An ontology is a formal collection of pieces of knowledge that specify the behaviour of entities in a domain. Our domain is physical-chemical-biological systems, processes that we describe with a set of concepts or principles. These ontologies are not used to reason about the system, but to construct process models that adhere to these concepts, in particular the conservation principles and the behaviour of materials, the geometrical concepts in space and time. Simplicity of the ontology is a design criteria, both in the definition and implementation of its utilisation. A simple generic structure building on defining the containment as a directed graph, which is populated with tokens. The two enable us to apply our concept in a very broad field of contexts. So whilst we discuss the structure based on physical systems with control, it can be applied much wider. The extension to multi-scale models is or particular interest.
