Strengths and limitations of formal ontologies in the biomedical domain

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology of different kinds of logical resources, with a focus on description logics.The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals.We advocate a clear distinction of the four kinds of representation in order to provide a more rational basis for using of ontologies and related artifacts to advance integration of data and interoperability of associated reasoning systems.We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies when the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models.