The EcoCyc and MetaCyc databases

By Peter D. Karp, M. Riley, Milton H. Saier Jr., Ian T. Paulsen, Suzanne M. Paley, A. Pellegrini-Toole. Nucleic Acids Res., 2000

322 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4736bb7737f4555ad6e71babca8e68a8abd74157

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Citations in the corpus

Subnetwork hierarchies of biochemical pathways (2002, methodology): “…we use (the same data set as in Jeong et al., 2001) were constructed from the WIT database1 (Overbeek et al., 2000) consisting of 43 organisms from 1Similar information can be obtained from the KEGG (Kanehisa and Goto, 2000), EcoCyc (Karp et al., 2000) and EMP (Selkov et al., 1996) databases.”
Creating the gene ontology resource: design and implementation. (2001, background): “These types of classifications have been applied in a manner that supports the ability to search for genes by physiological roles in databases such as EcoCyc and MetaCyc (Karp et al. 2000).”
Regulation of gene expression in flux balance models of metabolism. (2001, background): “Databases have already been developed and made available online which detail the known regulation of E. coli (Karp et al., 2000; Salgado et al., 2001); such information, made available for this and other organisms, will enable the construction of genome-scale metabolic/regulatory microbial models.”
A new approach to decoding life: systems biology. (2001, unknown): “For instance, the Database of Interacting Proteins (137), BIND (10), and MIPS (90a) contain searchable indices of known protein-protein interactions; TRANSFAC (133) and SCPD (142) catalog interactions between proteins and DNA (i.e., transcriptionfactor interactions), and databases of metabolic pathw”
An automated method for finding molecular complexes in large protein interaction networks (2003, unknown): “This graph theory approach has been used by other biomolecular interaction database projects such as DIP [16], CSNDB [17], TRANSPATH [18], EcoCyc [ 19 ] and WIT [20] and is discussed by Wagner and Fell [21].”
The MetaCyc database of metabolic pathways and enzymes - a 2019 update (2019, background): “org) (pronounced ‘met-a-sike’, as in ‘encyclopedia’) is a highly curated reference database of metabolism from all domains of life that has been curated for over 20 years (1).”