Abstract
OWL ontologies are extensively used in the clinical sciences, with ontologies such as SNOMED CT being a component of the health information systems of several countries. Preserving privacy of information in ontology-based systems (e.g., preventing unauthorised access to system's data and ontological knowledge) is a critical requirement, especially when the system is accessed by numerous users with different privileges and is distributed across applications. Unauthorised disclosure, for example, of medical information from SNOMED-based systems could be disastrous for government organisations, companies and, most importantly, for the patients themselves. It is to be expected that privacy-related issues will become increasingly important as ontology-based technologies are integrated in mainstream applications. In this short paper, I discuss several challenges and open problems, and sketch possible research directions.