The BioPAX validator

Igor Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Summary: BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation-detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a commandline tool, Java library and online web service for BioPAX that performs 4100 classes of consistency checks. Availability and implementation: The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at biopax, and the latest stable version of the web application is available at Contact: or

Original languageEnglish (US)
Pages (from-to)2659-2660
Number of pages2
Issue number20
StatePublished - Oct 15 2013
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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