Ontologies are being ever more commonly used in biomedical informatics. The paper provides a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonized. The authors argue that one key foundation for both ontology evaluation and harmonization is the adoption of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonization is becoming ever more urgent. An example of such harmonization within the ACGT project is described, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.