Bringing data from curated pathway resources to Cytoscape with OmniPath

Francesco Ceccarelli; Denes Turei; Attila Gabor; Julio Saez-Rodriguez

doi:10.1093/bioinformatics/btz968

Bringing data from curated pathway resources to Cytoscape with OmniPath

Bioinformatics. 2020 Apr 15;36(8):2632-2633. doi: 10.1093/bioinformatics/btz968.

Authors

Francesco Ceccarelli^{1

2}, Denes Turei^{1

3}, Attila Gabor^{1

4}, Julio Saez-Rodriguez^{1

4}

Affiliations

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.

PMID: 31886476
DOI: 10.1093/bioinformatics/btz968

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual
Software*