Automation of ReactomeFIViz via CyREST API

Area of Science:

• Bioinformatics
• Systems Biology
• Computational Biology

Background:

• Pathway- and network-based analyses offer enhanced insights compared to gene-based approaches, particularly for complex diseases like cancer.
• ReactomeFIViz is a Cytoscape application that utilizes curated Reactome pathways and functional interaction networks for data analysis and visualization.
• There is a need to integrate such tools into automated bioinformatics pipelines and workflows.

Purpose of the Study:

• To develop a CyREST API for the ReactomeFIViz Cytoscape app.
• To expose key functionalities of ReactomeFIViz through the API for programmatic access.
• To enable automated pathway- and network-based data analysis and visualization.

Main Methods:

• Development of a CyREST API to interface with ReactomeFIViz functionalities.
• Exposing major features of ReactomeFIViz via the API endpoints.
• Demonstration of API usage in a Python-based notebook for a specific use case.

Main Results:

• A functional CyREST API for ReactomeFIViz has been successfully developed.
• The API allows for automated execution of pathway- and network-based analyses.
• A use case illustrates the practical application of the API in a Python notebook.

Conclusions:

• The new CyREST API provides a convenient and powerful tool for automated bioinformatics analyses.
• This API facilitates the integration of ReactomeFIViz into larger computational pipelines and workflows.
• The development empowers researchers to perform advanced pathway and network analysis programmatically.