cPath: open source software for collecting, storing, and querying biological pathways. Results: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

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References in zbMATH (referenced in 3 articles )

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  1. De Matteis, Giovanni; Graudenzi, Alex; Antoniotti, Marco: A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development (2013)
  2. Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Llavori, Rafael Berlanga; Perlasca, Paolo; Valentini, Giorgio; Manset, David: XML-based approaches for the integration of heterogeneous bio-molecular data (2009) ioport
  3. Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter: BNDB [8211] the biochemical network database (2007) ioport