Software

Presenting and exploring biological pathways with PathVisio

Martijn P van Iersel¹ , Thomas Kelder¹ , Alexander R Pico^2,3 , Kristina Hanspers^2,3 , Susan Coort¹ , Bruce R Conklin^2,3 and Chris Evelo¹

¹  Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands

²  Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA

³  Departments of Medicine, and Molecular and Cellular Pharmacology, University of California, San Francisco, CA 94158, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:399doi:10.1186/1471-2105-9-399

Published:	25 September 2008

Abstract

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 http://www.pathvisio.org webcite.

Conclusion

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