From biopax

BioPAX : Biological Pathways Exchange

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

• BioPAX Specification
• BioPAX Software
• BioPAX Community

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Level3Announcement

Using BioPAX

• For biologists and computational biologists interested in downloading and analyzing pathway data
  • Specification: The BioPAX format is defined in OWL and is represented in the RDF/XML Syntax).
    • Level 3 Ontology (browse) webprotege covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
    • Level 2 Ontology (browse) Support metabolic pathways, molecular interactions, protein post-translational modifications and the PSI-MI
    • Level 1 Ontology (browse) Supports metabolic pathways
  • Pathways in BioPAX format
    • 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.
    • Reactome - Level 2 format: Download link available on each pathway page or on the Reactome download page.
    • BioModels Database - Level 2 format: Download link available on each model page.
    • INOH pathway database - Level 2 format: 57 signal transduction pathways with more than 1300 interactions are available from Pathway data page.
    • PathCase - save pathways and search results in BioPAX
    • Pathway Interaction Database - some pathways curated by NCI-Nature and many others imported from BioCarta
  • Biological software supporting BioPAX
• For developers interested in building software using BioPAX
  • Paxtools
  • Introduction to OWL Web Ontology Language for Medical and Biosciences Applications
  • Tutorial on accessing BioPAX content using Jena
  • Software Development Tools

Documentation

• Level 3 Documentation (pdf)
• Level 2 Documentation (pdf) another, automatically generated version
• Level 1 Documentation (pdf) another, automatically generated version

• BioPAX Homepage: http://www.biopax.org/. Note: BioPAX activity is now mostly documented on this wiki.
• FAQ
• Presentations and Publications

Community

• Mailing Lists:
  • biopax discuss - This is the main mailing list for all BioPAX community discussion.
• Old Mailing list (Archives still available)
  • biopax-discuss
  • biopax-announce
  • biopax-boston
• BioPAX Tutorial at ICSB 2010, register here

BioPAX Workgroup Coordination

• Level 4 Workgroups
• Level 3 BioPAX Workgroup Coordination Page
• Next Workshop: COMBINE 2010 Edinburgh, UK
• Last Workshop: NYC2009
• See Past meetings to find notes from previous meetings.

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