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Announcing BioPAX Level 3 v1.0

We are delighted to announce the release of BioPAX Level 3, version 1.0 and the acceptance of the BioPAX paper in Nature Biotechnology.

BioPAX Level 3 is a major advance over Level 2 and adds support for:

  • Physical entities in diverse states
  • Generic physical entities
  • Gene regulation networks
  • Genetic interactions
  • Degradation

Version 1.0 fixes some bugs and completes documentation of the OWL file since the last release candidate.

This release of BioPAX can be found at http://www.biopax.org/release/biopax-level3.owl and full documentation on this release is available at http://www.biopax.org/release/biopax-level3-documentation.pdf

Please note that this release is not backward compatible and there are significant changes from Level 2 to Level 3. A converter from Level 2 to Level 3 is available as a part of the Paxtools Java library.

We thank everyone in the community for their contribution to BioPAX. Level 3 is a significant milestone in the BioPAX project, with this release offering an almost complete pathway exchange format. Congratulations to one and all on this auspicious achievement.

Best wishes, Nadia Anwar, Emek Demir, Gary Bader, Chris Sander