Ontologies play a key role in the advent of the Semantic Web. An important problem when dealing with ontologies is the modification of an existing ontology in response to a certain need for change. This problem is a complex and multifaceted one, because it can take several different forms and includes several related subproblems, like heterogeneity resolution or keeping track of ontology versions. As a result, it is being addressed by several different, but closely related and often overlapping research disciplines. Unfortunately, the boundaries of each such discipline are not clear, as the same term is often used with different meanings in the relevant literature, creating a certain amount of confusion. The purpose of this paper is to identify the exact relationships between these research areas and to determine the boundaries of each field, by performing a broad review of the relevant literature.

Abstract. The ultimate goal of the biomedical informatics project PrognoChip is the identification of classification and prognosis molecular markers for breast cancer. This requires not only an understanding of the genetic basis of the disease, based on the patient's tumor gene expression profiles but also the correlation of this data with knowledge normally processed in the clinical setting. In this paper, we present the Mediator component of the PrognoChip Integrated Clinico-Genomics Environment (ICGE), through which the integration of the clinical and genomic information subsystems is achieved. The biomedical investigator can form clinico-genomic queries through the webbased graphical user interface of the Mediator. This is split into several query forms, allowing cancerous sample selection (along with their associated gene expression profiles and patient characteristics), based on criteria of interest. After a query is formed, the Mediator translates it into an equivalent set of local subqueries, which are executed directly against the constituent databases. Then, results are combined for presentation to the user and/or transmission to the Data Mining tools for analysis.