The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

By Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, I. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller and 5 more. Nucleic Acids Res., 2015

803 citations recorded by the source corpus.

The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/89c433d6a7160bba49ef164fa93c3036d9f7ac5e

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Citations in the corpus

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018, methodology): “The database channel is based on manually curated interaction records assembled by expert curators, at KEGG (41), Reactome (50), BioCyc (51) and Gene Ontology (52), as well as legacy datasets from PID and BioCarta.”
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor (2018, methodology): “MetaCyc is a pathway database that collects only experimentally verified pathways with curated reversibility information and mass-balanced reactions [26].”
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes (2018, methodology): “Proteomes are associated with KEGG pathways based on KO term assignments, and are associated with MetaCyc pathways (19) based on gene annotations with Enzyme Commission numbers derived from KO terms.”
U.S. immigration westernizes the human gut microbiome (2018, neutral): “Resulting functional pathways were mapped to and colored by the top-level categories of the MetaCyc (Caspi et al., 2008) ontology.”