Table 1 Formal approaches to the meaning facets of bio-models
From: Structure, function, and behaviour of computational models in systems biology
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 | ||||||||