Difference between revisions of "Specification"

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=Specification=
 
=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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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].)
  
 
==Level3==
 
==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
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** [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/webprotege/ WebProtégé view]
 
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=L3Data BioPAX Level 3 Data Sources]
 
* [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=L3Data BioPAX Level 3 Data Sources]
 
* Developer resources
 
* Developer resources
** [http://biopax.hg.sourceforge.net/hgweb/biopax BioPAX Mercurial home] - browse the Mercurial versioning system repository from the root
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** [http://biopax.hg.sourceforge.net/hgweb/biopax the latest BioPAX sources (Mercurial SCM)] - browse the Hg repository from the root (all BioPAX Levels)
** [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/ BioPAX L3 docs and examples]
** [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://biopax.hg.sourceforge.net/hgweb/biopax/biopax/raw-file/default/Level3/specification/biopax-level3.owl the latest rev. of BioPAX Level 3 ontology]
** [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/log/default/Level3/specification/biopax-level3.owl BioPAX Level 3 OWL revision history]
** [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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=== Posters ===
** [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file/default/Level3/examples Examples]
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* 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...
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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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=== BioPAX Development Logs ===
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* [http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/rss-log Changelog (RSS)]
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* [http://biopax.hg.sourceforge.net/hgweb/biopax/paxtools/rss-log Changelog (RSS)]
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* [http://biopax.hg.sourceforge.net/hgweb/biopax/validator/rss-log Changelog (RSS)]
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==Level2==
 
==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]
 
** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level2.owl Auto-generated ontology documentation]
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==Level1==
 
==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://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level1.owl Auto-generated ontology documentation]
 
** [http://www.mygrid.org.uk/OWL/Presentation?url=http://www.biopax.org/release/biopax-level1.owl 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)]
 
  
 
__NOTOC__
 
__NOTOC__

Revision as of 21:54, 21 February 2013

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.

(See other wiki pages in the Category:LEVEL3.)

Level3

Posters

Presentations

Publications

BioPAX Development Logs


Level2

Level1