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Extraction and use of Electronic Health Record (EHR) data is common in retrospective observational studies. However, electronic extraction and use of EHR data is rare during longitudinal prospective studies. One of the reasons is the amount of processing needed to assess data quality and assure consistency in meaning and format across multiple investigational sites. We report a case study of and lessons learned from acquisition and processing of EHR data in an ongoing basis during a clinical study.