Desktop Application
Bring the power of BioCyc.org securely in-house, with the abilities to create and
edit PGDBs, perform metabolic modeling, and query/update using APIs.
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]
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.
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]
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]
Linking to MetaCyc
Users are encouraged to link their Web site or application to MetaCyc as described here.
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.
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