EcoCyc: A comprehensive view of Escherichia coli biology

By I. Keseler, César Bonavides-Martínez, Julio Collado-Vides, S. Gama-Castro, R. Gunsalus, D. A. Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne M. Paley, Ian T. Paulsen and 4 more. Nucleic Acids Res., 2008

407 citations recorded by the source corpus.

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; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d460d469cae87c66916211d14c6373ee855dd1e5

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Citations in the corpus

Fate of low molecular weight organic substances in an arable soil: From microbial uptake to utilisation and stabilisation (2014, background): “, 2009), carboxylic acids enter from side branches of the citric acid cycle (Caspi et al., 2012; Keseler et al., 2009), and amino acids enter glycolysis or the citric acid cycle from individual side branches at different steps (Apostel et al.”
The NCBI BioSystems database (2009, methodology): “Presently, NCBI BioSystems contains pathways from KEGG (2), Human Reactome (3) and EcoCyc (9) for a total of about 100 000 BioSystem records.”
Database resources of the National Center for Biotechnology Information (2006, methodology): “Currently, Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (35–37), BioCyc (38), Reactome (39), the Pathway Interaction Database (40), WikiPathways (41,42) and Gene Ontology (43).”
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Capturing the mutational landscape of the beta-lactamase TEM-1 (2013, background): “First, about a fourth of all proteins in a bacterial species such as Escherichia coli are enzymes (19).”
BioPAX – A community standard for pathway data sharing (2010, neutral): “• Gene regulatory networks involve transcription and translation events and their control 12,14 .”
Database resources of the National Center for Biotechnology Information (2014, methodology): “Currently Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (49–51), BioCyc (52), Reactome (53), the Pathway Interaction Database (54), WikiPathways (55,56) and Gene Ontology (57).”
Metabolomics in pesticide research and development: review and future perspectives (2011, neutral): “…http://eros.fiehnlab.ucdavis.edu:8080/binbase-compound/ Fiehn et al. (2005) BioCyc http://biocyc.org/ Karp et al. (2005), Caspi et al. (2008), Keseler et al. (2009) BioMeta http://biometa.cmbi.ru.nl/ Ott and Vriend (2006) ChEBI http://www.ebi.ac.uk/chebi/ Degtyarenko et al. (2008) ChemDB…”
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 (2016, methodology): “An initiative to represent ET pathways in EcoCyc was first described in 2009 (10) along with the subsequent addition of 11 ET pathways.”
Using graph theory to analyze biological networks (2011, background): “Among the several databases holding information about biochemical networks some of the most popular are the Kyoto Encyclopedia of Genes and Genomes (KEGG) [40], EcoCyc [41], BioCyc [42] and metaTIGER [43].”
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011, methodology): “EcoCyc was used to identify gene functions, and several genes with verified metabolic functions were then added to iJO1366.”
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Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm (2010, background): “The quaternary structure of each selected structure was determined using the PQS web server [80] and was verified, where possible, with the EcoCyc database; it should be noted that correct identification of a protein’s quaternary structure is a non-trivial undertaking, and the PQS predictions are un”
Database resources of the National Center for Biotechnology Information (2011, methodology): “Currently Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (32–34), BioCyc (35), Reactome (36), the Pathway Interaction Database (37) and WikiPathways (38,39).”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, background): “Arabidopsis thaliana ARATH TAIR (11) Dicot plant Caenorhabditis elegans CAEEL WormBase (12) Nematode worm Danio rerio DANRE Ensembl, ZFIN (13) Zebrafish Dictyostelium discoideum DICDI DictyBase (14) Cellular slime mold Drosophila melanogaster DROME FlyBase (15) Fruit fly Escherichia coli ECOLI EcoCy”