The BioPAX validator

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. © The Author 2013. Published by Oxford University Press.