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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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==[[Level3Announcement]]==
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==[http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html BioPAX Paper Published in Nature Biotechnology ]==
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== Using BioPAX ==
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*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
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**<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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*** [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]) [http://biopax.org/webprotege/ webprotege] covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
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***[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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***[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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** <b>[[Data|Pathways in BioPAX format]]</b>
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***[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 and Level 3 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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***[http://www.signaling-gateway.org/molecule/ UCSD Nature Molecule Pages]- Level 3 format: Download link available on each molecule page.
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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://groups.google.com/group/biopax-discuss?lnk=li The BioPAX Forum]
*[http://www.biopax.org/release/biopax-level3-documentation.pdf Level 3 Documentation (pdf)]
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* [[Level3Announcement | BioPAX Level3 Announcenment]]
*[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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* [[Specification | BioPAX Specification and Documentation]]
*[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 Governance]]
 
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* [[L4Workgroups | BioPAX Workgroups]] and [[BioPAX People Pages]] (Add yourself!)
* BioPAX Homepage: http://www.biopax.org/. Note: BioPAX activity is now mostly documented on this wiki.
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* [[L4ProposalsList | BioPAX Proposals]]
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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]]
* [[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] please [http://www.surveymonkey.com/s/9GP9KJ3 register] as soon as possible.
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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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----
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== [[Special:Categories | Wiki Pages by Category]] ==
  
 
==Note==
 
==Note==
 
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We encourage everyone to simply pick a [[Special:Random|Random Page]] to review and edit.
BioPAX wiki pages were auto-converted from the MoinMoin to MediaWiki, and this was not perfect. We encourage everyone to review and fix them, e.g., by simply picking up a [[Special:Random|Random Page]].
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[http://archive.biopaxwiki.org Original Wiki Archive] is still 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>. 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 PDF, OWL, etc., cannot <br/>(there is no simple solution, because the wiki is SourceForge's globally configured and shared application). So, we manually uploaded them to [http://sourceforge.net/projects/biopax/files "/other" directory]
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* 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.