Related Experiment Video
Updated: Sep 27, 2025
A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
Published on: September 20, 2018
Using Natural Language Processing to Improve Discrete Data Capture From Interpretive Cervical Biopsy Diagnoses at a
Soora Wi1, Patricia E Goldhoff1, Laurie A Fuller1
1From Kaiser Permanente, TPMG Regional Laboratories, Berkeley, California (Wi, Goldhoff, Fuller, Grewal, Lorey).
Context.—:
The terminology used by pathologists to describe and grade dysplasia and premalignant changes of the cervical epithelium has evolved over time. Unfortunately, coexistence of different classification systems combined with nonstandardized interpretive text has created multiple layers of interpretive ambiguity.
Objective.—:
To use natural language processing (NLP) to automate and expedite translation of interpretive text to a single most severe, and thus actionable, cervical intraepithelial neoplasia (CIN) diagnosis.
Design.—:
We developed and applied NLP algorithms to 35 847 unstructured cervical pathology reports and assessed NLP performance in identifying the most severe diagnosis, compared to expert manual review. NLP performance was determined by calculating precision, recall, and F score.
Results.—:
The NLP algorithms yielded a precision of 0.957, a recall of 0.925, and an F score of 0.94. Additionally, we estimated that the time to evaluate each monthly biopsy file was significantly reduced, from 30 hours to 0.5 hours.
Conclusions.—:
A set of validated NLP algorithms applied to pathology reports can rapidly and efficiently assign a discrete, actionable diagnosis using CIN classification to assist with clinical management of cervical pathology and disease. Moreover, discrete diagnostic data encoded as CIN terminology can enhance the efficiency of clinical research.
