A large number of biomedical ontologies exist, covering diverse
domains. Their integration into a common ontological framework is a
difficult yet rewarding task. In particular, there are ontologies
that describe a canonical view of a domain. The Foundational Model of Anatomy
and many other ontologies that describe structure or anatomy fall into
this category of ontologies. On the other hand, some ontologies
represent pathologies or exceptions to the canonical cases. Integration
of these two kinds of ontologies is particularly challenging, because
inconsistencies may arise that must be avoided.
We show where non-monotonic phenomena occur in the integration of
the two types of ontologies we discuss, and propose a solution to the problem
of their integration.