The code in this repository has been ported into python and the R code contained here will not receive further updates. You can find the python code here: https://github.com/FinnishCancerRegistry/gleason_extraction_py.
This repository contains the programme developed in the peer-reviewed study "Accurate pattern-based extraction of complex Gleason score expressions from pathology reports" (https://doi.org/10.1016/j.jbi.2021.103850).
The study was conducted at the Finnish Cancer Registry (https://cancerregistry.fi/).
To browse the repository in the state it was in at the completion of the study, go to https://github.com/WetRobot/gleason_extraction/tree/7946cc2ae5403937a4b5ac30e6a74166af6b7507.
Contents:
example.R: run this to see how it all works.x_confusion_funs.R: contains functions which define confusion statistics (sensitivity, etc.)x_gleason_extraction_funs.R: the regular expressions and how they are used are defined here.x_pattern_extraction_funs.R: more general pattern extraction functions.x_util_funs.R: general utility functions.