shaojunyu / deid2020

Class project for de-identification BMI 500 all 2020

de-id

Perl and Python code for de-identifying electronic medical records

Prerequisites

Python

• Python 3.5.2

Perl

• Perl 5, Version 28, Subversion 0 (v5.28.0)

Running insturctions

Python Code

De-identification

1- Change to the python directory

2- run python deid.py id.text phone.phi

In which:

• id.text contains Patient Notes.
• phone.phi is the output file that will be created.

Stats

1- change to the python directory

2- run python stats.py id.deid id-phi.phrase phone.phi

In which:

• id.deid is the gold standard that is category-blind.
• id-phi.phrase is the gold standard with the categories included.
• phone.phi is the test file that the stats is run on.