BioPAX Roadmap

Level	Scope of Ontology					Data Source Compatibility
	Physical Entities	Interactions		Pathways	Metadata / Utility Classes
Level 1	Small molecules	Biochemical Reactions		Metabolic pathways	X-refs	KEGG, BioCyc, WIT/PUMA2, aMAZE
	Proteins	Enzyme Catalyses			Participants
	RNA	Transport Catalyses
	Complexes	Assembly of Complexes
	Biological Rationale: Capture knowledge about simple metabolic pathways.
Level 2	DNA	Binding Interactions		Molecular interaction networks	Evidence	BIND, IntAct, HPRD, MINT, DIP, PSI format
					Confidence
	Biological Rationale: Add support for molecular binding interactions.
Level 3	Genes	Molecular states		Signal transduction	External controlled	Transpath, PATIKA, CSNDB, Reactome, INOH
		Gene regulation		networks	Vocabularies
					States
	Biological Rationale: Add support for signaling pathways and regulation of gene expression.
Level 4	Generic physical	Genetic interactions		Genetic networks		FlyBase
	entities	Generic interactions		Generic pathways		MIPS
	Biological Rationale: Add support for genetic interactions, generic entities and processes.
Future Levels	Environmental effects		Abstract associations (e.g. co-occurrence in: pathways, literature abstracts, cell compartments, etc.)	Networks of abstract relationships	Experimental	PubGene
					descriptions	GeneWays
	Cells				Provenance
	Cell compartments
	Photons
	Biological Rationale: Capture abstract relationships between biological entities, cell-level interactions.

Note: Feedback from the community and potential users could lead to modifications in this document.