The BioPAX validator

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

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

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 sf.net/p/ biopax, and the latest stable version of the web application is available at biopax.org/validator. Contact: igor.rodchenkov@utoronto.ca or gary.bader@utoronto.ca.

Original languageEnglish (US)
Pages (from-to)2659-2660
Number of pages2
JournalBioinformatics
Volume29
Issue number20
DOIs
StatePublished - Oct 15 2013

ASJC Scopus subject areas

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

Fingerprint Dive into the research topics of 'The BioPAX validator'. Together they form a unique fingerprint.

  • Cite this

    Rodchenkov, I., Demir, E., Sander, C., & Bader, G. D. (2013). The BioPAX validator. Bioinformatics, 29(20), 2659-2660. https://doi.org/10.1093/bioinformatics/btt452