Mediator-based Interoperation in Computational Biology: A Characterization of the Mediator Concept

The interoperation of information from various data sources, internet services and applications is a central topic in scientific research. Due to the fact that today interoperation requires a high degree of user knowledge and domain expertise in order to combine services in life science applications, we need a smarter mediator-based interoperation. In particular, biologists cannot answer questions by consultation of a single information source. In combining heterogeneous services we identify two different processes: an explicit user-defined biological business process and an implicit mediation process. In this context, mediators are subjects of the latter process, defining transformation steps in order to solve syntactic as well as semantic mismatches. Computational biology is a diverse and dynamic field. Therefore it is not possible to standardize data structures and working processes. Thus, one should simplify or standardize the mediation process. Based on an analysis of related mediator architectures we give a precise characterization of mediators in general. We identify several features a mediator has to provide. A major factor is the introspection mechanism in order to expose features of previously unknown mediators. This mechanism should be processable by users and machines, as far as possible. Introspection has to discover syntactic as well as semantic knowledge of the capabilities of a concrete mediator. We build an ontology-based mediator profile for this purpose. It is useful not only for generating concrete interface descriptions but also for specialized registries. Qualified mediator registries are a first step towards a smart mediation process.