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 documentation.  The latest version is BioPAX Level 3, and it is recommended that users adopt or migrate to this version.
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(See other wiki pages in the [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Category:LEVEL3 Category: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].)
  
==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://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-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/release/biopax-level3.owl Official BioPAX Level 3 OWL file] - Status: Final, Release v1.0 July 2010
** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level3.owl OWL ontology HTML presentation view]
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* [http://www.biopax.org/owldoc/Level3/ OWLDoc - ontology HTML view]
** [http://www.biopax.org/webprotege/ WebProtégé view]
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* [http://www.biopax.org/webprotege/ WebProtégé view]
* [L3Data BioPAX Level 3 Data Sources]
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* [http://github.com/BioPAX/specification The latest BioPAX and examples (on Github)]
* [http://sourceforge.net/p/biopax/code/ current BioPAX ontology and examples (Mercurial SCM)]
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=== Posters ===
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==BioPAX Level2==
* Presented at [http://www.iscb.org/cms_addon/conferences/ismb2010/posterlist.php?cat=E ISMB]|[http://www.iscb.org/uploaded/css/58/17048.pdf Abstract]|[http://www.biopax.org/Documentation/BioPAXISMB2010_NADIA.pdf PDF]
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* Presented at [http://www.iscb.org/cshals2010-program/cshals2010-call-for-posters CSHALS 2010]|[http://www.iscb.org/cms_addon/conferences/cshals2010/posters/BioPAXCSHALS10.pdf PDF]
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* Presented at [http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/  IB2010]|[http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/posterpdfs/BioPAXL32009_NADIA.pdf PDF]
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=== Presentations  ===
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*[http://www.biopax.org/Documentation/Level3updateWorkshopNov2009.ppt Level 3 Presentation NOV2009 ]
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*[http://www.biopax.org/Documentation/BioPAXTutorialNov2009.pdf BioPAX Tutorial NOV 2009 ]
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*%TODO add more... (HARMONY'11, COMBINE'12, HARMONY'12, HARMONY'13, etc...)
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=== Publications ===
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*The BioPAX community standard for pathway data sharing. [http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html Nature Biotechnology 28, 935–942 (2010)]
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==Level2==
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* 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://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.owl Official BioPAX Level 2 OWL file] - Status: Final. Recommend using Level 3.
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** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level2/examples BioPAX L2 Examples]
 
** [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://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.owl Official BioPAX Level 1 OWL file] - Status: Final. Recommend using Level 3.

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