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. 2012 Mar 15;28(6):889-90.
doi: 10.1093/bioinformatics/btr694. Epub 2011 Dec 22.

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

Kumar Chandan  1 , Martijn P van Iersel, Mirit I Aladjem, Kurt W Kohn, Augustin Luna
Affiliations

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

Kumar Chandan et al. Bioinformatics. .

Abstract

The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings.

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Figures

Fig. 1.
Fig. 1.
A pathway diagram being validated using the PathVisio-Validator plugin.
See this image and copyright information in PMC

References

    1. Beltrame L., et al. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics. 2011;27:2127–2133. - PMC - PubMed
    1. Czauderna T., et al. Editing, validating and translating of SBGN maps. Bioinformatics. 2010;26:2340–2341. - PMC - PubMed
    1. Demir E., et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 2010;28:935–942. - PMC - PubMed
    1. Hucka M., et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524–531. - 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. 2011a;12:167. - PMC - PubMed

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