Difference between revisions of "Main Page"

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(Using BioPAX)
(Using BioPAX)
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** <b>[[Data|Pathways in BioPAX format]]</b>
 
** <b>[[Data|Pathways in BioPAX format]]</b>
 
***[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.
 
***[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.
***[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://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].
 
***[http://www.ebi.ac.uk/biomodels/ BioModels Database] - Level 2 format: Download link available on each model page.
 
***[http://www.ebi.ac.uk/biomodels/ BioModels Database] - Level 2 format: Download link available on each model page.
 
***[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].
 
***[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].

Revision as of 20:56, 20 September 2010

BioPAX : Biological Pathways Exchange

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


Level3Announcement

BioPAX Paper Published in Nature Biotechnology

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 #, ##, ###,..)