A computable case definition for patients with SARS-CoV2 testing that occurred outside the hospital

JAMIA Open. 2023 Jul 5;6(3):ooad047. doi: 10.1093/jamiaopen/ooad047. eCollection 2023 Oct.


Objective: To identify a cohort of COVID-19 cases, including when evidence of virus positivity was only mentioned in the clinical text, not in structured laboratory data in the electronic health record (EHR).

Materials and methods: Statistical classifiers were trained on feature representations derived from unstructured text in patient EHRs. We used a proxy dataset of patients with COVID-19 polymerase chain reaction (PCR) tests for training. We selected a model based on performance on our proxy dataset and applied it to instances without COVID-19 PCR tests. A physician reviewed a sample of these instances to validate the classifier.

Results: On the test split of the proxy dataset, our best classifier obtained 0.56 F1, 0.6 precision, and 0.52 recall scores for SARS-CoV2 positive cases. In an expert validation, the classifier correctly identified 97.6% (81/84) as COVID-19 positive and 97.8% (91/93) as not SARS-CoV2 positive. The classifier labeled an additional 960 cases as not having SARS-CoV2 lab tests in hospital, and only 177 of those cases had the ICD-10 code for COVID-19.

Discussion: Proxy dataset performance may be worse because these instances sometimes include discussion of pending lab tests. The most predictive features are meaningful and interpretable. The type of external test that was performed is rarely mentioned.

Conclusion: COVID-19 cases that had testing done outside of the hospital can be reliably detected from the text in EHRs. Training on a proxy dataset was a suitable method for developing a highly performant classifier without labor-intensive labeling efforts.

Keywords: COVID-19; machine learning; natural language processing; text classification.

Associated data

  • Dryad/10.5061/dryad.51c59zwdj