A document(PhysiomeOntologiesAndTools) on physiome ontologies and tools discusses some of the ideas influencing the view on model representation.

Two key ideas out of this are

  1. the goals of human and machine-level aspects of model representation.
  2. the idea of levels of process for developing a biological model. This being 'conceptual -> mathematical -> instances(formulation) -> simulation'.

Model representation means the rules or data structures used to represent models so that we accurately capture the structures within the different levels of the process in (2) and can unambiguously interpret these from the model through human or machine-level interfaces.

Ontologies are relevant to this project at two levels, the goals of ontologies and the current solutions or systems in ontologies. The former is useful in this section, where the goals of model representation align well with the goals of the Web Ontology Group(WebOntologyGroup) community, who are very ontology focused. The latter, solutions or systems, represent the chosen systems we are designing to fulfil our goals. CellML ontologies(CellMLOntologies) should be the section to refer to for that information. It is likely that we will also follow the technologies of the WebOntologyGroup from a system-view as well as their goals.

The CellML language is designed for representing cellular models. A sub-section, CellMLEvolution, is a start on documenting some ideas that should influence the evolution of the language.