Automated extraction of Biomarker information from pathology reports.

ABSTRACT:

Background

Pathology reports are written in free-text form, which precludes efficient data gathering. We aimed to overcome this limitation and design an automated system for extracting biomarker profiles from accumulated pathology reports.

Methods

We designed a new data model for representing biomarker knowledge. The automated system parses immunohistochemistry reports based on a "slide paragraph" unit defined as a set of immunohistochemistry findings obtained for the same tissue slide. Pathology reports are parsed using context-free grammar for immunohistochemistry, and using a tree-like structure for surgical pathology. The performance of the approach was validated on manually annotated pathology reports of 100 randomly selected patients managed at Seoul National Universit

SUBMITTER: Lee J 

PROVIDER: S-EPMC5963015 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature