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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Rafael Riudavets Puig1, Stian Holmås2, Vladimir Mironov2

  • 1Computational Biology and Gene Regulation Group, Center for Molecular Medicine Norway, University of Oslo, Oslo, Norway.

Current Protocols in Bioinformatics
|September 28, 2020
PubMed
Summary
This summary is machine-generated.

The BioGateway App enables researchers to build and explore complex biological networks using curated data. This tool facilitates the discovery of gene regulatory relationships and protein interactions within the Cytoscape environment.

Keywords:
Cytoscape AppRDF triple storeSPARQL queriesexploratory network buildingtranscription factor regulation resource

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Biological network analysis is crucial for understanding complex molecular interactions.
  • Integrating diverse biological data sources remains a significant challenge.
  • Existing tools may lack intuitive interfaces for complex query construction.

Purpose of the Study:

  • To introduce the BioGateway App, a Cytoscape plugin for interactive biological network construction.
  • To demonstrate the utility of BioGateway in querying and visualizing integrated biological data.
  • To provide practical use cases for exploring gene regulatory and protein-protein interactions.

Main Methods:

  • Utilizing the BioGateway App plugin within the Cytoscape network editor.
  • Querying the Biogateway Resource Description Framework (RDF) triple store via a Graphical User Interface.
  • Building complex SPARQL queries for data retrieval and network generation.
  • Leveraging Cytoscape's filtering and refinement capabilities for network analysis.

Main Results:

  • Successful interactive construction of biological networks from curated resources like UniProtKB, IntAct, and Gene Ontology.
  • Demonstration of use cases for human gene and protein data, including disease-related molecular relationships and protein kinase activity.
  • Exploration of potential downstream effects of targeted protein inhibition.
  • Examples provided for exploring network information in other species.

Conclusions:

  • The BioGateway App offers an intuitive interface for building and exploring complex biological networks.
  • It effectively integrates data from multiple curated resources, facilitating the assessment of gene regulatory and protein-protein interactions.
  • The tool enhances biological data exploration within the Cytoscape framework, supporting diverse research applications.