BioPAX Data Exchange Ontology for Biological Pathway Databases

BioPAX Group1, BioPAX

The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.

Systems biology mark-up languages, such as CellML ( and SBML (, address a pathway simulation use case, but are not designed to handle the wider range of use cases intended for BioPAX. In the areas where they overlap, BioPAX will be compatible with these and other important standards such as PSI ( This will decrease the burden on end-users and allow for a common standard to be developed in the future.

BioPAX is being developed as both an OWL ontology using the Generic Knowledge Base Editor (GKB,, and concurrently as an XML Schema using XMLSpy. We are designing both versions of BioPAX so that XSLT translators will be able to provide translation between them. The rationale behind dual syntaxes for the exchange format stems from the fact that OWL is a more powerful representation language, but XML Schema is currently in much wider use. Since the utility of a data exchange format depends on it being widely accepted, we feel it is necessary to create a version of BioPAX in both of these syntaxes.

The primary use of the BioPAX data exchange format will be enabling data sharing between pathway databases like aMAZE, BIND, DIP, EcoCyc, IntAct, and WIT. BioPAX could also facilitate the creation of a centralized public repository for pathway data (the desire for such a repository was one of the driving forces behind formation of the BioPAX effort).

Another intended use of the BioPAX format is to provide a standard format for software tools that must access pathway data (pathway visualization programs, expression analysis tools, and pathway simulation tools).

Members of the community interested in BioPAX are encouraged to participate, promote and provide feedback to BioPAX. The BioPAX web site ( contains documentation, activities, and mailing lists for feedback and discussion.