Difference between revisions of "Specification"

From BiopaxWiki
Jump to: navigation, search
m (BioPAX Level3)
 
(46 intermediate revisions by 3 users not shown)
Line 1: Line 1:
=Specification=
+
[[Category:SPECIFICATION]]
This pages provides links to the '''current''' BioPAX specification and associated documentation sourcefore.
+
  
* BioPAX OWL
+
This pages provides links to the BioPAX specifications and documentation.  The latest version is BioPAX Level 3, and it is recommended that users adopt or migrate to this version. (See other wiki pages in the [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Category:LEVEL3 Category:LEVEL3].)
* BioPAX Data
+
 
* Examples
+
==BioPAX Level3==
* Documents
+
* Supports metabolic pathways, signaling pathways (including states of molecules and generic molecules), gene regulatory networks, molecular interactions, genetic interactions. Not backwards compatible with Level 2.
* Presentations
+
* [http://www.biopax.org/release/biopax-level3-documentation.pdf Official BioPAX Level 3 Documentation] - Status: Final, Release v1.0 July 2010
 +
* [http://www.biopax.org/release/biopax-level3.owl Official BioPAX Level 3 OWL file] - Status: Final, Release v1.0 July 2010
 +
* [http://www.biopax.org/owldoc/Level3/ OWLDoc - ontology HTML view]
 +
* [http://www.biopax.org/webprotege/ WebProtégé view]
 +
* [http://github.com/BioPAX/specification The latest BioPAX and examples (on Github)]
 +
 
 +
==BioPAX Level2==
 +
* Supports metabolic pathways, signaling pathways, molecular interactions. Backwards compatible with Level 1.
 +
* [http://www.biopax.org/release/biopax-level2.owl Official BioPAX Level 2 OWL file] - Status: Final. Recommend using Level 3.
 +
* [http://www.biopax.org/release/biopax-level2-documentation.pdf Official BioPAX Level 2 Documentation (PDF)] - Status: Final. Recommend using Level 3.
 +
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data Sources]
 +
* Developer resources
 +
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ BioPAX L2 sources (CVS)] - all versions from the previously used CVS version management system.
 +
** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level2/examples BioPAX L2 Examples]
 +
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/biopax-level2-documentation.pdf?view=log Documentation]
 +
** [http://www.biopax.org/owldoc/Level2/ Auto-generated ontology documentation]
 +
 
 +
==BioPAX Level1==
 +
* Supports metabolic pathways.
 +
* [http://www.biopax.org/release/biopax-level1.owl Official BioPAX Level 1 OWL file] - Status: Final. Recommend using Level 3.
 +
* [http://www.biopax.org/release/biopax-level1-documentation.pdf Official BioPAX Level 1 Documentation] - Status: Final. Recommend using Level 3.
 +
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_1_Data BioPAX Level 1 Data Sources]
 +
* Developer resources
 +
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ BioPAX CVS home] - all versions from the previously used CVS version management system.
 +
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ BioPAX Examples]
 +
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-level1-documentation.pdf?view=log Documentation]
 +
** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level1.owl Auto-generated ontology documentation]
 +
 
 +
 
 +
__NOTOC__

Latest revision as of 14:49, 25 June 2015


This pages provides links to the BioPAX specifications and documentation. The latest version is BioPAX Level 3, and it is recommended that users adopt or migrate to this version. (See other wiki pages in the Category:LEVEL3.)

BioPAX Level3

BioPAX Level2

BioPAX Level1