Difference between revisions of "Specification"

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=Specification=
 
=Specification=
This pages provides links to the BioPAX specifications and associated documentation on sourceforge.  
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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.
  
[http://www.biopax.org/release/biopax-level3.owl The Latest Officially Released OWL]
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==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://biopax.org/release/biopax-level3.owl Official BioPAX Level 3 OWL file] - Status: Draft, but ready to use. Should be finalized by June.2010
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* [http://biopax.org/release/biopax-level3-documentation.pdf Official BioPAX Level 3 Documentation] - Status: Draft. Should be finalized by June.2010
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* BioPAX Level 3 Data Sources - Coming soon
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* Developer resources
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release3/ Mercurial home] - all versions from the Mercurial version management system on Sourceforge
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** [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/file/default/Level3/specification 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.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]
  
==[http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/ Level3]==
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==Level2==
* [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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* Supports metabolic pathways, signaling pathways, molecular interactions. Backwards compatible with Level 1.
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/specification BioPAX Level 3 OWL] '''*Revision Look*'''
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* [http://biopax.org/release/biopax-level2.owl Official BioPAX Level 2 OWL file] - Status: Final. Recommend using Level 3.
* [[BioPAX Level 3 Data]]
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* [http://biopax.org/release/biopax-level2-documentation.pdf Official BioPAX Level 2 Documentation] - Status: Final. Recommend using Level 3.
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/examples Examples]
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* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data Sources]
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/docs Documents]
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* Developer resources
* [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.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ CVS home] - all versions from the previously used CVS version management system on Sourceforge
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ BioPAX 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.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level2.owl Auto-generated ontology documentation]
  
== [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release2/ Level2]==
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==Level1==
* [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.
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_2_Data BioPAX Level 2 Data]
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* [http://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/release2/ BioPAX Examples]
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* [http://biopax.org/release/biopax-level1-documentation.pdf Official BioPAX Level 1 Documentation] - 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_1_Data BioPAX Level 1 Data Sources]
* [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level2.owl Auto-generated ontology documentation]
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* Developer resources
 
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ CVS home] - all versions from the previously used CVS version management system on Sourceforge
==[http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/ Level1]==
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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-short-demo-pathway.owl?view=log BioPAX Level 1 OWL]
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** [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-level1-documentation.pdf?view=log Documentation]
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAX_Level_1_Data BioPAX Level 1 Data]
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** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level1.owl Auto-generated ontology documentation]
* [http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/release1/biopax-level1-documentation.pdf?view=log Documents]
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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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=== Logs ===
 
=== Logs ===
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* You can use these to follow the latest BioPAX development progress
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/atom-log Changelog (Atom)]
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/atom-log Changelog (Atom)]
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/rss-log Changelog (RSS)]
 
* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/rss-log Changelog (RSS)]
  
 
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Revision as of 22:46, 21 May 2010

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.

Level3

Level2

Level1

Logs