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

K. Chandan, M.P. van Iersel, M.I. Aladjem, K.W. Kohn, A. Luna

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Abstract

Purpose: 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 amongst 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. AVAILABILITY: The PathVisio-Validator plugin works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X, and Linux. The plugin along with the instructions, example rulesets for Groovy and Schematron, and Java source code can be downloaded at http://pathvisio.org/wiki/PathVisioValidatorHelp. The software is developed under the open source Apache 2.0 License and is freely available for both commercial and academic use. CONTACT: augustin@mail.nih.gov or chandankmit@gmail.com.
Original languageEnglish
Pages (from-to)889-890
Number of pages2
JournalBioinformatics
Volume28
Issue number6
DOIs
Publication statusPublished - 1 Jan 2012

Cite this

Chandan, K., van Iersel, M. P., Aladjem, M. I., Kohn, K. W., & Luna, A. (2012). PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. Bioinformatics, 28(6), 889-890. https://doi.org/10.1093/bioinformatics/btr694