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Introduction to BioCyc and Pathway Tools

BioCyc and Pathway Tools accelerate science by providing extensive data for sequenced genomes, and a wide suite of bioinformatics tools.

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 three sources:
  • Computational inferences: Our Pathway Tools software predicts the metabolic pathways of an organism, predicts which genes code for missing enzymes in metabolic pathways, and predicts operons.

  • Imported data: BioCyc integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt, and gene-essentiality datasets.

  • Manual curation: The Tier 1 and Tier 2 PGDBs have received literature-based curation to enter new gene functions, pathways, protein complexes, regulation, and more.

BioCyc data files may be downloaded to your site, and BioCyc data can be queried via web services.

BioCyc.org Website

BioCyc.org provides a suite of bioinformatics tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway analysis.
  • Search and Visualization: Multiple search tools enable users to find genes, pathways, and metabolites of interest, which are presented in corresponding information pages. A variety of visualization tools are provided, such as metabolic-pathway diagrams, and zoomable diagrams depicting the complete metabolic charts of each organism [example].

  • Genome Browser: The BioCyc genome browser [example] enables analysis of positional genome datasets via tracks.

  • Omics Data Analysis: Tools include statistical over-representation analysis; and visualization of gene expression, proteomics, or metabolomics data on metabolic-chart diagrams [example] and on the Omics Dashboard [example].

  • SmartTables: Biologist-friendly analysis capabilities for groups of genes or metabolites that are stored in your BioCyc account.

  • Metabolic Route Search: Search for reactions paths connecting specified metabolites in the metabolic network, with the option of adding new reactions from the MetaCyc DB.

  • Comparative Analysis: Tools include comparison of pathways, metabolites, transporters, and regulatory networks -- (see menu command Analysis -> Comparative Analysis).

Pathway Tools Software

Pathway Tools is the software used to create BioCyc databases and it powers the BioCyc.org website.

Installing Pathway Tools at your site brings these advantages:

  • Install a private local set of BioCyc PGDBs on your intranet

  • Create new PGDBs from your own genome data

  • Edit PGDBs interactively to add new gene functions and pathways

  • Build quantitative metabolic flux models using Flux-Balance Analysis with the MetaFlux tool

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

  • The genome of an organism -- its chromosome(s), genes, and genome sequence
  • The product of each gene
  • The metabolic network of the organism -- its pathways, reactions, enzymes, and metabolites
  • The transporter complement of the organism
  • The regulatory network of the organism, including its operons, transcription factors, and the interactions between transcription factors and their small-molecule ligands and DNA binding sites

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:

  • The Pathway/Genome Navigator supports querying, visualization, and analysis of PGDBs
  • The Pathway/Genome Editors support interactive updating and refinement of PGDBs
  • PathoLogic performs computational inferences such as pathway prediction
  • MetaFlux enables creation of quantitative metabolic models from PGDBs

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 Pages

BioCyc contains home pages for the following organisms. You can visit these pages as an easy entrez into the BioCyc genomes for these organisms.

 EcoCyc EcoCyc.org
 MetaCyc MetaCyc.org
 HumanCyc HumanCyc.org
 Bacillus subtilis 168BsubCyc.org
 Helicobacter pyloriHelicobacter.biocyc.org
 Listeria monocytogenesListeria.biocyc.org
 Mycobacterium tuberculosisMycobacterium.biocyc.org
 Pseudomonas aeruginosaPseudomonas.biocyc.org
 Peptoclostridium difficileClostridium.biocyc.org
 Saccharomyces cerevisiae yeast.biocyc.org
 Salmonella enterica Salmonella.biocyc.org
 Shigella flexneriShigella.biocyc.org
 Vibrio choleraeVibrio.biocyc.org