Table 1.

Formal approaches to the meaning facets of bio-models

Formal	Language element/	Intrinsic meaning facet
approach	Ontology branch	Structure			Function			Behaviour
		(S1)	(S2)	(S3)	(F1)	(F2)	(F3)	(B1)	(B2)	(B3)
SBML	species		x
	reaction			x
	kineticLaw			x
	initialAmount					x
	parameter					x
SBO	“modelling framework”	x
SED-ML	Simulation				x
	Change					x
KiSAO	“modeling and simulation						x
	algorithm”
DYML	feature							x
	constraints					x
TEDDY	“temporal behaviour”							x
	“behaviour diversification”							x
Temporal logics								x
SBRML	Result								x	x
Fielded Text									x	x
Formal	Language element/	Extrinsic meaning facet
approach	Ontology branch	Structure			Function			Behaviour
		(S1)	(S2)	(S3)	(F1)	(F2)	(F3)	(B1)	(B2)	(B3)
UniProt			x
NCBI Taxonomy		x
Database
Gene ontology	“Biological Process”	x						x
SBO	“physical entity representation”		x
	“systems description parameter”		x
	“occurring entity representation”			x
	“systems biology representation”			x
Reactome				x
Cell type						x
Ontology
SABIO-RK						x
FuGE	Material					x
	Investigation						x
	Data								x	x
SBRML	Result								x	x
Fielded Text									x	x

Formal approaches (languages, ontologies and biological resources) for computer representations of bio-models and their contribution to the formalisation of the meaning facets as shown for the example models by Tyson. An “x” means that the respective formal approach or some given aspect (language element or ontology branch) of it is able to represent the specific meaning facet or at least parts of it. The table is divided into intrinsic (top) and extrinsic (bottom) meaning facets.