What is cPath?
cPath is a database and software suite for storing, visualizing, and analyzing biological pathways.
Main features:
- Import pipeline capable of aggregrating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome.
- Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats.
- Data visualization and analysis via Cytoscape.
- Simple HTTP URL based XML web service.
- Complete software is freely available for local install. Easy to install and administer.
- Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG), and aims to meet "silver-level" requirements for software interoperability and data exchange.
Who do I contact for additional information regarding cPath?
For scientific questions regarding cPath, please contact Gary Bader. For technical / programming questions regarding cPath, please contact Ethan Cerami or Benjamin Gross.
What is Cytoscape? How can I visualize cPath data in Cytoscape?
Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape is open source software, and available for download from the cytoscape.org web site. Cytoscape is written in Java, and therefore runs on Windows, Mac OS X, and Linux.
Cytoscape includes a built-in PlugIn framework for adding new features and functionality. The cPath PlugIn enables Cytoscape users to directly query, retrieve and visualize interactions retrieved from the cPath database.
How can I programmatically access cPath? How do I use the Web Services API?
cPath provides a complete Web Services API for programmatically accessing cPath data. Complete details are available at the Web Services API Help Page.