The Cytoscape BioGateway App: explorative network building from the BioGateway triple store

Stian Holmås; Rafel Riudavets Puig; Marcio Luis Acencio; Vladimir Mironov; Martin Kuiper

doi:10.1093/bioinformatics/btz835

The Cytoscape BioGateway App: explorative network building from the BioGateway triple store

Bioinformatics. 2019 Nov 9;36(6):1966-1967. doi: 10.1093/bioinformatics/btz835. Online ahead of print.

Authors

Stian Holmås¹, Rafel Riudavets Puig¹, Marcio Luis Acencio², Vladimir Mironov¹, Martin Kuiper¹

Affiliations

¹ Semantic Systems Biology group, Department of Biology.
² Gastrin Systems Biology group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.

Abstract

Summary: The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are visualised using the inherent flexibility of the Cytoscape framework, and network links can be checked against curated database records or against the original publication.

Availability: Install through the Cytoscape application manager or visit www.biogateway.eu for download and tutorial documents.

Supplementary information: Supplementary information is available at Bioinformatics online.