Difference between revisions of "Specification"

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=Specification=
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[[Category:SPECIFICATION]]
This pages provides links to the BioPAX specifications and associated documentation.  The latest version is BioPAX Level 3 and it is recommended that users adopt or migrate to this version.
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==Level3==
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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].)
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==BioPAX Level3==
 
* 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.
 
* 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.
* [http://biopax.org/release/biopax-level3.owl Official BioPAX Level 3 OWL file] - Status: Final, Release v1.0 July 2010
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* [http://www.biopax.org/release/biopax-level3-documentation.pdf Official BioPAX Level 3 Documentation] - Status: Final, Release v1.0 July 2010
* [http://biopax.org/release/biopax-level3-documentation.pdf Official BioPAX Level 3 Documentation] - Status: Final, Release v1.0 July 2010
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* [http://www.biopax.org/release/biopax-level3.owl Official BioPAX Level 3 OWL file] - Status: Final, Release v1.0 July 2010
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=L3Data BioPAX Level 3 Data Sources]
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* [http://www.biopax.org/owldoc/Level3/ OWLDoc - ontology HTML view]
* Developer resources
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* [http://www.biopax.org/webprotege/ WebProtégé view]
** [http://biopax.hg.sourceforge.net/hgweb/biopax BioPAX Mercurial home] - browse the Mercurial versioning system repository from the root
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* [http://sourceforge.net/p/biopax/code/ The latest BioPAX and examples (Mercurial SCM)]
** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/raw-file/default/Level3/specification/biopax-level3.owl BioPAX Level 3 OWL] - Current OWL
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** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/log/default/Level3/specification/biopax-level3.owl BioPAX Level 3 OWL] - Revision history
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** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level3.owl Auto-generated ontology documentation]
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** [http://biopax.org/webprotege/ webprotege]  
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** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/docs Documentation]
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** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/examples Examples]
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==Level2==
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==BioPAX Level2==
 
* Supports metabolic pathways, signaling pathways, molecular interactions. Backwards compatible with Level 1.
 
* Supports metabolic pathways, signaling pathways, molecular interactions. Backwards compatible with Level 1.
* [http://biopax.org/release/biopax-level2.owl Official BioPAX Level 2 OWL file] - Status: Final. Recommend using Level 3.
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* [http://www.biopax.org/release/biopax-level2.owl Official BioPAX Level 2 OWL file] - Status: Final. Recommend using Level 3.
* [http://biopax.org/release/biopax-level2-documentation.pdf Official BioPAX Level 2 Documentation] - Status: Final. Recommend using Level 3.
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* [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]
 
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data Sources]
 
* Developer resources
 
* Developer resources
** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ BioPAX CVS home] - all versions from the previously used CVS version management system.
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** [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.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ BioPAX Examples]
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** [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://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/biopax-level2-documentation.pdf?view=log Documentation]
** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level2.owl Auto-generated ontology documentation]
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** [http://www.biopax.org/owldoc/Level2/ Auto-generated ontology documentation]
  
==Level1==
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==BioPAX Level1==
 
* Supports metabolic pathways.
 
* Supports metabolic pathways.
* [http://biopax.org/release/biopax-level1.owl Official BioPAX Level 1 OWL file] - Status: Final. Recommend using Level 3.
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* [http://www.biopax.org/release/biopax-level1.owl Official BioPAX Level 1 OWL file] - Status: Final. Recommend using Level 3.
* [http://biopax.org/release/biopax-level1-documentation.pdf Official BioPAX Level 1 Documentation] - Status: Final. Recommend using Level 3.
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* [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]
 
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_1_Data BioPAX Level 1 Data Sources]
 
* Developer resources
 
* Developer resources
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ BioPAX Examples]
 
** [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://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]
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** [http://www.biopax.org/owldoc/Level1/ Auto-generated ontology documentation]
  
== Other ==
 
===Follow the BioPAX development logs===
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/atom-log Changelog (Atom)]
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/rss-log Changelog (RSS)]
 
  
 
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Revision as of 00:31, 19 May 2013


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