  There is a growing need to semantically process and integrate clinical data
from different sources for Clinical Data Management and Clinical Decision
Support in the healthcare IT industry. In the clinical practice domain, the
semantic gap between clinical information systems and domain ontologies is
quite often difficult to bridge in one step. In this paper, we report our
experience in using a two-step formalization approach to formalize clinical
data, i.e. from database schemas to local formalisms and from local formalisms
to domain (unifying) formalisms. We use N3 rules to explicitly and formally
state the mapping from local ontologies to domain ontologies. The resulting
data expressed in domain formalisms can be integrated and analyzed, though
originating from very distinct sources. Practices of applying the two-step
approach in the infectious disorders and cancer domains are introduced.
