The Web Ontology Language (OWL) provides a modelling paradigm that is especially well suited for developing models of large, structurally complex domains such as those found in Health Care and the Life Sciences. OWL’s declarative nature combined with powerful reasoning tools has effectively supported the development of very large and complex anatomy, disease, and clinical ontologies. OWL, however, is not a programming language, so using these models in applications necessitates both a technical means of integrating OWL models with programs and considerable methodological sophistication in knowing how to integrate them. In this paper, we present an analytical framework for evaluating various OWL-Java combination approaches. We have developed a software framework for what we call hybrid modelling, that is, building models in which part of the model exists and is developed directly in Java and part of the model exists and is developed directly in OWL. We analyse the advantages and disadvantages of hybrid modelling both in comparison to other approaches and by means of a case study of a large medical records system.