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. 2011 Aug 1;27(15):2165-6.
doi: 10.1093/bioinformatics/btr336. Epub 2011 Jun 2.

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

Augustin Luna  1 , Margot L Sunshine, Martijn P van Iersel, Mirit I Aladjem, Kurt W Kohn
Affiliations

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

Augustin Luna et al. Bioinformatics. .

Abstract

Motivation: A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the Molecular Interaction Map (MIM) notation. Together with the core PathVisio application, this plugin presents a simple to use and cross-platform application for the construction of complex MIM diagrams with the ability to annotate diagram elements with comments, literature references and links to external databases. This tool extends the capabilities of the PathVisio pathway editor by providing both MIM-specific glyphs and support for a MIM-specific markup language file format for exchange with other MIM-compatible tools and diagram validation.

Availability: The PathVisio-MIM plugin is freely available and works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. Information about MIM notation and the MIMML format is available at http://discover.nci.nih.gov/mim. The plugin, along with diagram examples, instructions and Java source code, may be downloaded at http://discover.nci.nih.gov/mim/mim_pathvisio.html.

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Figures

Fig. 1.
Fig. 1.
Screenshot of PathVisio diagram editor with PathVisio-MIM plugin loaded. MIM-specific glyphs are shown in the right-hand side panel.
See this image and copyright information in PMC

References

    1. Freeman T.C., et al. The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. BMC Syst. Biol. 2010;4:65. - PMC - PubMed
    1. Kohn K.W., et al. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol. Biol. Cell. 2006;17:1–13. - PMC - PubMed
    1. Le Novère N., et al. The systems biology graphical notation. Nat. Biotechnol. 2009;27:735–741. - PubMed
    1. Luna A., et al. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-based format, an API, and a validation method. BMC Bioinformatics. 2011;12:167. - PMC - PubMed
    1. van Iersel M.P., et al. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008;9:399. - PMC - PubMed

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