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Generating high-quality data abstractions from scanned clinical records: text-mining-assisted extraction of endometrial carcinoma pathology features as proof of principle

Authors :
Anthony Nguyen
Amanda B. Spurdle
Sharon E. Johnatty
John O'Dwyer
Thanh Vu
Penelope M. Webb
Source :
BMJ Open, Vol 10, Iss 6 (2020), BMJ Open
Publication Year :
2020
Publisher :
BMJ Publishing Group, 2020.

Abstract

ObjectiveMedical research studies often rely on the manual collection of data from scanned typewritten clinical records, which can be laborious, time consuming and error prone because of the need to review individual clinical records. We aimed to use text mining to assist with the extraction of clinical features from complex text-based scanned pathology records for medical research studies.DesignText mining performance was measured by extracting and annotating three distinct pathological features from scanned photocopies of endometrial carcinoma clinical pathology reports, and comparing results to manually abstracted terms. Inclusion and exclusion keyword trigger terms to capture leiomyomas, endometriosis and adenomyosis were provided based on expert knowledge. Terms were expanded with character variations based on common optical character recognition (OCR) error patterns as well as negation phrases found in sample reports. The approach was evaluated on an unseen test set of 1293 scanned pathology reports originating from laboratories across Australia.SettingScanned typewritten pathology reports for women aged 18–79 years with newly diagnosed endometrial cancer (2005–2007) in Australia.ResultsHigh concordance with final abstracted codes was observed for identifying the presence of three pathology features (94%–98% F-measure). The approach was more consistent and reliable than manual abstractions, identifying 3%–14% additional feature instances.ConclusionKeyword trigger-based automation with OCR error correction and negation handling proved not only to be rapid and convenient, but also providing consistent and reliable data abstractions from scanned clinical records. In conjunction with manual review, it can assist in the generation of high-quality data abstractions for medical research studies.

Details

Language :
English
ISSN :
20446055
Volume :
10
Issue :
6
Database :
OpenAIRE
Journal :
BMJ Open
Accession number :
edsair.doi.dedup.....0e6a403e92e91ab505044ae9ea9ea639