The BioPAX Validator

High quality biological pathway knowledge is easier to analyze and integrate at a much greater level of detail and with standard tools. To help detect and fix syntax and semantic issues introduced in the course of biological pathway data modeling and exporting to BioPAX, we created this BioPAX Validator, with dozens of custom criteria, some of which cannot be expressed in OWL or rule definition languages. These rules originate from the BioPAX specification and the community best practice, are expressed in Java as generic classes built mostly around the Paxtools API, and embraced by the aspect-oriented framework (AOP). It reports all the issues at once, in several categories and levels, and the normalized BioPAX Level3 model (optional), auto-converting BioPAX Level 1, 2 to 3 if required (before it checks the rules). There are also Java console and library version of the BioPAX Validator.

Start Validating

How to cite:

Igor Rodchenkov, Emek Demir, Chris Sander, and Gary D. Bader. The BioPAX Validator. Bioinformatics (2013) 29 (20): 2659-2660 first published online August 5, 2013 doi: 10.1093/bioinformatics/btt452 Open Access


Please feel free to post your comments and suggestions at the Validator Wiki or BioPAX issue tracker.