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BioPAX Level 4 Workgroups

An outline of the Level4 Workgroups suggested at the November 2009 meeting in NYC are listed below.

  • Visualization and exchange

The option of an extension to BioPAX to deliver layout (basic coordinates). After a long discussion in Novemeber, it was agreed that this would be a duplication of work and that 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/

This would encompass extending BioPAX to enable the capture and exchange of generic reactions and generic pathways and extensions tot he entityreference class.

  • Semantic web/linking/CVs

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

  • Validation/best practices

Form rules and best practices for data and documenting and delivering these into the BioPAX validator.

  • Quantitative modeling vs. static relationship/SBML/CellML/VirtualCell

With respect to reaction rates and rate laws, some people using BioPAX 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.