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BioPAX Level 4 Workgroups

Five Level 4 Workgroups were suggested at the November 2009 meeting in NYC.

The option of an extension to BioPAX to deliver layout (x,y coordinates only). A complete visualization extension for BioPAX would be a duplication of work and eventually SBGN will provide visualization exchange. In the interim, a workgroup could formulate a simple format for pathway visualization. This group would coordinate with SBGN.

  • Semantics: Generics/polymers/logic/ Status: Seeking Co-ordinator

Works toward extending BioPAX e.g. to enable the capture and exchange of generic reactions and generic pathways and extensions to the entityreference class.

Semantic web community wish list including Linked Data Project, Linking to other ontologies and ontology mapping, additional controlled vocabularies and architecture of controlled vocabularies are all areas where BioPAX needed improvement.

  • Validation/best practices Status: Initiated - Point of Contact Igor Rodchenkov

Develop rules and best practices for data and documenting and deliver these into the BioPAX validator.

  • Quantitative modeling vs. static relationship/SBML/CellML/VirtualCell Status: Started - Point of Contact Oliver Ruebenacker

With respect to reaction rates and rate laws, some BioPAX users would like to have a stronger link between BioPAX and SBML. In order to provide a technical link between BioPAX and SBML, this group will create a proposal and help to define a better bridge between the two languages and ultimately delegate to SBML.