Difference between revisions of "Main Page"

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== Using BioPAX ==
 
== Using BioPAX ==
 
*<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 defined (in [http://www.w3.org/TR/owl-features/ OWL XML]).
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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 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]) 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]

Revision as of 19:01, 27 May 2010

BioPAX : Biological Pathways Exchange

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


Using BioPAX

Documentation

Community

BioPAX Workgroup Coordination


Note

Many (but not all) BioPAX Wiki Pages Have Been Recently Auto-converted from the MoinMoin to MediaWiki.
The Convertion Was Not Perfect, So We Encourage Everyone to Edit, Starting from the Original biopaxwiki Front Page or Picking up a Random Page.

The Original Wiki Archive Will Be Available Soon (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]]. Therefore, this has to be changed manually to [[Page/SubPage]]
  • 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)
  • list items: you may find some pages look ugly due to extra spaces before * or # or broken nested lists (must be *, **, ***, etc. or #, ##, ###,..)