Introduction to BioCyc
The BioCyc collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes and metabolic pathways of thousands of sequenced organisms. BioCyc PGDBs are generated by software that predict the metabolic pathways of completely sequenced organisms, predict which genes code for missing enzymes in metabolic pathways, and predict operons. BioCyc also integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.
BioCyc databases (DBs) are organized into tiers according to the amount of manual updating they have received.
BioCyc Software Tools
How to Learn More About BioCycThe following additional information exists about the BioCyc site:
BioCyc data files may be downloaded to your site, and BioCyc data can be queried via web services. And you can install BioCyc on computers at your site, running it as a local Web server, and/or as a desktop application. The desktop application has a number of capabilities that the Web server does not [desktop mode]; we highly recommend it for frequent BioCyc users.
Definitions of Terminology on the BioCyc WebsiteHere we define a few key terms. See the glossary for more definitions.
Pathway/Genome Database (PGDB). A database that describes
Tier 1 PGDB. PGDBs in Tier 1 have received at least one year of literature-based curation by scientists. For example, the EcoCyc DB is the result of more than 20 person-years of effort to enter information from the E. coli literature about the metabolism, transport, and genetic regulatory processes of this organism. More information about curation practices is available in the Curator Guide.
Tier 2 PGDB. PGDBs in Tier 2 were generated by the PathoLogic program, which predicted their metabolic pathways; their operons (for bacteria only); and some missing enzymes in their predicted pathways (pathway hole fillers). The resulting PGDBs underwent manual review by a person to remove false-positive pathway predictions that they could detect, and to perform refinements such as defining protein complexes. The resulting PGDBs also underwent a period of literature-based curation, such as to enter metabolic pathways that had been experimentally elucidated in the organism but that were not inferred by PathoLogic. [list of Tier 2 PGDBs]
Tier 3 PGDB. PGDBs in Tier 3 were generated by PathoLogic, which predicted metabolic pathways, operons (for bacteria only), pathway hole fillers, and transport reactions. The resulting PGDBs did not undergo manual review of the pathway predictions, nor subsequent literature curation. Therefore, the pathway predictions should be treated with due caution. [list of Tier 3 PGDBs]
Pathway Tools Software. Pathway Tools is used to construct, update, visualize, query, and analyze PGDBs, such as the BioCyc collection. It is freely available to academics interested in creating PGDBs for organisms of interest to them. Components of Pathway Tools are:
BioCyc: The collection of PGDBs at URL http://BioCyc.com/ is called the BioCyc Database Collection. EcoCyc and MetaCyc are component databases within the BioCyc collection.
BioCyc Organism Home PagesBioCyc contains home pages for the following organisms. You can visit these pages as an easy entrez into the BioCyc genomes for these organisms.
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