The BioPAX Validator

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

doi:10.1093/bioinformatics/btt452

Igor Rodchenkov, Emek Demir + Show 2 more

Open Access

https://doi.org/10.1093/bioinformatics/btt452

Copy DOI

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 command-line tool, Java library and online web service for BioPAX that performs >100 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

Highlights

BioPAX (Demir et al, 2010) is a community-developed standard language for biological pathway data
BioPAX is defined in Web Ontology Language (OWL) and can represent a broad spectrum of biological processes including metabolic and signaling pathways, molecular interactions and gene networks
We developed a comprehensive BioPAX Validator that recognizes syntactic errors, semantic inconsistencies and violations of best practices in BioPAX models

Summary

Introduction

BioPAX (Demir et al, 2010) is a community-developed standard language for biological pathway data. BioPAX is defined in Web Ontology Language (OWL) and can represent a broad spectrum of biological processes including metabolic and signaling pathways, molecular interactions and gene networks. Checking some of these rules requires accessing external databases and non-OWL ontologies.

Results

Conclusion