Flexible data integration and ontology-based data access to medical records

The ASSIST project aims to facilitate cervical cancer research by integrating medical records containing both phenotypic and genotypic data, and residing in different medical centres or hospitals. The goal of ASSIST is to enable the evaluation of medical hypotheses and the conduct of association studies in an intuitive manner, thereby allowing medical researchers to identify risk factors that can then be used at the point of care to identify women who are at high risk of developing cervical cancer. This paper presents the current status of the ASSIST medical knowledgebase. In particular, we discuss the challenges faced in constructing the ASSIST integrated resource and in enabling query processing through a domain ontology, and the solutions provided using the AutoMed heterogeneous data integration system. We focus on data cleansing issues, on data integration issues related to integrating relational medical data sources into an independent domain ontology and also on query processing. Of particular interest is the challenge of providing an easily maintainable integrated resource in a setting where the data sources and the domain ontology are developed independently and are therefore both highly likely to evolve over time.