MetaCyc

Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract The MetaCyc 'metabolic pathway' database contains pathways from over 2,000 different organisms. MetaCyc describes metabolic pathways, reactions, enzymes, and substrate compounds.

The MetaCyc data were gathered from a variety of literature and on-line sources and contain citations to the source of each pathway.

It stores predominantly qualitative information rather than quantitative data, although the manufacturer has begun capturing some quantitative data such as enzyme kinetics data. "MetaCyc" is pronounced "met-a- sike". It rhymes with "encyclopedia".

Products features/capabilities include:

1) A unique property of MetaCyc is that it is curated from the scientific experimental literature according to an extensive process, such that:

• a) More than 2,000 different organisms are represented.
• b) The majority of pathways occur in microorganisms and plants.
• c) More than 1,580 metabolic pathways are stored, with more than 8,800 enzymatic reactions and more than 26,000 associated literature citations.
• d) MetaCyc stores all enzyme-catalyzed reactions that have been assigned 'Enzyme Commission' numbers (EC numbers) by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).
• e) MetaCyc also stores hundreds of additional enzyme-catalyzed reactions that have Not yet been assigned an EC number.

2) 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:

• a) 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 (see G6G Abstract Number 20235).
• b) 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.
• c) 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.

3) Database Contents -- MetaCyc stores pathways involved in:

• a) Primary metabolism - defined as the metabolism of primary compounds.
• b) Secondary metabolism - described as the metabolism of secondary compounds, defined simply as compounds other than primary compounds.

MetaCyc also stores compounds, proteins, protein complexes and genes associated with these pathways.

MetaCyc is extensively linked to other biological databases 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 many enzymes within the database (DB), but MetaCyc contains No sequence data. It does contain links to external sequence databases.

4) Query and Visualization --

MetaCyc data can be browsed and queried in several different ways. For pathways, proteins, reactions and compounds, the MetaCyc site supports:

• a) Text-based searching, when trying to find information without knowing exactly how an object is named.
• b) Browsing using ontologies, when one wants to search by proceeding from general categories to specific instances.
• c) Direct queries, when an identifier is known.

Comparison features combine MetaCyc with other BioCyc databases (see G6G Abstract Number 20230) to provide additional ways for viewing data.

Examples for Cross-Species comparisons include:

• a) Comparing specific pathways between two (2) or more organisms.
• b) Comparing the genomic maps of two (2) or more organisms.

Additionally, a desktop version of the software provides substantially more advanced capabilities.

When installed locally with 'multiple organism-specific' databases, the desktop version enables several advanced capabilities, such as:

• a) Comparing the overall metabolic networks of different organisms.

5) Underlying Software -- MetaCyc is based on the same retrieval and visualization software used by EcoCyc (see G6G Abstract Number 20231).

6) Updating -- The Web version of the MetaCyc database is updated quarterly.

System Requirements

See G6G Abstract Number 20230 or BioCyc

Manufacturer

• Bioinformatics Research Group
• Dr Peter D Karp
• Director, Bioinformatics Research Group
• Artificial Intelligence Center
• SRI International
• 333 Ravenswood Avenue
• Menlo Park, CA 94025-3493
• Phone: (650) 859-2000
• ptools-info@ai.sri.com
• biocyc-support@ai.sri.com

Manufacturer Web Site MetaCyc

Price Free for academic institutions. Fee required for commercial use. Licence required.

G6G Abstract Number 20232

G6G Manufacturer Number 102506