BioPAX-SBGN Mapping

This page may serve as a point of coordination for collaborative development of a BioPAX<->SBGN mapping.

http://sbgn.org/

As of 01/19/09 a substantial amount of BioPAX Level 3 concepts can be represented in SBGN PD. Most important outstanding issues are:

Generics- Classes of proteins, small molecules that behave in the same manner in the context of some interaction and/or pathway. This currently can not be represented in SBGN. See Generics

Features- Currently SBGN employs a strict close world semantics for features which was recently changed to open world in BioPAX L3. TODO: add e-mail discussion summary here.

Gene Regulation: This is both work in progress in BioPAX L3 and SBGN. A mapping has not been done.

Genetic Interactions: Currently are not covered by SBGN PD as these are not really processes. These can be later covered in ER or AF.

Figure 1 : A mapping of some BioPAX concepts to SBGN.

Of interest:

http://www.csml.org/