BioPAX - Biological Pathway Exchange
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.
Status and Development
BioPAX Level 3 was finalized by the community in November 2009 and covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions. The current release of the BioPAX Level 3 can be found in the links below and the most up to date version is available to download from sourceforge.
- http://www.biopax.org/release/biopax-level3.owl
- http://www.biopax.org/release/biopax-level3-documentation.pdf
Community/Participate
BioPAX is a community process, please see Contributions, Editors and SAB. We are currently working on BioPAX Level 4. Current activity is documented in the Proposals and Workgroups section, on the BioPAX wiki and in the mailing lists that are listed below.