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Perl and Python code for de-identifying electronic medical records

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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.

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