Presenting and exploring biological pathways with PathVisio

M.P. van Iersel, T.A.J. Kelder, A.R. Pico, K. Hanspers, S.L. Coort, B.R. Conklin, C. Evelo

Research output: Contribution to journalArticleAcademicpeer-review

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. CONCLUSION: PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.
Original languageEnglish
Pages (from-to)399
JournalBMC Bioinformatics
Volume9
DOIs
Publication statusPublished - 1 Jan 2008

Cite this

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