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 on sourcefore.
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==[http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/ 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].)
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/74b8ecef5f15/Level3/specification BioPAX Level 3 OWL] '''*Current Specification*'''
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* [[BioPAX Level 3 Data]]
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* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/74b8ecef5f15/Level3/examples Examples]
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* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/74b8ecef5f15/Level3/docs Documents]
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==BioPAX Level3==
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* 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.
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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
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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
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* [http://www.biopax.org/owldoc/Level3/ OWLDoc - ontology HTML view]
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* [http://www.biopax.org/webprotege/ WebProtégé view]
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* [http://github.com/BioPAX/specification The latest BioPAX and examples (on Github)]
  
== [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ Level2]==
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==BioPAX Level2==
* [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/biopax-level2.owl?view=log BioPAX Level 2 OWL]
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* Supports metabolic pathways, signaling pathways, molecular interactions. Backwards compatible with Level 1.
* [https://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data]
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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.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ BioPAX Examples]
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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://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/biopax-level2-documentation.pdf?view=log Documents]
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* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data Sources]
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* Developer resources
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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.
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** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level2/examples BioPAX L2 Examples]
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/biopax-level2-documentation.pdf?view=log Documentation]
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** [http://www.biopax.org/owldoc/Level2/ Auto-generated ontology documentation]
  
==[http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ Level1]==
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==BioPAX Level1==
* [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-short-demo-pathway.owl?view=log BioPAX Level 1 OWL]
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* Supports metabolic pathways.
* [https://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_1_Data BioPAX Level 1 Data]
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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.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-level1-documentation.pdf?view=log Documents]
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* [http://www.biopax.org/release/biopax-level1-documentation.pdf Official BioPAX Level 1 Documentation] - Status: Final. Recommend using Level 3.
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* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_1_Data BioPAX Level 1 Data Sources]
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* Developer resources
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ 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/release1/ BioPAX Examples]
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-level1-documentation.pdf?view=log Documentation]
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** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level1.owl Auto-generated ontology documentation]
  
  
 
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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