Automatic generation of case-detection algorithms to identify children with asthma from large electronic health record databases
Purpose: Most electronic health record databases contain unstructured free-text narratives, which cannot be easily analyzed. Case-detection algorithms are usually created manually and often rely only on using coded information such as International Classification of Diseases version 9 codes. We applied a machine-learning approach to generate and evaluate an automated case-detection algorithm that uses both free-text and coded information to identify asthma cases. Methods: The Integrated Primary Care Information (IPCI) database was searched for potential asthma patients aged 5-18years using a broad query on asthma-related codes, drugs, and free text. A training set of 5032 patients was created by manually annotating the potential patients as definite, probable, or doubtful asthma cases or non-asthma cases. The rule-learning program RIPPER was then used to generate algorithms to distinguish cases from non-cases. An over-sampling method was used to balance the performance of the automated algorithm to meet our study requirements. Performance of the automated algorithm was evaluated against the manually annotated set. Results: The selected algorithm yielded a positive predictive value (PPV) of 0.66, sensitivity of 0.98, and specificity of 0.95 when identifying only definite asthma cases; a PPV of 0.82, sensitivity of 0.96, and specificity of 0.90 when identifying both definite and probable asthma cases; and a PPV of 0.57, sensitivity of 0.95, and specificity of 0.67 for the scenario identifying definite, probable, and doubtful asthma cases. Conclusions: The automated algorithm shows good performance in detecting cases of asthma utilizing both free-text and coded data. This algorithm will facilitate large-scale studies of asthma in the IPCI database.
|Keywords||Automated case definition, Case-detection algorithms, Electronic medical records, Machine learning, Pharmacoepidemiology|
|Persistent URL||dx.doi.org/10.1002/pds.3438, hdl.handle.net/1765/40923|
|Journal||Pharmacoepidemiology and Drug Safety: an international journal|
Afzal, M.Z, Engelkes, M, Verhamme, K.M.C, Janssens, H.M, Sturkenboom, M.C.J.M, Kors, J.A, & Schuemie, M.J. (2013). Automatic generation of case-detection algorithms to identify children with asthma from large electronic health record databases. Pharmacoepidemiology and Drug Safety: an international journal, 22(8), 826–833. doi:10.1002/pds.3438