FrontPage

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. Please Get Involved!. This is the Wiki documenting and discussing the project. You might want to have a look at Tips on Using this Wiki.

Note: To edit wiki pages, sign up for an account, then add yourself to the editor list.

Using BioPAX

• For biologists and computational biologists interested in downloading and analyzing pathway data

  • Ontology: The BioPAX format defined (in OWL XML).

    • Level 3, Version 0.92 (Release Candidate 3) covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions. BioPAX Level 3 is currently under development and review by pathway databases and is scheduled for release by mid-2008. Level 3 Documentation

    • Level 2 Ontology ( browse) Support metabolic pathways, molecular interactions, protein post-translational modifications and the PSI-MI

    • Level 1 Ontology ( browse) Supports metabolic pathways

    • Level 2 is recommended. It is backwards compatible with Level 1.

    • See documentation below.

  • 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

  • Introduction to OWL Web Ontology Language for Medical and Biosciences Applications

  • Tutorial on accessing BioPAX content using Jena

  • Software Development Tools

Documentation

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

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

• Level 3 Documentation (pdf)

• BioPAX homepage: http://www.biopax.org/. Note: BioPAX activity is now mostly documented on this wiki.

• Presentations and Publications

• Mailing lists: biopax-discuss (main user mailing list), biopax-announce, biopax-boston, biopax admin

• FAQ

BioPAX Workgroup Coordination

Main BioPAX Workgroup Coordination Page

• Recent Workshop: Oct.15-16, 2007, SRI, Menlo Park

• See Past meetings to find notes from previous meetings.