Presenting and exploring biological pathways with PathVisio

被引：251

作者：

van Iersel, Martijn P. ^{[1
]}

Kelder, Thomas ^{[1
]}

Pico, Alexander R. ^{[2
,3
,4
]}

Hanspers, Kristina ^{[2
,3
,4
]}

Coort, Susan ^{[1
]}

Conklin, Bruce R. ^{[2
,3
,4
]}

Evelo, Chris ^{[1
]}

机构：

[1] BiGCaT Maastricht Univ, Dept Bioinformat, NL-6229 ER Maastricht, Netherlands

[2] Gladstone Inst Cardiovasc Dis, San Francisco, CA 94158 USA

[3] Univ Calif San Francisco, Dept Med, San Francisco, CA 94158 USA

[4] Univ Calif San Francisco, Dept Mol & Cellular Pharmacol, San Francisco, CA 94158 USA

来源：

BMC BIOINFORMATICS | 2008年 / 9卷 / 1期

关键词：

D O I：

10.1186/1471-2105-9-399

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

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