Introduction to BioCyc and Pathway Tools

BioCyc is a database collection and website that couples rich and high-quality data with extensive bioinformatics tools.

The Pathway Tools software -- the software that underlies BioCyc -- can be installed at your site to create BioCyc-like databases for genomes of interest. The software will compute metabolic reconstructions for sequenced genomes, and can be used to create quantitative metabolic models.

BioCyc Benefits: Better Science, Faster

BioCyc accelerates your science: BioCyc enables better science:

BioCyc Database Collection

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes, metabolic pathways, and (in some cases) regulatory networks of thousands of sequenced organisms. Each database combines information from several sources:

The EcoCyc database is freely available to all users because its curation is supported by NIH funding. Also free is the database for the cyanobacterium Arthrospira platensis NIES-39 as an example of a Tier 3 database. The other BioCyc databases are available via subscription, which supports their curation. To obtain free access to the other BioCyc databases for teaching purposes, please click here.

BioCyc data files may be downloaded to your site, and BioCyc data can be queried via web services. Bioinformatics Tools provides a suite of bioinformatics tools (see Tools menu) for accessing and analyzing the BioCyc databases. The tools provide search and visualization, omics data analysis, and comparative genomics and comparative pathway analysis:

Pathway Tools Software

Pathway Tools is an enterprise genome and pathway data management tool and is among the most extensive bioinformatics software packages. It is the software used to create BioCyc databases and it powers the website and several additional websites. Its capabilities are described in detail here. Please click here to see Pathway Tools testimonials.

Pathway Tools can run as both a desktop application and as a web server.

Installing Pathway Tools at your site brings these advantages:

How to Learn More About BioCyc

The following additional information exists about the BioCyc site:

Definitions of Terminology on the BioCyc Website

Here 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, such as EcoCyc, MetaCyc, and HumanCyc, have received at least one year of literature-based curation by scientists. 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); protein complexes; 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 is called the BioCyc Database Collection. EcoCyc and MetaCyc are component databases within the BioCyc collection.

BioCyc Organism Home Pages

BioCyc contains home pages for the following organisms. You can visit these pages to pre-select these organism databases for searches.

 Bacillus subtilis
 Saccharomyces cerevisiae
 Salmonella enterica