WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization [v1; ref status: indexed, http://f1000r.es/3ij]

• Main Authors: Martina Kutmon, Samad Lotia, Chris T Evelo, Alexander R Pico
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2014-07-01
• Series: F1000Research
• Subjects: Bioinformatics; Theory & Simulation
• Online Access: http://f1000research.com/articles/3-152/v1

In this paper we present the open-source WikiPathways app for Cytoscape (http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 2000 downloads between its first release in August 2013 and the submission of the paper in May 2014 highlight the importance and adoption of the app in the network biology field.