BioPAX is a standard for communicating the knowledge about biochemical processes. The BioPAX Validator is to help detect and fix syntax and non-trivial semantic issues introduced in the course of biological pathway data modeling, mapping, and exporting to BioPAX. "Valid" pathway knowledge is easier to analyze and merge at a much greater level of detail and with more generic, standard tools. The BioPAX Validator has dozens of custom rules defined, some of which cannot be expressed in OWL or related rule definition languages. These rules come from the BioPAX specification and community best practices, are expressed in plain Java and embraced by the validator's original cross-cutting error reporting framework. The rules are, basically, generic Java classes built around Paxtools API. They can check across several BioPAX entities, check entire BioPAX model, can be nested, can overlap in their subjects, can check "real-time" (on a property change). The BioPAX Validator can run on the web, command line, or - integrated into other java applications.

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