CyTargetLinker app update: A flexible solution for network extension in Cytoscape.

Area of Science:

• Network biology
• Bioinformatics
• Computational biology

Background:

• CyTargetLinker is an open-source Cytoscape app for extending biological networks.
• It utilizes linksets to integrate relevant data and knowledge.
• Previous versions lacked advanced automation capabilities.

Purpose of the Study:

• To introduce new automation features to the CyTargetLinker app.
• To enable programmatic execution of CyTargetLinker functionalities for enhanced reproducibility.
• To demonstrate the app's utility in diverse network extension use cases.

Main Methods:

• Implemented automation features for command-line execution within Cytoscape.
• Enabled programmatic use with external tools like R, Jupyter, and Python.
• Developed three use cases showcasing automated workflows and network extension.

Main Results:

• Successfully demonstrated automated network extension with compound-target interactions and disease-gene annotations.
• Showcased a workflow for integrating differentially expressed genes with pathway associations.
• Created a non-biological author-article-journal network using a two-step extension.

Conclusions:

• The enhanced CyTargetLinker app improves workflow sharing, repeatability, and reproducibility in network biology.
• The new automation features increase the app's applicability and adoption in biomedical research.
• CyTargetLinker continues to be a relevant tool for network data integration and analysis.