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

doi:10.1093/bioinformatics/btr694

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

^*Corresponding author for this work

Bioinformatica

Research output: Contribution to journal › Article › Academic › peer-review

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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 language	English
Pages (from-to)	889-890
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/btr694
Publication status	Published - 1 Jan 2012

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Cite this

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title = "PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.",

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.",

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N2 - 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.

AB - 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.

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