Enhancing an enterprise data warehouse for research with data extracted using natural language processing

This study aims to develop a generalizable architecture for enhancing an enterprise data warehouse for research (EDW4R) with results from a natural language processing (NLP) model, which allows discrete data derived from clinical notes to be made broadly available for research use without need for NLP expertise. The study also quantifies the additional value that information extracted from clinical narratives brings to EDW4R.

Clinical notes written during one month at an academic health center were used to evaluate the performance of an existing NLP model and to quantify its value added to the structured data. Manual review was utilized for performance analysis. The architecture for enhancing the EDW4R is described in detail to enable reproducibility.

Two weeks were needed to enhance EDW4R with data from 250 million clinical notes. NLP generated 16 and 39% increase in data availability for two variables.

Our architecture is highly generalizable to a new NLP model. The positive predictive value obtained by an independent team showed only slightly lower NLP performance than the values reported by the NLP developers. The NLP showed significant value added to data already available in structured format.

Given the value added by data extracted using NLP, it is important to enhance EDW4R with these data to enable research teams without NLP expertise to benefit from value added by NLP models.