Abstract
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.
Highlights
MetaCyc (MetaCyc.org) is a highly curated reference database of small-molecule metabolism from all domains of life
In addition to its role as a general reference on metabolism, MetaCyc can be used by the PathoLogic component of the Pathway Tools software [2] as a reference database to computationally predict the metabolic network of any organism that has a sequenced and annotated genome [3]
The predicted metabolic network is captured in the form of a Pathway/Genome Database (PGDB)
Summary
MetaCyc (MetaCyc.org) is a highly curated reference database of small-molecule metabolism from all domains of life. In addition to its role as a general reference on metabolism, MetaCyc can be used by the PathoLogic component of the Pathway Tools software [2] as a reference database to computationally predict the metabolic network of any organism that has a sequenced and annotated genome [3]. Since the last Nucleic Acids Research publication we have added several important capabilities to the SmartTables, including: r Creating ‘frozen’ copies: This feature allows a user to publish a set of PGDB objects, such as a gene or metabolite list, within a publically readable, non-modifiable Smart-
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