Abstract: To provide support for the analysis of biochemical pathways a
database system based on a model that represents the characteristics of the
domain is needed. This domain has proven to be difficult to model by using
conventional data modelling techniques. We are building an ontology for
biochemical pathways, which acts as the basis for the generation of a database
on the same domain, allowing the definition of complex queries and complex data
representation. The ontology is used as a modelling and analysis tool which
allows the expression of complex semantics based on a first-order logic
representation language. The induction capabilities of the system can help the
scientist in formulating and testing research hypotheses that are difficult to
express with the standard relational database mechanisms. An ontology
representing the shared formalisation of the knowledge in a scientific domain
can also be used as data integration tool clarifying the mapping of concepts to
the developers of different databases. In this paper we describe the general
structure of our system, concentrating on the ontology-based database as the
key component of the system.
