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another important area of cpath development concerns the improvement of the software performance. for the newest version, we enhanced the performance of the identifier mapping services, adding support for psi-mi (through the psi-mi bridge) and additional formats, and for mapping the data stores of the underlying cytoscape data sources.


we have developed the cpath database and web application that will be included in version 3 of the cytoscape cybrowser plug-in. cpath stores pathway data in psi-mi-compliant xml format (psi-mi version 1.1, which is compatible with psi-mi version 1.0), and provides a uniform, standards-based way of storing and querying pathway information. cpath can store pathway data from multiple databases, including reactome, kegg, the cellmap, and others. its powerful query engine can be used to link to external resources (e.g., medline, go), as well as for querying cpath data in ways not previously possible.


the current version of cpath is freely available for academic use under a license that permits unrestricted use, distribution, and reproduction in any medium, provided that the product is not sold commercially and that the terms of the license are at least as restrictive as the gpl. the cpath server api allows application developers to create an application-specific database and integration layer, and allows the cpath database to be queried through a web service. all cpath software is freely available under the lgpl open source license for academic and commercial use.


the main cpath software consists of the cpath database and the cpath web application. cpath stores pathway information in psi-mi format, and provides a standard way of storing and querying pathway data. the cpath database is an open source database (code available at http://www.pathways.org) that is implemented in the scripting language python. its key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources, a built-in support for psi-mi and biopax exchange formats, a web service interface for searching and retrieving pathway data sets, and thorough documentation. it is free, open source software that can be installed locally, used in a web server context, and modified as necessary by an individual or an academic institution. the cpath web application is a python-based data integration toolkit for constructing, querying, and presenting pathway data. its main features include: a uniform, standards-based way of storing and querying pathway data; an api, which gives applications access to the cpath database through a web service; and a standards-based web service interface for accessing pathway data from outside cpath. 84d34552a1