There are currently two ways to use data from MetNetDB in third-party applications. The first is through the Cytoscape XML builder. This Java applet can compile pathways from MetNetDB into XML files readable by Cytoscape. Files built by this applet contain up-to-date information about each pathway, so any changes made to the database will be immediately reflected in the XML. This is the preferred method for building files used by Cytoscape and its FCModeler plugins.
The second is via the MetNet SBML site. This site contains pre-compiled pathway information in SBML (Systems Biology Markup Language) format. These files are readable by a variety of bioinformatics applications (visit the SBML homepage for a partial list of applications that support SBML). Please note that this feature is still under development, so the SBML files do not contain as much information as the Cytoscape XML files. Also, these files are only compiled periodically, so their information may not be as recent as files built by the Cytoscape XML applet.