Figure 1

Taxonomy of a basic upper-level ontology to facilitate integration of in vivo and in silico entities. Our basic upper-level ontology distinguishes between representation of in vivo entities (Biological entity) and in silico entities (Model entity). The sub-classes of Biological entity included in the upper-level ontology are Physical object, Process, Function and Quality. These classes are further extended by classes from biomedical reference ontologies (e.g., classes from ChEBI, Celltype, FMA, GO and PATO). Sub-classes of Model entity include Model and Model component, and these classes can be extended with SBML-specific classes.