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

doi:10.1186/1471-2105-9-399

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 journal › Article › Academic › peer-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 language	English
Pages (from-to)	399
Journal	BMC Bioinformatics
Volume	9
DOIs	https://doi.org/10.1186/1471-2105-9-399
Publication status	Published - 1 Jan 2008

Access to Document

10.1186/1471-2105-9-399Licence: CC BY

Cite this

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title = "Presenting and exploring biological pathways with PathVisio",

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.",

author = "{van Iersel}, M.P. and T.A.J. Kelder and A.R. Pico and K. Hanspers and S.L. Coort and B.R. Conklin and C. Evelo",

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doi = "10.1186/1471-2105-9-399",

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T1 - Presenting and exploring biological pathways with PathVisio

AU - van Iersel, M.P.

AU - Kelder, T.A.J.

AU - Pico, A.R.

AU - Hanspers, K.

AU - Coort, S.L.

AU - Conklin, B.R.

AU - Evelo, C.

PY - 2008/1/1

Y1 - 2008/1/1

N2 - 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.

AB - 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.

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DO - 10.1186/1471-2105-9-399

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