcoCyc in the 2013 NAR Database Issue (2) , many improvements to EcoCyc, the Pathway Tools software, the BioCyc family of websites and the display and analysis tools available  ... 
doi:10.1093/nar/gkw1003 pmid:27899573 pmcid:PMC5210515 fatcat:27ttoout2zgfdgwa5rvtbc3xqu

Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the EcoCyc Database

A. Mackie, S. Paley, I. M. Keseler, A. Shearer, I. T. Paulsen, P. D. Karp
2013 Journal of Bacteriology  
from high-throughput phenotype microarrays into the EcoCyc database.  ...  We also integrated six data sets describing 16,119 observations of the growth of single-gene knockout mutants of E. coli K-12 into EcoCyc, which are relevant to antimicrobial drug design, provide clues  ...  We integrated the following growth data into a single collection available in the EcoCyc database (1) and in the supplemental files: (i) a collection of observations of the growth or nongrowth of laboratory  ... 
doi:10.1128/jb.01209-13 pmid:24363340 pmcid:PMC3957686 fatcat:i72wcqgl4ba5ldo7m5hnioor74

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Daniel S Weaver, Ingrid M Keseler, Amanda Mackie, Ian T Paulsen, Peter D Karp
2014 BMC Systems Biology  
Interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database.  ...  The model's derivation from EcoCyc enables query and visualization via the EcoCyc website, facilitating model reuse and validation by inspection.  ...  The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes  ... 
doi:10.1186/1752-0509-8-79 pmid:24974895 pmcid:PMC4086706 fatcat:au6jk2wu2fdprfmvcru6hxai4u

EcoCyc: The Resource and the Lessons Learned [chapter]

Peter D. Karp, Monica Riley
Bioinformatics: Databases and Systems  
It is useful to organize pathway databases as a collection of multiple types of biological objects: pathways, reactions, enzymes, genes, and compounds.  ...  This organization is to be contrasted with that of biological databases such as GenBank, Swiss-Prot, and PDB, which contain only a single type of biological object. Metabolic information is complex.  ... 
doi:10.1007/0-306-46903-0_5 fatcat:n2sivmsn6zbnrdvu47gkte77li

Dead End Metabolites - Defining the Known Unknowns of the E. coli Metabolic Network

Amanda Mackie, Ingrid M. Keseler, Laura Nolan, Peter D. Karp, Ian T. Paulsen, John Parkinson
2013 PLoS ONE  
The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration  ...  The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.  ...  DEMs remaining in the EcoCyc database.  ... 
doi:10.1371/journal.pone.0075210 pmid:24086468 pmcid:PMC3781023 fatcat:7vjwrrg2hvfkxkp5fvczfekavu

Comparison of annotation terms between automated and curated E. coli K12 databases

ReddySailaja Marpuri, Claire A Rinehart
2009 BMC Bioinformatics  
Methods were developed to compare these additional terms to the EcoCyc database and it was found that approximately 17% of the BASys predicted ontology's matched the EcoCyc database.  ...  BASys and EcoCyc were the databases used for comparison (3 and 4) .  ... 
doi:10.1186/1471-2105-10-s7-a10 fatcat:jh2ywbmu7jfvjdglrx7pekgnsu

EcoCyc: a comprehensive database resource for Escherichia coli

I. M. Keseler
2004 Nucleic Acids Research  
EcoCyc database.  ...  The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12.  ...  This work was supported by grant RR07861 from the NIH National Center for Research Resources.  ... 
doi:10.1093/nar/gki108 pmid:15608210 pmcid:PMC540062 fatcat:pryrhmotizgw5ndaofvwqw7coq

EcoCyc: fusing model organism databases with systems biology

Ingrid M. Keseler, Amanda Mackie, Martin Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol Fulcher, Araceli M. Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado (+12 others)
2012 Nucleic Acids Research  
EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655.  ...  Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology.  ...  The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes  ... 
doi:10.1093/nar/gks1027 pmid:23143106 pmcid:PMC3531154 fatcat:2g6l2e4twbdxdgnmeyhmetycmy

EcoCyc: A comprehensive view of Escherichia coli biology

I. M. Keseler, C. Bonavides-Martinez, J. Collado-Vides, S. Gama-Castro, R. P. Gunsalus, D. A. Johnson, M. Krummenacker, L. M. Nolan, S. Paley, I. T. Paulsen, M. Peralta-Gil, A. Santos-Zavaleta (+2 others)
2009 Nucleic Acids Research  
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network;  ...  ACKNOWLEDGEMENTS We thank Dr Robert Landick for suggesting the graphtrack display.  ...  OVERVIEW OF EcoCyc CONTENT Since the last NAR Database Issue publication on EcoCyc four years ago (1), significant additions and changes to the content and features of EcoCyc have occurred.  ... 
doi:10.1093/nar/gkn751 pmid:18974181 pmcid:PMC2686493 fatcat:tk5atoclqfbiza3tcyayuksfue

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism

P. Karp
1998 Nucleic Acids Research  
The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signaltransduction pathways, and its tRNAs.  ...  The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways.  ...  The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1093/nar/26.1.50 pmid:9399798 pmcid:PMC147256 fatcat:64pqxezo4jau7gahzp7bs4mxqe

Multidimensional annotation of the Escherichia coli K-12 genome

P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola (+2 others)
2007 Nucleic Acids Research  
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.  ...  Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites.  ...  We are grateful to Dr Robert Gunsalus for comments on this manuscript, and for his many suggestions regarding EcoCyc.  ... 
doi:10.1093/nar/gkm740 pmid:17940092 pmcid:PMC2190727 fatcat:nafpzty6i5hb5cocwmquj6gzka
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