Presenting and exploring biological pathways with PathVisio.
- Author(s): van Iersel, Martijn P
- Kelder, Thomas
- Pico, Alexander R
- Hanspers, Kristina
- Coort, Susan
- Conklin, Bruce R
- Evelo, Chris
- et al.
Published Web Locationhttps://doi.org/10.1186/1471-2105-9-399
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.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.PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.