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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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.
Original languageEnglish
Pages (from-to)399
JournalBMC Bioinformatics
Publication statusPublished - 1 Jan 2008


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