cPath: open source software for collecting, storing, and querying biological pathways

Abstract

Background: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required.

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.

Figure 1

cPath Open Source Pathway Database Software Overview. cPath is open source software for collecting, storing, and querying biological pathways. At left, multiple databases can be imported into cPath via standard exchange formats. At right, cPath data can be viewed via a standard web browser or exported via an XML-based web service API, making cPath data available to third-party applications for pathway visualization and analysis.

Figure 2

Browsing Pathways using cPath. cPath provides a web interface for querying biological pathways. This screenshot is of the human Androgen receptor pathway from the Cancer Cell Map [48].

Figure 3

Sample Cytoscape Plugin for Interfacing with cPath. The Cytoscape Expression Viewer plugin enables researchers to visualize expression data on biological pathways. The plugin utilizes the cPath web service API to retrieve pathway data, such as the Kit receptor pathway from the Cancer Cell Map [48].