Presenting and exploring biological pathways with PathVisio

BMC Bioinformatics. 2008 Sep 25;9:399. doi: 10.1186/1471-2105-9-399.


Background: Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects. The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs.

Results: PathVisio can be combined with other bioinformatics tools to open up three possible uses: visual compilation of biological knowledge, interpretation of high-throughput expression datasets, and computational augmentation of pathways with interaction information. PathVisio is open source software and available at

Conclusion: PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.

Publication types

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

MeSH terms

  • Algorithms*
  • Computer Graphics*
  • Computer Simulation
  • Models, Biological*
  • Proteome / metabolism*
  • Signal Transduction / physiology*
  • Software*
  • User-Computer Interface*


  • Proteome