Table 3.

BioPAX covers five main types of biological pathways and coverage has increased over time with new levels of the ontology.

Type of Biological Pathway	Main BioPAX Classes Used	Introduced
Metabolic pathways	All types of physical entities (most common use of protein, small molecule, complex), All types of conversion events (most common use of BiochemicalReaction, ComplexAssembly and Transport), Catalysis, Modulation and Pathway	Level 1
Signaling pathways	All types of physical entities (most common use of protein, complex), All types of conversion events (most common use of BiochemicalReaction, ComplexAssembly, Transport and Degradation), Control, Catalysis, Modulation, MolecularInteraction, Pathway	Level 2
Molecular interactions	All types of physical entities (most common use of protein, complex, small molecule), MolecularInteraction, Pathway	Level 2
Gene regulatory networks	All types of physical entities, TemplateReaction, TemplateReactionRegulation	Level 3
Genetic interactions	Gene, GeneticInteraction	Level 3