The EcoCyc Database

By Peter D. Karp, M. Riley, Milton H. Saier Jr., Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, A. Pellegrini-Toole, César Bonavides-Martínez, S. Gama-Castro. Nucleic Acids Res., 2002

562 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f6f9a5260b6e8c1bfe1d614daeb76b58dba73b8e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Prolinks: a database of protein functional linkages derived from coevolution (2004, methodology): “We used the EcoCyc library of E. coli multiprotein complexes [27] to assess the ability of the Proteome Navigator to identify direct protein physical interactions.”
Enzyme-specific profiles for genome annotation: PRIAM. (2003, background): “Once enzyme-coding genes are detected, they can be reported in pathway-oriented databases such as WIT (7), ECOCYC (8), METACYC (9), KEGG (10) or UMBBD (11).”
Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003, methodology): “Annotation updates to the E. coli genome (55), coupled with previously published data and organism-speciﬁc databases, including EcoCyc (27), have enabled expansion of Edwards and Palsson’s metabolic model.”
A novel method for accurate operon predictions in all sequenced prokaryotes (2005, background): “This latter result explains why a previous study focusing only on E.coli and B.subtilis reached the conclusion that distance models can be applied across species (9); however, our results suggest that this is not true in general.”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, background): “Information about substrate and cofactor utilization can be obtained from organism-specific biochemical studies and may also be listed in organism-specific databases (e.g., Ecocyc 43 ).”
Computational prediction of human metabolic pathways from the complete human genome (2004, methodology): “Both were originally developed for the EcoCyc project [2,3].”
The Pathway Tools software (2002, methodology): “The PathoLogic inference process predicts the metabolicpathway complement of S from its genome by comparison to the MetaCyc pathway DB (Karp et al., 2002).”
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks (2003, unknown): “∗To whom correspondence should be addressed.”
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms (2003, methodology): “Several methods and metabolic databases are available to reconstruct an organism specific metabolic network from genome information, such as KEGG (http://www.genome.ad.jp/kegg), WIT (wit.mcs.anl.gov/WIT) and EcoCyc (biocyc.org/ecocyc/) (Ogata et al., 1999; Overbeek et al., 2000; Karp et al., 2002).”
AraCyc: A Biochemical Pathway Database for Arabidopsis1 (2003, methodology): “In this work, we used Pathway Tools software (Karp et al., 2002a) to build a database for Arabidopsis metabolism .”
MetaCyc: a multiorganism database of metabolic pathways and enzymes (2005, background): “EcoCyc ( 3 ), a model organism DB (MOD) for Escherichia coli.”
Graph theory and networks in Biology. (2006, background): “coli [17, 43–47], and are stored in databases such as the KEGG [17] or BioCyc [18] databases.”
Bio-ontologies: current trends and future directions (2006, methodology): “Rich, high-fidelity models of biology, such as can be provided by ontologies, are also seen as a way of providing a means of forming knowledge bases such as EcoCyc [7], RiboWeb [8] and PharmGKB [9].”