Bringing data from curated pathway resources to Cytoscape with OmniPath

Author:

Ceccarelli Francesco12,Turei Denes13,Gabor Attila14,Saez-Rodriguez Julio14

Affiliation:

1. Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen 52074, Germany

2. Computer Laboratory, University of Cambridge, CB3 0FD, Cambridge, UK

3. European Molecular Biology Laboratory (EMBL)

4. Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany

Abstract

Abstract Summary Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools. Availability and implementation The OmniPath App has been developed for Cytoscape 3 in the Java programing language. The latest source code and the plugin can be found at: https://github.com/saezlab/Omnipath_Cytoscape and http://apps.cytoscape.org/apps/omnipath, respectively. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

Joint Research Center for Computational Biomedicine

Bayer AG

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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