A controlled trial of automated classification of negation from clinical notes

BACKGROUND: Identification of negation in electronic health records is essential if we are to understand the computable meaning of the records: Our objective is to compare the accuracy of an automated mechanism for assignment of Negation to clinical concepts within a compositional expression with Human Assigned Negation. Also to perform a failure analysis to identify the causes of poorly identified negation (i.e. Missed Conceptual Representation, Inaccurate Conceptual Representation, Missed Negation, Inaccurate identification of Negation). METHODS: 41 Clinical Documents (Medical Evaluations; sometimes outside of Mayo these are referred to as History and Physical Examinations) were parsed using the Mayo Vocabulary Server Parsing Engine. SNOMED-CT™ was used to provide concept coverage for the clinical concepts in the record. These records resulted in identification of Concepts and textual clues to Negation. These records were reviewed by an independent medical terminologist, and the results were tallied in a spreadsheet. Where questions on the review arose Internal Medicine Faculty were employed to make a final determination. RESULTS: SNOMED-CT was used to provide concept coverage of the 14,792 Concepts in 41 Health Records from John's Hopkins University. Of these, 1,823 Concepts were identified as negative by Human review. The sensitivity (Recall) of the assignment of negation was 97.2% (p < 0.001, Pearson Chi-Square test; when compared to a coin flip). The specificity of assignment of negation was 98.8%. The positive likelihood ratio of the negation was 81. The positive predictive value (Precision) was 91.2% CONCLUSION: Automated assignment of negation to concepts identified in health records based on review of the text is feasible and practical. Lexical assignment of negation is a good test of true Negativity as judged by the high sensitivity, specificity and positive likelihood ratio of the test. SNOMED-CT had overall coverage of 88.7% of the concepts being negated.