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BMC Bioinformatics. 2008 Sep 25;9:399. doi: 10.1186/1471-2105-9-399.

Presenting and exploring biological pathways with PathVisio.

Author information

  • 1Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands. martijn.vaniersel@bigcat.unimaas.nl

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.

PMID:
18817533
[PubMed - indexed for MEDLINE]
PMCID:
PMC2569944
Free PMC Article
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