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Bioinformatics. 2019 Dec 30. pii: btz968. doi: 10.1093/bioinformatics/btz968. [Epub ahead of print]

Bringing data from curated pathway resources to Cytoscape with OmniPath.

Author information

1
RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074, Aachen, Germany.
2
University of Cambridge, United Kingdom.
3
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
4
Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.

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 programming 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.

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