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='''[http://www.biopax.org BioPAX] : Biological Pathways Exchange'''=
 
='''[http://www.biopax.org BioPAX] : Biological Pathways Exchange'''=
  
BioPAX is a collaborative effort to create a data exchange format for biological pathway data.  
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BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
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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.
  
* [[:Category:SPECIFICATION|BioPAX Specification]]
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== Coordination ==
* [[:Category:SOFTWARE|BioPAX Software]]
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* [[:Category:COMMUNITY|BioPAX Community]]
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----
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* [http://groups.google.com/group/biopax-discuss?lnk=li The BioPAX Forum]
== Using BioPAX ==
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* [[Level3Announcement | BioPAX Level3 Announcenment]]
*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
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* [[Specification | BioPAX Specification and Documentation]]  
**<b>[[Specification]]</b>: The BioPAX format is defined in [http://www.w3.org/TR/owl-features/ OWL] and is represented in the RDF/XML Syntax).
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* [[BioPAX Governance]]
*** [http://www.biopax.org/release/biopax-level3.owl Level 3 Ontology] ([http://phoebus.cs.man.ac.uk:9999/OWL/Presentation?url=http://www.biopax.org/release/biopax-level3.owl browse]) covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
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* [[L4Workgroups | BioPAX Workgroups]] and [[BioPAX People Pages]] (Add yourself!)
***[http://www.biopax.org/release/biopax-level2.owl Level 2 Ontology] ([http://phoebus.cs.man.ac.uk:9999/OWL/Presentation?url=http://www.biopax.org/release/biopax-level2.owl browse]) Support metabolic pathways, molecular interactions, protein post-translational modifications and the [http://psidev.sourceforge.net/ PSI-MI]
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* [[L4ProposalsList | BioPAX Proposals]]
***[http://www.biopax.org/release/biopax-level1.owl Level 1 Ontology] ([http://phoebus.cs.man.ac.uk:9999/OWL/Presentation?url=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level1.owl browse]) Supports metabolic pathways
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* Next Workshops: [http://co.mbine.org/events/COMBINE_2014 COMBINE 2014], [http://co.mbine.org/events/HARMONY_2014 HARMONY 2014]
** <b>[[Data|Pathways in BioPAX format]]</b>
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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)]
***[http://biocyc.org/download.shtml BioCyc] - For freely available datasets visit http://biocyc.org/open-reg.shtml. For full dataset (free to academics, fees apply to industry), visit http://biocyc.org/flat-file-reg.shtml .  You can get the entire set of organisms in one file (named biopax.owl) or each individually (each one also named biopax.owl.
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***[http://reactome.org Reactome] - Level 2 format:  Download link available on each pathway page or [http://reactome.org/download/index.html on the Reactome download page].
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***[http://www.ebi.ac.uk/biomodels/ BioModels Database] - Level 2 format: Download link available on each model page.
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***[http://www.inoh.org/ INOH pathway database] - Level 2 format: 57 signal transduction pathways with more than 1300 interactions are available from [http://www.inoh.org/download.html#PathwayData Pathway data page].
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***[http://nashua.cwru.edu/PathwaysWeb/ PathCase] - save pathways and search results in BioPAX
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***[http://pid.nci.nih.gov/PID/browse_pathways.shtml Pathway Interaction Database] - some pathways curated by NCI-Nature and many others imported from [[BioCarta]]
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**<b>[[Biological software supporting BioPAX]]</b>
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*<b>For developers interested in building software using BioPAX</b>
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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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== [[Documents | Documentation]] ==
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*[http://www.biopax.org/release/biopax-level3-documentation.pdf Level 3 Documentation (pdf)]
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*[http://biopax.org/release/biopax-level2-documentation.pdf Level 2 Documentation (pdf)] [http://www.biopax.org/release/biopax-level2.owl another, automatically generated version]
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*[http://www.biopax.org/release/biopax-level1-documentation.pdf Level 1 Documentation (pdf)] [http://www.biopax.org/release/biopax-level1.owl another, automatically generated version]
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* BioPAX Homepage: http://www.biopax.org/. Note: BioPAX activity is now mostly documented on this wiki.
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* [[FAQ]]
 
* [[FAQ]]
* [[Presentations and Publications]]
 
  
== Community ==
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==For biologists==
* Mailing Lists:  
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<strong>and computational biologists interested in downloading and analyzing pathway data:</strong>
**[http://groups.google.com/group/biopax-discuss?lnk=li biopax discuss] - This is the main mailing list for all BioPAX community discussion.
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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.
* Old Mailing list (Archives still available)
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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]
**[http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]  
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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
** [http://www.biopax.org/mailman/listinfo/biopax-announce biopax-announce]
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*[[Data|Pathways in BioPAX format]]
**[http://groups.google.com/group/BioPAX-Boston biopax-boston]
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*[[Biological software supporting BioPAX]]
* BioPAX Tutorial at [[ICSB 2010 Tutorial| ICSB 2010]], [https://participants.congrex.com/scripts/jmevent/Registration.asp?Client_Id='CSLG'&Project_Id='101004'&Form_Id=1&Form_Number=2&Stand_Id=0&A=&Language_Code=&template_id= register here]
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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]]
  
== BioPAX Workgroup Coordination ==
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==Archive==
*[[L4Workgroups| Level 4 Workgroups]]
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* [[Presentations_and_Publications | Previous Presentations and Publications]]
*Level 4 [[BioPAX Workgroup Coordination L4]] Page
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* [[Past meetings]]
*Level 3 [[BioPAX Workgroup Coordination]] Page
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* [http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]  
* Next Workshop: [http://sbml.org/Events/Forums/COMBINE_2010 COMBINE 2010 Edinburgh, UK]
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* [http://groups.google.com/group/BioPAX-Boston biopax-boston]
* Last Workshop: [[NYC2009]]
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* [http://archive.biopaxwiki.org Original Wiki Archive]
* See [[Past meetings]] to find notes from previous meetings.
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== [[Special:Categories | Wiki Pages by Category]] ==
  
 
==Note==
 
==Note==
Many (but not all) BioPAX Wiki Pages Have Been Recently Auto-converted from the MoinMoin to MediaWiki. <br/>
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We encourage everyone to simply pick a [[Special:Random|Random Page]] to review and edit.
The Conversion Was Not Perfect, So We Encourage Everyone to Edit, Starting from the [[FrontPage|Original biopaxwiki Front Page]]
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or Picking up a [[Special:Random|Random Page]].
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The [http://archive.biopaxwiki.org Original Wiki Archive] is available (readonly).
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Known Issues:
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* not all pages were copied, but they are available in the archive (exception: see the next issue)
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* after the conversion, a sub-page name became, e.g., "Page/SubPage", but the parent "Page" still refers to it as <nowiki>[[/SubPage]]</nowiki>. Therefore, this has to be changed manually to <nowiki>[[Page/SubPage]]</nowiki>
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* attachments were not copied; images can be easily uploaded and linked, but others: PDF, OWL, etc., cannot (there seems to be no simple solution, as the MediaWiki is globally configured, shared application at SourceForge). So, we manually uploaded them to http://sourceforge.net/projects/biopax/files (directory '''/other''')
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* list items: you may find some pages look ugly due to extra spaces before <nowiki>* or #</nowiki> or broken nested lists (must be <nowiki>*, **, ***, etc. or #, ##, ###,..</nowiki>)
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__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.