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In this paper, we present a framework which enables medical decision making in the presence of partial information. At its core is ontology-based automated reasoning, machine learning techniques are integrated to enhance existing patient datasets in order to address the issue of missing data. Our approach supports interoperability between different health information systems. This is clarified in a sample implementation that combines three separate datasets (patient data, drug-drug interactions and drug prescription rules) to demonstrate the effectiveness of our algorithms in producing effective medical decisions. In short, we demonstrate the potential for machine learning to support a task where there is a critical need from medical professionals by coping with missing or noisy patient data and enabling the use of multiple medical datasets.