About MetaCyc


Guide To MetaCyc
Querying Examples
Update History
Advisory Board
Webinars

Services

Join MetaCyc Mailing List
Faster MetaCyc Search
Web Services
SRI AI Center
Carnegie Institution of Washington
Chemaxon


Overview | Motivations | Contents | Querying & Visualization | Development | Software | Updating | Linking

Database Overview

MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways. It stores predominantly qualitative information rather than quantitative data, although we have begun capturing some quantitative data such as enzyme kinetics data. "MetaCyc" is pronounced "met-a-sike". It sounds like "encyclopedia".

A unique property of MetaCyc is that it is curated [def] from the scientific experimental literature according to an extensive process [more], such that:

  • More than 1900 different organisms are represented
  • The majority of pathways occur in microorganisms and plants
  • More than 1530 metabolic pathways are stored, with more than 8,600 enzymatic reactions and more than 24,000 associated literature citations
  • MetaCyc stores all enzyme-catalyzed reactions that have been assigned EC numbers by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)
  • MetaCyc also stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number

Motivations

The MetaCyc mission is to serve a broad community of researchers from genetics, molecular biology, microbiology, biochemistry, genomics, bioinformatics, metabolic engineering, and systems biology in support of the following tasks:

Support computational metabolic network prediction. One of MetaCyc's primary applications is to serve as a reference database for computationally predicting the metabolic network of an organism from its annotated genome, such as by the PathoLogic algorithm, part of Pathway Tools. [example]

Provide an encyclopedic reference on pathways and enzymes. MetaCyc is used as a readily accessible source of up-to-date, literature-curated information on metabolic pathways and enzymes by researchers for basic research and genome analysis, and by students and teachers for educational purposes. [example]

Support metabolic engineering. Metabolic engineers use MetaCyc as an encyclopedia of metabolic pathways and enzymes that may be genetically engineered into an organism to alter its metabolism. [example]

[top]

Database Contents

MetaCyc stores pathways involved in:
  • Primary metabolism [def]
  • Secondary metabolism [def]
MetaCyc also stores compounds, proteins, protein complexes and genes associated with these pathways.

MetaCyc is extensively linked to other biological databases [list] containing protein and nucleic-acid sequence data, bibliographic data and protein structures.

Unlike EcoCyc, MetaCyc provides little genomic data. MetaCyc does contain objects for the genes that encode most of the enzymes within the DB, but MetaCyc contains no sequence data. It does contain links to external sequence databases.

[top]

Query and Visualization

MetaCyc data can be browsed and queried in several different ways. For pathways, proteins, reactions and compounds, the MetaCyc site supports:
  • Text-based searching, when trying to find information without knowing exactly how an object is named [example]
  • Browsing using ontologies, when one wants to search by proceeding from general categories to specific instances [example]
  • Direct queries, when an identifier is known [example]

Comparison features combine MetaCyc with other BioCyc databases to provide additional ways for viewing data. Examples for Cross-Species comparisons include:

  • Comparing specific pathways between two or more organisms [example]
  • Comparing the genomic maps of two or more organisms [example]
Additionally, a desktop version of the software provides substantially more powerful capabilities. When installed locally with multiple organism-specific databases, the desktop version enables several powerful capabilities, such as:

  • Comparing the overall metabolic networks of different organisms [example]
The desktop version can be downloaded here.

[top]

The MetaCyc Data Universe

MetaCyc inter-relates pathway information (including reactions and their substrates) with genes and their protein products. The diagram below depicts the hyperlinks that are typically available within MetaCyc, allowing the user to navigate among pathways, genes, enzymes, etc.

[Click on the data object to access MetaCyc data]

Overall view of the MetaCyc data universe enzymes pathways compounds reactions genes

Linking to MetaCyc

Users are encouraged to link their Web site or application to MetaCyc as described here.

[top]

Development

MetaCyc is a collaborative project between SRI International, the Boyce Thomson Institute for Plant Research, and the Carnegie Institution of Washington. Since its beginning in 1998, MetaCyc's data have been gathered from a variety of literature and on-line sources. A staff of several full-time curators update MetaCyc on an ongoing basis using a literature-based strategy. [def] [more]

[top]

Underlying Software

MetaCyc is based on the same retrieval and visualization software used by EcoCyc and other BioCyc databases - the Pathway Tools platform -- which can be obtained here.

[top]

Updating

The Web version of the MetaCyc database is updated quarterly. [MetaCyc release history ]

[top]