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

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


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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Graphics*
  • Software*
  • Systems Biology / methods*