Bringing data from curated pathway resources to Cytoscape with OmniPath

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


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: and, respectively.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual
  • Software*