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Large electronic health records database available at a national level offer great opportunity for research in rare diseases and orphan drugs. Methods and data used in pharmacoepidemiology present a great potential for epidemiology, drug utilization studies, drug safety, drug effectiveness and pharmacoeconomics. This review presents the different sources of data in Europe, with a special focus on the French situation, with the recent implementation of SNDS (système national des données de santé [French national health data wharehouse]).