The BioPAX validator

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

Research output: Contribution to journalArticle

3 Citations (Scopus)

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
Externally publishedYes

Fingerprint

Informatics
Critical Pathways
Licensure
Semantics
Inconsistency
Documentation
Libraries
Pathway
Language
Normalize
Data Exchange
Electronic data interchange
Syntactics
Web Application
Uniformity
Open Source
Web services
Java
Web Services
Availability

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

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

The BioPAX validator. / Rodchenkov, Igor; Demir, Emek; Sander, Chris; Bader, Gary D.

In: Bioinformatics, Vol. 29, No. 20, 15.10.2013, p. 2659-2660.

Research output: Contribution to journalArticle

Rodchenkov, I, Demir, E, Sander, C & Bader, GD 2013, 'The BioPAX validator', Bioinformatics, vol. 29, no. 20, pp. 2659-2660. https://doi.org/10.1093/bioinformatics/btt452
Rodchenkov I, Demir E, Sander C, Bader GD. The BioPAX validator. Bioinformatics. 2013 Oct 15;29(20):2659-2660. https://doi.org/10.1093/bioinformatics/btt452
Rodchenkov, Igor ; Demir, Emek ; Sander, Chris ; Bader, Gary D. / The BioPAX validator. In: Bioinformatics. 2013 ; Vol. 29, No. 20. pp. 2659-2660.
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