Extracting Clinical Features From Dictated Ambulatory Consult Notes Using a Commercially Available Natural Language Processing Tool: Pilot, Retrospective, Cross-Sectional Validation Study

JMIR Med Inform. 2019 Nov 1;7(4):e12575. doi: 10.2196/12575.


Background: The increasing adoption of electronic health records (EHRs) in clinical practice holds the promise of improving care and advancing research by serving as a rich source of data, but most EHRs allow clinicians to enter data in a text format without much structure. Natural language processing (NLP) may reduce reliance on manual abstraction of these text data by extracting clinical features directly from unstructured clinical digital text data and converting them into structured data.

Objective: This study aimed to assess the performance of a commercially available NLP tool for extracting clinical features from free-text consult notes.

Methods: We conducted a pilot, retrospective, cross-sectional study of the accuracy of NLP from dictated consult notes from our tuberculosis clinic with manual chart abstraction as the reference standard. Consult notes for 130 patients were extracted and processed using NLP. We extracted 15 clinical features from these consult notes and grouped them a priori into categories of simple, moderate, and complex for analysis.

Results: For the primary outcome of overall accuracy, NLP performed best for features classified as simple, achieving an overall accuracy of 96% (95% CI 94.3-97.6). Performance was slightly lower for features of moderate clinical and linguistic complexity at 93% (95% CI 91.1-94.4), and lowest for complex features at 91% (95% CI 87.3-93.1).

Conclusions: The findings of this study support the use of NLP for extracting clinical features from dictated consult notes in the setting of a tuberculosis clinic. Further research is needed to fully establish the validity of NLP for this and other purposes.

Keywords: electronic health record; natural language processing; tuberculosis.