Igor Rodchenkov edited this page Sep 13, 2018 · 5 revisions

The BioPAX Validator

(We're still migrating wiki pages and docs from Sourceforge to here...)

The BioPAX Validator helps improve BioPAX data quality. It implements and checks many syntax and semantic rules and best practices, which in most cases cannot be formally defined neither using OWL restrictions nor - any rule definition language.
In 11/2008, Pathway Commons team came up with the BioPAX Validator requirements and design. The first version was released in May 2009.

For information about BioPAX ontology classes and properties, please refer to the specification, owldoc, webprotege.


Other software that performs non-trivial data validation:


We can imagine different levels of contribution, depending on how familiar you are with the project and what time and resources you are going to grant. Regardless the category or level all the tasks are important.


  • try it online or download the latest version;
  • report problems (use the issue tracker);
  • grab the sources and create more BioPAX rule tests that generate example OWL files (a very important and excellent exercise) - in the org.biopax.validator.Level3RulesUnitTest or TestContextTest class;
  • feel free to ask questions at biopax-discuss@googlegroups.com (http://groups.google.com/group/biopax-discuss).


  • implement a rule labeled with "*" at the BioPAXRules page;
  • help debug/test/tune;
  • make web service accept/send zipped BioPAX data;


  • improve auto-fix and normalization;
  • boost performance;
  • getting rid of AspectJ LTW? (load-time weaving is not required anymore when biopax-validator is used as java library, but then it will ignore all issues that occur in the Paxtools' BioPAX reader while converting from RDF/XML, such as illegal biopax property range);
  • integration with visualization and modelling tools (add more web api);
  • add advanced rules that may require using external tools (e.g., check organism, check that sequence match the xref, etc...)


Goal When Comments
biopax-validator v1.0 alpha 20-Apr-09 [done]
biopax-validator beta 07-May-09 [done]
Trying at IOB May-09 Toronto-Bangalore
XML configuration for the DB synonyms in Xrefs; limit DB usage (allow/deny) May-09 [done]
New features: ''FIXIT'' behavior, errors threshold, and warnings Jun-09 [done]
Web service and Web site (draft) Jun-09 [done]
biopax-validator v1.0 beta 2 Aug-09 [done]
Re-design: simpleIO instead JenaIO; errors - only via AOP; simpler interfaces; a basis for the future multi-thread validation Jul-Aug [done]
Implementing rules Aug-Oct-09
Present the validator at the BioPAX meeting Nov-09 [done] NYC USA
Assembly or convert BioPAX models online Collaborate with [http://www.bilkent.edu.tr/~bcbi/chibe.html ChiBE]
Begin v2.0 development Dec-09 [done] biopax hg (Mercurial) repository; fix/normalization behavior, maven2
Basic CV rule change: do not use the Generic Schema Validator module, nor Ontology Manager; use OLS directly Dec-09 [done]
BioPAX Validator 1.0 Release 31-Dec-09 [done] v1.0.6 is the last 1.x one
BioPAX Validator 2.0 2010 [done] normalization, error threshold, new web look, etc... http://www.biopax.org/validator
BioPAX Validator 2.0.0 Release by April-23 (HARMONY) improved error messages, normalization and auto-fix, ontology manager configuration, docs/examples
BioPAX Validator 2.1.0 Release by end of May 2012 (HARMONY meeting) add categories, review rules and messages, improve normalizer, upgrade ontology manager, paxtools, and other dependencies, etc.
BioPAX Validator 3.0.0 Release January 2013 [done] "notstrict" validation profile added; improved auto-fix and normalization; improved console app; improved web style, etc.
BioPAX Validator 3.0.1 Release April 2013 TODO: fix bugs; improve validating of multiple large files (from a directory)
BioPAX Validator 3.0.2 Release Summer 2013 [done]
BioPAX Validator 3.0.3 Release December 2013 [done]
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