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. CONCLUSION: PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.
van Iersel, M. P., Kelder, T. A. J., Pico, A. R., Hanspers, K., Coort, S. L., Conklin, B. R., & Evelo, C. (2008). Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics, 9, 399. https://doi.org/10.1186/1471-2105-9-399