Abstract: The long-term objective of our work is the computational
construction of complex cellular systems. Therefore, input data must be
prepared systematically first. In the field of biological data information is
spread out over hundreds of molecular databases. Different approaches of data
integration have been already applied in the past to provide a homogeneous
access to these databases. Actually, a system is required to store integrated
data of different type locally and to search for networks found in the
integrated dataset. Finally, the analysis of these networks can answer
different questions, e.g. the role of biochemical substances in regulatory
systems or the reasoning of metabolic diseases. In this article a novel object-oriented modelling approach in the
field of biochemical networks is presented. Molecular objects are modelled
conceptually using object classes, internally based on the object model OMG
IDL. Specific object services are implemented automatically for each model and
object instances are built using data integration. In combination with that, a
specific view concept based on access paths has been implemented to model
biochemical reaction rules automatically. Together with the application of
graphical methods, pathways and cliques are computed by the system. They
provide the topology of cellular process networks. The system has been
implemented using Java and CORBA.
Keywords: object-oriented modelling, data integration, network analysis, Java, CORBA
