Difference between revisions of "Main Page"

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*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
 
*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
 
**<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).
 
**<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).
*** [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.
+
*** [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.
 
***[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]
 
***[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]
 
***[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
 
***[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

Revision as of 14:34, 28 July 2010

BioPAX : Biological Pathways Exchange

BioPAX is a collaborative effort to create a data exchange format for biological pathway data.


Level3Announcement

Using BioPAX

Documentation

Community

BioPAX Workgroup Coordination


Note

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 Random Page.

Original Wiki Archive is still available (readonly).

Known Issues:

  • not all pages were copied, but they are available in the archive (exception: see the next issue)
  • after the conversion, a sub-page name became, e.g., "Page/SubPage", but the parent "Page" still refers to it as [[/SubPage]]. This has to be changed manually to [[Page/SubPage]]
  • attachments were not copied; images can be easily uploaded and linked, but PDF, OWL, etc., cannot
    (there is no simple solution, because the wiki is SourceForge's globally configured and shared application). So, we manually uploaded them to "/other" directory
  • you may find some pages look ugly due to extra spaces before * or # or broken nested lists (must be *, **, ***, etc. or #, ##, ###,..)