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

Collection with item attached
2006_11
Item details URL
http://open-repository.kisti.re.kr/cube/handle/open_repository/153897.do
Title
cPath: open source software for collecting, storing, and querying biological pathways
Description
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.
provenance
Made available in Cube on 2015-09-19T07:32:49Z (GMT). No. of bitstreams: 0
language
en
creator
Cerami, Ethan G
Bader, Gary D
Gross, Benjamin E
Sander, Chris
date
2006-11-13
accessioned
2015-09-19T07:32:49Z
available
2015-09-19T07:32:49Z
issued
2015-09-19
identifier
http://www.biomedcentral.com/1471-2105/7/497
uri
http://open-repository.kisti.re.kr/cube/handle/open_repository/153897.do
publisher
BioMed Central Ltd.
rights
Copyright 2006 Cerami et al; licensee BioMed Central Ltd.
type
Software


Files in This Item
1471-2105-7-497.pdf852.5KBDownloadView
1471-2105-7-497.xml110.6KBDownloadView