Abstract
BackgroundBiological 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.ResultsWe 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.ConclusioncPath 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.
Highlights
Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases
A blueprint for how these parts are assembled is required to explain how the system works [3]. This wiring diagram for a cell consists of multiple biological data types, including metabolic pathways, signal transduction pathways, proteinprotein interaction networks, gene regulatory networks and genetic interactions
Biologists, computational biologists, and software developers can utilize cPath for content aggregation, query and analysis. cPath can serve as a modular, core software layer in larger pathway information systems that are capable of visualizing, analyzing, and modeling biological pathways
Summary
Overview Using cPath, researchers can import interaction and pathway data from multiple sources, access such data via a standard web interface, and export data to third-party applications via a standards-based web service (Figure 1). A researcher can import a UniProt to Affymetrix mapping file, when a new protein with a matching UniProt identifier is subsequently imported into cPath, it is annotated with all known Affymetrix probe set identifiers This is useful for tools that link gene expression data to pathways. The cPath web service is not tied to a specific operating system or programming language, and uses a REST-based (Representational State Transfer) architecture [49], which has only two requirements: queries must be specified as Internet URLs, and response documents must be specified as XML documents This REST-based approach is considerably simpler than other web service options, such as SOAP [50], and enables developers to interactively experiment with the cPath web service with just a standard web browser. Since early 2004, the cPath web service has handled more than 537,000 queries from over 5,800 distinct hosts (IP addresses), mostly from Cytoscape users using the cPath query plugin
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