Development of a Semi-Automated Chart Review for Assessing the Development of Radiation Pneumonitis: using Natural Language Processing (Preprint)

Background: Health research frequently requires manual chart reviews to identify patients in a study-specific cohort and examine their clinical outcomes. Manual chart review is a labor-intensive process that requires significant time investment for clinical researchers. Objective: This study aims to evaluate the feasibility and accuracy of an assisted chart review program, using an in-house rule-based text-extraction program written in Python, to identify patients who developed radiation pneumonitis (RP) after receiving curative radiotherapy. Methods: A retrospective manual chart review was completed for patients who received curative radiotherapy for stage 2-3 lung cancer from January 1, 2013 to December 31, 2015, at British Columbia Cancer, Kelowna Centre. In the manual chart review, RP diagnosis and grading were recorded using the Common Terminology Criteria for Adverse Events version 5.0. From the charts of 50 sample patients, a total of 1413 clinical documents were obtained for review from the electronic medical record system. The text-extraction program was built using the Natural Language Toolkit Python platform (and regular expressions, also known as RegEx). Python version 3.7.2 was used to run the text-extraction program. The output of the text-extraction program was a list of the full sentences containing the key terms, document IDs, and dates from which these sentences were extracted. The results from the manual review were used as the gold standard in this study, with which the results of the text-extraction program were compared. Results: Fifty percent (25/50) of the sample patients developed grade ≥1 RP; the natural language processing program was able to ascertain 92% (23/25) of these patients (sensitivity 0.92, 95% CI 0.74-0.99; specificity 0.36, 95% CI 0.18-0.57). Furthermore, the text-extraction program was able to correctly identify all 9 patients with grade ≥2 RP, which are patients with clinically significant symptoms (sensitivity 1.0, 95% CI 0.66-1.0; specificity 0.27, 95% CI 0.14-0.43). The program was useful for distinguishing patients with RP from those without RP. The text-extraction program in this study avoided unnecessary manual review of 22% (11/50) of the sample patients, as these patients were identified as grade 0 RP and would not require further manual review in subsequent studies. Conclusions: This feasibility study showed that the text-extraction program was able to assist with the identification of patients who developed RP after curative radiotherapy. The program streamlines the manual chart review further by identifying the key sentences of interest. This work has the potential to improve future clinical research, as the text-extraction program shows promise in performing chart review in a more time-efficient manner, compared with the traditional labor-intensive manual chart review.