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:

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:

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

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:

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:

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:

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 Web Site MetaCyc

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

G6G Abstract Number 20232

G6G Manufacturer Number 102506