A mechanism is provided for implement a discrepancy detection mechanism for detecting discrepancies between clinical notes and administrative records. Clinical concepts are extracted from the clinical notes and the administrative records in a patient's electronic medical records (EMRs). The extracted clinical concepts are filtered based on semantic type information to identify concepts that reference diseases or syndromes while also removing negated instances. Utilizing the positive mentions of diseases in clinical notes, the positive mentions of diseases or syndromes in the clinical notes are compared against each positive entry in the administrative records. A discrepancy summary is then generated for diseases or syndromes that failed to translate correctly from clinical notes to the administrative records in the patient's EMRs.