Electronic health records (EHRs) are an important source of data for detection of adverse drug reactions (ADRs). However, adverse events are frequently due not to medications but to the patients' underlying conditions. Mining to detect ADRs from EHR data must account for confounders. We developed an automated method using natural-language processing (NLP) and a knowledge source to differentiate cases in which the patient's disease is responsible for the event rather than a drug. Our method was applied to 199,920 hospitalization records, concentrating on two serious ADRs: rhabdomyolysis (n = 687) and agranulocytosis (n = 772). Our method automatically identified 75% of the cases, those with disease etiology. The sensitivity and specificity were 93.8% (confidence interval: 88.9-96.7%) and 91.8% (confidence interval: 84.0-96.2%), respectively. The method resulted in considerable saving of time: for every 1 h spent in development, there was a saving of at least 20 h in manual review. The review of the remaining 25% of the cases therefore became more feasible, allowing us to identify the medications that had caused the ADRs.
