OBJECTIVES: Recently, ontological principles have been applied to numerous biomedical vocabularies, with the intention to identify mistakes and poor modeling decisions. No doubt, such applications are useful and necessary for terminological systems like SNOMEDCT based on an axiomatic logical formalism.

METHODS: In the following review, ontology is dealt with by focussing on particularly two aspects: the problem of ISA-overloading and the intrusion of epistemology-loaded terms in biomedical vocabularies. Both aspects are considered with respect to three types of biomedical vocabularies.

RESULTS: Opposed to concept-oriented terminological systems, the purpose-specific organization of descriptors in thesauri and classes in statistical classifications on an extra aggregation level make it impossible to apply ontological principles. On the contrary, their intended purpose presupposes specific mechanisms that are in conflict with those principles.

CONCLUSIONS: Interestingly, for thesauri and classifications there are rather similar initiatives linking the extra level of descriptors and classes on the one hand and an intermediate concept level on the other hand. Such an approach proved beneficial for maintaining and translating thesauri and classifications.