PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

Bioinformatics. 2013 Jun 1;29(11):1465-6. doi: 10.1093/bioinformatics/btt146. Epub 2013 Apr 1.


Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries.

Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at The plugin is free, open-source and licensed by the Apache 2.0 License.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genes
  • Humans
  • Lymphoma / genetics
  • Models, Biological*
  • Proteins / metabolism
  • Software*
  • Systems Biology / methods
  • User-Computer Interface


  • Proteins