Complex systems are full of unpredictable and uncertain behaviours that depend on many factors. Various fields of science have set themselves the task of studying these systems and predicting their behaviour under various premises with the help of computer models. Kwakkel et al. [1] published an uncertainty matrix to systematically record and communicate uncertainties about systems. This paper takes up the matrix, analyses the concepts of model and uncertainty in literature, and models them ontologically in the Modelling Uncertainties Ontology (MUNO), a BFO-based mid-level ontology for modelling uncertainties in models for many domains. MUNO is evaluated against requirements and competency questions. Based on the ontology, an RDF-shape is created and used as an example in a case study to annotate the uncertainties for an energy system model.

Energy is a fundamental phenomenon of physics, but energy also plays an important role in the representation of many domains, since many processes involve energy transformation or transfer. However, energy is represented very differently in existing ontologies. Even in ontologies that share BFO as top-level ontology, energy is sometimes treated as disposition, as quality, and as a material entity. As we discuss in the paper, there are reasons for each choice, which makes the ontological representation of energy a challenging subject. In this paper we present an ontological analysis of energy in a BFO-based mid-level ontology (MENO), including the different kinds of energy, their relations to dispositions as well as their realisation in processes.