Automatic generation of case-detection algorithms to identify children with asthma from large electronic health record databases

Pharmacoepidemiol Drug Saf. 2013 Aug;22(8):826-33. doi: 10.1002/pds.3438. Epub 2013 Apr 17.


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 5-18 years 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Algorithms*
  • Asthma / epidemiology*
  • Child
  • Child, Preschool
  • Databases, Factual
  • Electronic Data Processing
  • Electronic Health Records*
  • Humans
  • Predictive Value of Tests
  • Sensitivity and Specificity