cPath: open source software for collecting, storing, and querying biological pathways
作者： Ethan G Cerami , Gary D Bader , Benjamin E Gross , Chris Sander
关键词: Gene regulatory network 、 BioPAX : Biological Pathways Exchange 、 Computer science 、 Software design 、 ConsensusPathDB 、 Web application 、 CellML 、 Biological pathway 、 Web service 、 SBML 、 Metabolic pathway 、 Data mining 、 Interface (computing) 、 World Wide Web 、 DNA microarray
摘要: Biological pathways, including metabolic protein interaction networks, signal transduction and gene regulatory are currently represented in over 220 diverse databases. These data crucial for the study of specific biological processes, human diseases. Standard exchange formats pathway information, such as BioPAX, CellML, SBML PSI-MI, enable convenient collection this research, but mechanisms common storage communication required. We have developed cPath, an open source database web application collecting, storing, querying data. cPath makes it easy to aggregate custom sets available standard from multiple databases, present biologists via a customizable interface, export service third-party software, Cytoscape, visualization analysis. is software only, does not include new information. Key features include: built-in identifier mapping linking identical interactors external resources; support PSI-MI BioPAX formats; interface searching retrieving sets; thorough documentation. The freely under LGPL license academic commercial use. robust, scalable, modular, professional-grade platform pathways. It can serve core handling component information systems visualization, analysis modeling.
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