Automation of ReactomeFIViz via CyREST API [version 2; referees: 2 approved]

Guanming Wu, Fred Loney

Research output: Contribution to journalArticlepeer-review

Abstract

Pathway- and network-based approaches project seemingly unrelated genes onto the context of pathways and networks, enhancing the analysis power that cannot be achieved via gene-based approaches. Pathway and network approaches are routinely applied in large-scale data analysis for cancer and other complicated diseases. ReactomeFIViz is a Cytoscape app, providing features for researchers to perform pathway- and network-based data analysis and visualization by leveraging manually curated Reactome pathways and highly reliable Reactome functional interaction network. To facilitate adoption of this app in bioinformatics software pipeline and workflow development, we develop a CyREST API for ReactomeFIViz by exposing some major features in the app. We describe a use case to demonstrate the use of this API in a Python-based notebook, and believe the new API will provide the community a convenient and powerful tool to perform pathway- and network-based data analysis and visualization using our app in an automatic way.

Original languageEnglish (US)
Article number531
JournalF1000Research
Volume7
DOIs
StatePublished - 2018

Keywords

  • CyREST
  • Cytoscape
  • Pathway and network
  • Reactome
  • ReactomeFIViz

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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