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BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.  
 
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.  
Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is open and collaborative effort by the community of researchers, software developers, and institutions.
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Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in [http://www.w3.org/TR/owl-features/ OWL DL] and is represented in the RDF/XML format. [http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html BioPAX Paper] was published in Nature Biotechnology in 2010.
  
* [http://groups.google.com/group/biopax-discuss?lnk=li The BioPAX Forum] (BioPAX Discussion Google Group).
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== Coordination ==
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* [http://groups.google.com/group/biopax-discuss?lnk=li The BioPAX Forum]
 
* [[Level3Announcement | BioPAX Level3 Announcenment]]
 
* [[Level3Announcement | BioPAX Level3 Announcenment]]
 
* [[Specification | BioPAX Specification and Documentation]]  
 
* [[Specification | BioPAX Specification and Documentation]]  
* [[L4Workgroups | BioPAX Workgroups]]
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* [[BioPAX Governance]]
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* [[L4Workgroups | BioPAX Workgroups]] and [[BioPAX People Pages]] (Add yourself!)
 
* [[L4ProposalsList | BioPAX Proposals]]
 
* [[L4ProposalsList | BioPAX Proposals]]
* [http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html BioPAX Paper Published in Nature Biotechnology ]
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* Next Workshops: [http://co.mbine.org/events/COMBINE_2014 COMBINE 2014], [http://co.mbine.org/events/HARMONY_2014 HARMONY 2014]
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* Last Workshops:  [http://co.mbine.org/events/COMBINE_2013 COMBINE 2013], [http://co.mbine.org/events/HARMONY_2013 HARMONY 2013], [http://biocuration2014.events.oicr.on.ca/biocuration Biocuration 2014 (Toronto, ON)]
 
* [[FAQ]]
 
* [[FAQ]]
* Archives
 
** [[Presentations_and_Publications | Previous Presentations and Publications]]
 
** [http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]
 
** [http://groups.google.com/group/BioPAX-Boston biopax-boston]
 
** [http://archive.biopaxwiki.org Original Wiki Archive]
 
* [[Special:Categories | Wiki Pages by Category]]
 
  
== BioPAX Workgroup Coordination ==
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==For biologists==
*[[L4Workgroups| Level 4 Workgroups]]
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<strong>and computational biologists interested in downloading and analyzing pathway data:</strong>
<!-- *Level 4 [[BioPAX Workgroup Coordination L4]] Page -->
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* [http://www.biopax.org/release/biopax-level3.owl Level 3 Ontology] ([http://www.biopax.org/owldoc/Level3/ browse]) covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
*Level 3 [[BioPAX Workgroup Coordination]] Page
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*[http://www.biopax.org/release/biopax-level2.owl Level 2 Ontology] ([http://www.biopax.org/owldoc/Level2 browse]) supports metabolic pathways, molecular interactions, protein post-translational modifications and the [http://psidev.sourceforge.net/ PSI-MI]
* Next Workshop: [http://co.mbine.org/events/HARMONY_2013 Harmony 2013]
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*[http://www.biopax.org/release/biopax-level1.owl Level 1 Ontology] ([http://www.biopax.org/owldoc/Level1 browse]) supports metabolic pathways
* Last Workshop: [http://co.mbine.org/events/COMBINE_2012 COMBINE 2012 Toronto, ON]  
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*[[Data|Pathways in BioPAX format]]
* See [[Past meetings]] to find notes from previous meetings.
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*[[Biological software supporting BioPAX]]
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==For developers==
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<strong>interested in building software using BioPAX:</strong>
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*[http://sourceforge.net/projects/biopax The BioPAX Project at SourceForge]
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*[[Paxtools]]
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*[[BioPAXValidator]]
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*[http://www.medicalcomputing.net/owl1.html Introduction to OWL Web Ontology Language for Medical and Biosciences Applications]
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*[http://www.biopax.org/Docs/BioPAX-Jena_Tutorial.pdf Tutorial on accessing BioPAX content using Jena]
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*[[Software Development Tools]]
  
== Using BioPAX ==
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==Archive==
*<strong>For biologists and computational biologists interested in downloading and analyzing pathway data</strong>
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* [[Presentations_and_Publications | Previous Presentations and Publications]]
** [http://www.biopax.org/release/biopax-level3.owl Level 3 Ontology] ([http://biopax.sourceforge.net/biopax-site/owldoc/Level3/ browse]) covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
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* [[Past meetings]]
**[http://www.biopax.org/release/biopax-level2.owl Level 2 Ontology] ([http://biopax.sourceforge.net/biopax-site/owldoc/Level2 browse]) Support metabolic pathways, molecular interactions, protein post-translational modifications and the [http://psidev.sourceforge.net/ PSI-MI]
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* [http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]  
**[http://www.biopax.org/release/biopax-level1.owl Level 1 Ontology] ([http://biopax.sourceforge.net/biopax-site/owldoc/Level1 browse]) Supports metabolic pathways
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* [http://groups.google.com/group/BioPAX-Boston biopax-boston]
**[[Data|Pathways in BioPAX format]]
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* [http://archive.biopaxwiki.org Original Wiki Archive]
**[[Biological software supporting BioPAX]]
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*<strong>For developers interested in building software using BioPAX</strong>
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**[[Paxtools]]
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**[http://www.medicalcomputing.net/owl1.html Introduction to OWL Web Ontology Language for Medical and Biosciences Applications]
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**[http://www.biopax.org/Docs/BioPAX-Jena_Tutorial.pdf Tutorial on accessing BioPAX content using Jena]
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**[[Software Development Tools]]
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==Note==
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== [[Special:Categories | Wiki Pages by Category]] ==
  
Old BioPAX (MoinMoin) wiki was auto-converted to this MediaWiki. We encourage everyone to simply pick a [[Special:Random|Random Page]] to review and edit.
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==Note==
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We encourage everyone to simply pick a [[Special:Random|Random Page]] to review and edit.
  
 
__NOTOC__
 
__NOTOC__

Latest revision as of 07:30, 12 July 2014

BioPAX : Biological Pathways Exchange

BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in the RDF/XML format. BioPAX Paper was published in Nature Biotechnology in 2010.

Coordination

For biologists

and computational biologists interested in downloading and analyzing pathway data:

For developers

interested in building software using BioPAX:

Archive

Wiki Pages by Category

Note

We encourage everyone to simply pick a Random Page to review and edit.