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deid.pl
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deid.pl
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#!/usr/bin/perl
#**************************************************************************************************************
#file: deid.pl Original author: M. Douglass 2004
#Last revised: Apr 2009 DeID 1.1
#
#
#_______________________________________________________________________________
#
#deid.pl: De-identification algorithm -- scrubs PHI from free-text medical records
#(e.g. Discharge Summaries and Nursing Notes)
#
#Copyright (C) 2004-2007 Margaret Douglas and Ishna Neamatullah
#
#This code is free software; you can redistribute it and/or modify it under
#the terms of the GNU Library General Public License as published by the Free
#Software Foundation; either version 2 of the License, or (at your option) any
#later version.
#
#This library is distributed in the hope that it will be useful, but WITHOUT ANY
#WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
#PARTICULAR PURPOSE. See the GNU Library General Public License for more
#details.
#
#You should have received a copy of the GNU Library General Public License along
#with this code; if not, write to the Free Software Foundation, Inc., 59
#Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#
#You may contact the author by e-mail or postal mail
#(MIT Room E25-505, Cambridge, MA 02139 USA). For updates to this software,
#please visit PhysioNet (http://www.physionet.org/).
#_______________________________________________________________________________
#
# De-identification Algorithm: Scrubs PHI from free-text medical records
#(e.g. Discharge Summaries and Nursing Notes)
# Original version written by:
# Margaret Douglass (douglass AT alum DOT mit DOT edu)
# William Long (wjl AT mit DOT edu)
# Modified by:
# Ishna Neamatullah (ishna AT alum DOT mit DOT edu) in Sept 5, 2006
# Last modified by:
# Li-wei Lehman (lilehman AT alum DOT mit DOT edu) in April, 2009
#
# Command to run the software:
# perl deid.pl <filename> <config_filename>
#
# Input arguments:
# filename (without extension, where extension must be .text): file to be de-identified
# config_filename: configuration file
#
# Required library file: stat.pm
#
# Output files:
# filename.res: de-identified file
# filename.phi: file containing all PHI locations, used in calculating performance statistics
# filename.info: file containing information useful for debugging
# code performance statistics printed on screen if Gold Standard available for nursing notes (details in README)
#**************************************************************************************************************
#use Stat;
# Declaring some variables for algorithm run configuration
# Variables to switch on/off filter functions
$allfilters = "";
$ssnfilter = "";
$urlfilter = "";
$emailfilter = "";
$telfilter = "";
$unitfilter = "";
$agefilter = "";
$locfilter = "";
$datefilter = "";
$namefilter = "";
$us_state_filter = "";
$ds_specific_filter = ""; #filter for discharge summmary specific patterns
$gs_specific_filter = ""; #filter for gold std specific patterns
my $offset; # positive date shift in number of days
my $comparison = ""; # 1=comparison with gold standard, 0=no comparison with gold standard
# Variables to switch on/off dictionaries/lists
$alllists = "";
$pid_patientname_list = "";
$pid_dateshift_list = "";
$country_list = "";
$company_list = "";
$ethnicity_list = "";
$hospital_list = "";
$doctor_list = "";
$location_list = "";
$local_list = "";
$state_list = "";
use Time::Local;
my ($mday,$mon,$year) = (localtime(time))[3,4,5];
my $shortyear = substr($year,1,4);
my $longyear = '20'.$shortyear;
# Nursing note date as retrieved from the header
my $nn_year;
# Sets whether a de-identified version should be output: 0 = no new version of text output, 1 = fully de-identified version of text output
# Note: Generally keep output_deid_text = 1
$output_deid_text = 1;
#Default date used to de-identify the Gold Std if no default date is specified in the
#config file. You can change the default date by setting the "Default date" variable to
#some other dates (in MM/DD/YYYY format).
$DEFAULT_DATE = "01/01/2000";
#The "Two Digit Year Threshold" is used to determine whether
#to interpret the year as a year in the 1900's or 2000's.
#Must be a 1- or 2-digit number.
#Two digit years > Threshold are interepreted as in the 1900's
#Two digit years <= Threshold are interpreted as in the 2000's
$TWO_DIGIT_YEAR_THRESHOLD = 30;#change this default by setting "Two Digit Year Threshold" in config file.
# "Valid Year Low" and "Valid Year High" (must be 4-digit numbers) are
# used in certain date pattern checking routines to determine if a
# four digit number that appear in a potential
# date pattern is a year or not -- it is a valid year if it is
# in the range of [Valid Year Low, Valid Year High].
$VALID_YEAR_LOW = 1900;
$VALID_YEAR_HIGH = 2030;
my @known_phi;
my @known_first_name;
my @known_last_name;
# Hash that stores PHI information from de-identification
# KEY = (patient number), VALUE = array with each element = (%HASH with KEY = start-end, VALUE = array of types of PHI for the note number/index of the array)
%all_phi;
my %ID;
# Declares some global variables
%lhash = ();
@typename = ();
$ntype = 1;
@extend = ('phrases');
##########################################################################################
# Sets paths to lists and dictionaries in working directory that will be used in this algorithm
$date_shift_file = "shift.txt"; # contains mapping of PID to date offset
$countries_file = "lists/countries_unambig.txt";
$ethnicities_unambig_file = "lists/ethnicities_unambig.txt";
$companies_file = "lists/company_names_unambig.txt";
$companies_ambig_file = "lists/company_names_ambig.txt";
$common_words_file = "dict/common_words.txt";
$medical_words_file = "dict/sno_edited.txt";
$very_common_words_file = "dict/commonest_words.txt";
$female_unambig_file = "lists/female_names_unambig.txt";
$female_ambig_file = "lists/female_names_ambig.txt";
$female_popular_file = "lists/female_names_popular.txt";
$male_unambig_file = "lists/male_names_unambig.txt";
$male_ambig_file = "lists/male_names_ambig.txt";
$male_popular_file = "lists/male_names_popular.txt";
$last_unambig_file = "lists/last_names_unambig.txt";
$last_ambig_file = "lists/last_names_ambig.txt";
$last_popular_file = "lists/last_names_popular.txt";
#$last_name_prefixes_file = "lists/last_name_prefixes.txt";
$doctor_first_unambig_file = "lists/doctor_first_names.txt";
$doctor_last_unambig_file = "lists/doctor_last_names.txt";
$prefixes_unambig_file = "lists/prefixes_unambig.txt";
$locations_unambig_file = "lists/locations_unambig.txt";
$locations_ambig_file = "lists/locations_ambig.txt";
$local_places_ambig_file = "lists/local_places_ambig.txt";
$local_places_unambig_file = "lists/local_places_unambig.txt";
$hospital_file = "lists/stripped_hospitals.txt";
$last_name_prefix_file = "lists/last_name_prefixes.txt";
$patient_file = "lists/pid_patientname.txt"; # contains mapping of PID to patient name
$us_states_file = "lists/us_states.txt";
$us_states_abbre_file = "lists/us_states_abbre.txt";
$more_us_states_abbre_file = "lists/more_us_state_abbreviations.txt";
$us_area_code_file = "lists/us_area_code.txt";
$medical_phrases_file = "dict/medical_phrases.txt";
$unambig_common_words_file = "dict/notes_common.txt";
############################################################################################################
# Declares some arrays of context words that can be used to identify PHI
# Days of the month
@days = ("monday", "tuesday", "wednesday", "thursday", "friday", "saturday", "sunday");
# Titles that precede last names (ignore .'s)
@titles = ("MISTER", "DOCTOR", "DOCTORS", "MISS", "PROF", "PROFESSOR", "REV", "RABBI", "NURSE", "MD", "PRINCESS", "PRINCE", "DEACON", "DEACONESS", "CAREGIVER", "PRACTITIONER", "MR", "MS");
@strict_titles = ("Dr", "DRS", "Mrs"); #treat words after these strict_titles as PHI
%titles = ();
foreach $title (@titles){
$titles{$title} = 1;
}
# Name indicators that precede or follow names
@name_indicators = ("problem","problem:", "proxy", "daughter","daughters", "dtr", "son", "brother","sister", "mother", "mom", "father", "dad", "wife", "husband", "neice", "nephew", "spouse", "partner", "cousin", "aunt", "uncle", "granddaughter", "grandson", "grandmother", "grandmom", "grandfather", "granddad", "relative", "friend", "neighbor", "visitor", "family member", "lawyer", "priest", "rabbi", "coworker", "co-worker", "boyfriend", "girlfriend", "name is", "named", "rrt", "significant other", "jr", "caregiver", "proxys", "friends", "sons", "brothers", "sisters", "sister-in-law", "brother-in-law", "mother-in-law", "father-in-law", "son-in-law", "daughter-in-law", "dtr-in-law", "surname will be", "name will be", "name at discharge will be", "name at discharge is");
# Phrases that precede locations
@location_indicators = ("lives in", "resident of", "lived in", "lives at", "comes from", "called from", "visited from", "arrived from", "returned to");
@employment_indicators_pre = ("employee of", "employed by", "employed at", "CEO of", "manager at", "manager for", "manager of", "works at", "business");
# Hospital indicators that follow hospital names
@hospital_indicators = ("Hospital", "General Hospital", "Gen Hospital", "gen hosp", "hosp", "Medical Center", "Med Center", "Med Ctr", "Rehab", "Clinic", "Rehabilitation", "Campus", "health center", "cancer center", "development center", "community health center", "health and rehabilitation", "Medical", "transferred to", "transferred from", "transfered to", "transfered from");
# Location indicators that follow locations
@loc_indicators_suff = ("city", "town", "beach", "valley","county", "harbor", "ville", "creek", "springs", "mountain", "island", "lake", "lakes", "shore", "garden", "haven", "village", "grove", "hills", "hill", "shire", "cove", "coast", "alley", "street", "terrace", "boulevard", "parkway", "highway", "university", "college", "tower");
# Location indicators that are most likely preceded by locations
@loc_ind_suff_c = ("town", "ville", "harbor", "tower");
# Location indicators that precede locations
#@loc_indicators_pre = ("cape", "fort", "lake", "mount", "santa", "los", "great","east","west","north","south");
@loc_indicators_pre = ("cape", "fort", "lake", "mount", "santa", "los", "east","west","north","south");
@apt_indicators = ("apt", "suite"); #only check these after the street address is found
@street_add_suff = ("park", "drive", "street", "road", "lane", "boulevard", "blvd", "avenue", "highway", "circle","ave", "place", "rd", "st");
#Strict street address suffix: case-sensitive match on the following,
#and will be marked as PHI regardless of ambiguity (common words)
@strict_street_add_suff = ("Park", "Drive", "Street", "Road", "Lane", "Boulevard", "Blvd", "Avenue", "Highway","Ave",,"Rd", "PARK", "DRIVE", "STREET", "ROAD", "LANE", "BOULEVARD", "BLVD", "AVENUE", "HIGHWAY","AVE", "RD");
# Age indicators that follow ages
@age_indicators_suff = ("year old", "y\. o\.", "y\.o\.", "yo", "y", "years old", "year-old", "-year-old", "years-old", "-years-old", "years of age", "yrs of age");
# Age indicators that precede ages
@age_indicators_pre = ("age", "he is", "she is", "patient is");
# Digits, used in identifying ages
@digits = ("one","two","three","four","five","six","seven","eight","nine", "");
# Different variations of the 12 months
@months = ("January", "Jan", "February", "Feb", "March", "Mar", "April", "Apr", "May", "June", "Jun", "July", "Jul", "August", "Aug", "September", "Sept", "Sep", "October", "Oct", "November", "Nov", "December", "Dec");
######################################################################################
# If the correct number of input argument is provided, sets the input and output filenames.
if ($#ARGV == 1) {
$data_file = "$ARGV[0].text"; # data_file: input file
$output_file = "$ARGV[0].phi"; # output_file: file containing PHI locations
$debug_file = "$ARGV[0].info"; # debug_file: file used for debugging, contains PHI and non-PHI locations
$deid_text_file = "$ARGV[0].res"; # deid_text_file: de-identified text file
$gs_file = "$ARGV[0].deid"; # gs_file: Gold Standard of the input file
print "\n*******************************************************************************************************************\n";
print "De-Identification Algorithm: Identifies Protected Health Information (PHI) in Discharge Summaries and Nursing Notes";
print "\n*******************************************************************************************************************\n";
$config_file = $ARGV[1];
open CF, $config_file or die "Cannot open $config_file";
while ($cfline = <CF>) {
chomp $cfline;
if ($cfline =~ /\A[\#]+/){
next;
}
if ($cfline =~ /\bGold\s+standard\s+comparison\s*\=\s*([0-9])/ig) {
$comparison = ($1);
}
#Date default expects MM/DD/YYYY
if ($cfline =~ /\bDate\s+default\s*\=\s*(\d\d)\/(\d\d)\/(\d\d\d\d)/ig) {
my $mm = $1; $dd = $2; $yyyy = $3;
$DEFAULT_DATE = "$mm/$dd/$yyyy";
#print "Default date is $DEFAULT_DATE\n";
}
#The "Two Digit Year Threshold" is used to determine whether
#to interpret the year as a year in the 1900's or 2000's
if ($cfline =~ /\bTwo\s+Digit\s+Year\s+Threshold\s*=\s*(\d{1,2})/ig) {
$TWO_DIGIT_YEAR_THRESHOLD = "$1";
#print "Two Digit Year Threshold is $TWO_DIGIT_YEAR_THRESHOLD\n";
}
if ($cfline =~ /\bDate\s+offset\s*\=\s*([0-9]+)/ig) {
$offset = ($1);
#print "Date offset is $1\n";
}
if ($cfline =~ /\bSSN\s+filter\s*\=\s*([a-z])/ig) {
$ssnfilter = ($1);
}
if ($cfline =~ /\bURL\s+filter\s*\=\s*([a-z])/ig) {
$urlfilter = ($1);
}
if ($cfline =~ /\bEmail\s+filter\s*\=\s*([a-z])/ig) {
$emailfilter = ($1);
}
if ($cfline =~ /\bTelephone\s+filter\s*\=\s*([a-z])/ig) {
$telfilter = ($1);
}
if ($cfline =~ /\bUnit\s+number\s+filter\s*\=\s*([a-z])/ig) {
$unitfilter = ($1);
}
if ($cfline =~ /\bAge\s+filter\s*\=\s*([a-z])/ig) {
$agefilter = ($1);
}
if ($cfline =~ /\bLocation\s+filter\s*\=\s*([a-z])/ig) {
$locfilter = ($1);
}
if ($cfline =~ /\bDate\s+filter\s*\=\s*([a-z])/ig) {
$datefilter = ($1);
}
if ($cfline =~ /\bName\s+filter\s*\=\s*([a-z])/ig) {
$namefilter = ($1);
}
if ($cfline =~ /\bState\s+filter\s*\=\s*([a-z])/ig) {
$us_state_filter = ($1);
}
if ($cfline =~ /\bDS\s+filter\s*\=\s*([a-z])/ig) {
$ds_specific_filter = ($1);
}
if ($cfline =~ /\bGS\s+filter\s*\=\s*([a-z])/ig) {
$gs_specific_filter = ($1);
}
######################################################
#get the config info for dictionaries loading
if ($cfline =~ /\bPID\s+to\s+patient\s+name\s+mapping\s*\=\s*([a-z])/ig) {
$pid_patientname_list = ($1);
}
if ($cfline =~ /\bPID\s+to\s+date\s+offset\s+mapping\s*\=\s*([a-z])/ig) {
$pid_dateshift_list = ($1);
}
if ($cfline =~ /\bCountry\s+names\s*\=\s*([a-z])/ig) {
$country_list = ($1);
}
if ($cfline =~ /\bCompany\s+names\s*\=\s*([a-z])/ig) {
$company_list = ($1);
}
if ($cfline =~ /\bEthnicities\s*\=\s*([a-z])/ig) {
$ethnicity_list = ($1);
}
if ($cfline =~ /\bHospital\s+names\s*\=\s*([a-z])/ig) {
$hospital_list = ($1);
}
if ($cfline =~ /\bLocation\s+names\s*\=\s*([a-z])/ig) {
$location_list = ($1);
}
if ($cfline =~ /\bDoctor\s+names\s*\=\s*([a-z])/ig) {
$doctor_list = ($1);
}
if ($cfline =~ /\bLocalPlaces\s+names\s*\=\s*([a-z])/ig) {
$local_list = ($1);
}
if ($cfline =~ /\bState\s+names\s*\=\s*([a-z])/ig) {
$state_list = ($1);
}
}
}
# Prints an error message on the screen if number of arguments is incorrect
else {
print "\n===========================================================================================";
print "\nError: Wrong number of arguments entered";
print "\nThe algorithm takes 2 arguments:";
print "\n 1. filename (the filename of medical notes, without extension, where extension must be .text)";
print "\n 2. config_filename (the configuration filename)";
print "\nExample (for Gold Standard Comparison): perl deid.pl id deid.config";
print "\nExample (for output mode using Gold Standard): perl deid.pl id deid-output.config";
print "\nFor further documentation, please consult the README.txt file";
print "\n===========================================================================================\n";
exit;
}
# After setting file names and configuring the run, indicates that de-identification has commenced
print "\n\nStarting de-identification (version 1.1) ...\n\n";
#check if we can open the .phi file
open F, ">$output_file" or die "Cannot open $output_file";
close F;
# Calls setup to create some lookup lists in memory
setup();
if ($comparison==1) {
print "Running deid in performance comparison mode.\n";
print "Using PHI locations in $gs_file as comparison. Output files will be:\n";
print "$output_file: the PHI locations found by the code.\n";
print "$debug_file: debug info about the PHI locations.\n";
#check if the gold std file exists
open GS, $gs_file or die "Cannot open $gs_file. Make sure that the gold standard file exists!\n"; # GS = Gold Standard file
close GS;
}
else {
#check if we can open the .res file
open F, ">$deid_text_file" or die "Cannot open $deid_text_file";
close F;
print "Running deid in output mode. Output files will be: \n";
print "$output_file: the PHI locations found by the code.\n";
print "$deid_text_file: the scrubbed text.\n";
print "$debug_file: debug info about the PHI locations.\n";
}
deid();
# Calls function stat() to calculate code performance statistics, if comparison mode = 1
if ($comparison==1) {
require "stat.pm";
&stat($gs_file, $output_file);
}
# End of top level of code
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub numerically {
#print "a is $a b is $b\n";
$a <=> $b;
}
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Reads in a file and pushes each line onto an array. Returns the array.
sub preload {
my ($file) = @_;
my @res = ();
open FILE, $file or die "Cannot open file $file";
while ($line = <FILE>) {
chomp $line;
push(@res, uc($line));
}
close FILE;
return @res;
}
# End of preload()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Reads in a file and pushes each line onto an array. Returns the array.
sub preload_uc {
my ($file) = @_;
my @res = ();
open FILE, $file or die "Cannot open file $file";
while ($line = <FILE>) {
chomp $line;
push(@res, uc($line));
}
close FILE;
return @res;
}
# End of preload_uc()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Reads in a file and creates a dictionary that records each line in that file under the given association, by mapping the line to a '1' in the dictionary of the association
sub preload_assoc {
my ($file,$assoc) = @_;
open FILE, $file or die "Cannot open file $file";
while ($line = <FILE>) {
chomp $line;
$$assoc{uc($line)}=1;
}
close FILE;
}
# End of preload_assoc()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Reads in a file and calls setup_hash on each line
sub setup_hash {
my ($file, $tname) = @_;
my @entry;
$typename[$ntype]= $tname;
open FILE, $file or die "Cannot open file $file";
while ($line = <FILE>) {
chomp $line;
&setup_item($ntype,$line);
}
$ntype++;
close FILE;
}
# End of setup_hash()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Reads in a file and calls setup_hash on each line
sub setup_lst_hash {
my ($tname, @hlst) = @_;
$typename[$ntype]= $tname;
foreach $line (@hlst) {
&setup_item($ntype,$line);
}
$ntype++;
}
# End of setup_lst_hash()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub setup_item {
my ($type,$line) = @_;
my ($head, @lst) = split (/([^a-zA-Z0-9_\']+)/,uc($line));
my $ix = $type;
if(@lst){
push @extend, [@lst];
$ix = "$type,$#extend";
}
my $entry = $lhash{$head};
if ($entry){
$lhash{$head} .= "|" . $ix;
}
else{$lhash{$head}=$ix;
}
}
# End of setup_item()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub typename {
my ($num) = @_;
return($typename[$num]);
}
# End of typename()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Takes in an array of words and compares them with hashes of known PHI. Recognizes and adds PHI using addType().
sub lookhash {
my @txtlst = @_;
my $pos = 0;
my $npos = 0;
my $tl,$ty;
my $txt = 1; # item is text not separator
my $item;
while (@txtlst) {
$item = shift(@txtlst);
$npos = $pos + length($item);
if ($item =~ /([a-zA-Z\']+)/ig) {
if($item){
$item = uc($item);
$tl = $lhash{$item};
#if the term ends with 's, remove it and see if
#there is a match in PHI hash
#if (!($tl) && $item =~/([a-zA-Z\'\-]+)\'s$/ig) {
if (!($tl) && $item =~/([a-zA-Z\']+)\'s$/ig) {
$tl = $lhash {$1};
}
if($tl){
# Compares with known PHI by calling bestmatch()
($xpos, $done, @types)=&bestmatch($tl,@txtlst);
splice(@txtlst,0,$#txtlst-$done);
$npos += $xpos;
foreach $typ (@types){
#print "item $item, adding type $type for position $pos-$npos\n";
#print "type is $typ , key is $pos - $npos \n";
addType("$pos-$npos",$typ);
#print "positions are $pos-$npos, typ is $typ\n";
}
}
} #end if $item
$txt = 0;
} #end if $txt
else {
$txt = 1;
}
$pos = $npos;
}
}
# End of lookhash()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub bestmatch {
my ($tl,@txtlst) = @_;
my $pos = 0;
my $bestpos = 0;
my $bestrest = $#txtlst;
my @besttyp = ();
my ($type, $rest, $xpos, @nlst);
foreach $ck (split '\|',$tl) {
($type, $rest) = split ',',$ck;
if($rest) {
($xpos , @nlst) = &matchrest($rest,@txtlst);
if ($xpos) {
if($xpos > $bestpos) {
$bestrest = $#nlst; $bestpos = $xpos;
@besttyp = ($typename[$type]);
}
elsif($xpos == $bestpos) {
push @besttyp,$typename[$type];
}
}
}
elsif ($bestpos == 0) {
push @besttyp,$typename[$type];
}
}
return ($bestpos, $bestrest, @besttyp);
}
# End of bestmatch()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub matchrest {
my ($rest, @txtlst) = @_;
my @mlst = @{$extend[$rest]};
my $item;
my $pos = 0;
my $pm = 0;
my $tmppos = 0;
if ($mlst[0] eq '|') {
$pm = 1; shift(@mlst);
}
foreach $i (@mlst) {
if ($i !~ /([a-zA-Z\'\-]+)$/ig){
next;
}
$item = shift(@txtlst);
$pos += length($item);
while ( $#txtlst >= 0 && ($item !~ /([a-zA-Z\'\-]+)/ig)){
$item = shift(@txtlst);
$pos += length ($item);
#print "item is $item, len is $#txtlst";
}
if ($pm ? (uc($item) !~ /$i/) : ($i ne uc($item))) {
#print "pm is $pm, returning zero\n";
return 0;
}
}
return ($pos, @txtlst);
}
# End of matchrest()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Function: setup()
# Arguments: None
# Returns: None
# Called by: Topmost level of code
# Description: Creates some lookup lists to have in memory
sub setup {
# This part is not necessary
open LP, $last_name_prefix_file or die "Cannot open $last_name_prefix_file";
while ($line = <LP>) {
chomp $line;
$prefixes{uc($line)} = 1;
}
close LP;
#Added to reduce false positives
&setup_hash($medical_phrases_file,"MedicalPhrase");
# Sets up hashes of some PHI lists for direct identification
if ($namefilter =~ /y/) {
&setup_hash($female_unambig_file,"Female First Name (un)");
&setup_hash($female_ambig_file,"Female First Name (ambig)");
&setup_hash($male_unambig_file,"Male First Name (un)");
&setup_hash($male_ambig_file,"Male First Name (ambig)");
&setup_hash($last_unambig_file,"Last Name (un)");
&setup_hash($last_popular_file,"Last Name (popular/ambig)");
&setup_hash($last_ambig_file,"Last Name (ambig)");
&setup_hash($female_popular_file, "Female First Name (popular/ambig)");
&setup_hash($male_popular_file, "Male First Name (popular/ambig)");
if ($doctor_list =~ /y/) {
&setup_hash($doctor_first_unambig_file, "Doctor First Name");
&setup_hash($doctor_last_unambig_file, "Doctor Last Name");
}
}
if ($locfilter =~ /y/) {
if ($location_list =~ /y/) {
&setup_hash($locations_ambig_file,"Location (ambig)");
&setup_hash($locations_unambig_file,"Location (un)");
} else {
@loc_unambig = ();
@more_loc_unambig = ();
@loc_ambig = ();
}
if ($hospital_list =~ /y/) {
&setup_hash($hospital_file,"Hospital");
}
if ($ethnicity_list =~ /y/) {
&setup_hash($ethnicities_unambig_file, "Ethnicity");
}
if ($company_list =~ /y/) {
&setup_hash($companies_file, "Company");
&setup_hash($companies_ambig_file, "Company (ambig)");
}
if ($country_list =~ /y/) {
&setup_hash($countries_file, "Country");
}
if ($local_list =~ /y/){
&setup_hash($local_places_unambig_file, "Location (un)");
&setup_hash($local_places_ambig_file, "Location (ambig)");
}
}
# Preloads PHI in some lists into corresponding arrays
@female_popular = &preload($female_popular_file);
@male_popular = &preload($male_popular_file);
#@last_name_prefixes = &preload_uc($last_name_prefixes_file);
@prefixes_unambig = &preload_uc($prefixes_unambig_file);
if ($hospital_list =~ /y/) {
@hospital = &preload($hospital_file);
} else {@hospital = ();}
if ($state_list =~ /y/){
@us_states = &preload($us_states_file);
@us_states_abbre = &preload($us_states_abbre_file);
@more_us_states_abbre = &preload($more_us_states_abbre_file);
}
# Generates associations between PHI in some lists and PHI categories
&preload_assoc($common_words_file,"common_words");
&preload_assoc($medical_words_file,"common_words");
&preload_assoc($very_common_words_file,"very_common_words");
&preload_assoc($unambig_common_words_file, "unambig_common_words");
&preload_assoc($male_unambig_file, "male_unambig");
&preload_assoc($female_unambig_file, "female_unambig");
&preload_assoc($female_ambig_file, "female_ambig");
&preload_assoc($male_ambig_file, "male_ambig");
&preload_assoc($last_ambig_file, "last_ambig");
&preload_assoc($male_popular_file, "male_popular");
&preload_assoc($female_popular_file, "female_popular");
&preload_assoc($us_area_code_file,"us_area_code");
# Opens debug file for debugging
open D, ">".$debug_file;
close D;
}
# End of setup()
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
# Function: deid()
# Arguments: None
# Returns: None
# Called by: Topmost level of code
# Description: One of the 2 major branches of the code
# This function takes over de-identification if no performance statistic is required
# Function first loads the patient name list file.
# Then reads the medical text line by line.
# If the line indicates START_OF_RECORD, read the Patient ID (PID), Note ID (NID), (and Note Date if any) info
# Scan for PHI a paragraph at a time
# output PHI locations into .phi file
my $currentID;
my @known_phi;
my @known_first_name;
my @known_last_name;
my %pidPtNames; # key = pid, value = [0] first name [1] last name
#***********************************************************************************************************
#***********************************************************************************************************
#***********************************************************************************************************
sub deid {
$allText = "";
$allallText = "";
open DF, $data_file or die "Cannot open $data_file";
my $paraCount = 0;
my $stpos = 0;
my %deids; #key = start index, value = array of (end index, ID)
my %phiTerms; #key = lc(word), value = # of occurrences
my %phiT;
my %phiTT;
my $noteDate;
my $line;
$currentID = 0; #initialize current ID to a non-existent PID 0
# Code runs through text by paragraph so things that extend over lines aren't missed
$para = "";
#load the patient name file
if ($pid_patientname_list =~ /y/) {
open PF, $patient_file or die "Cannot open $patient_file";
while ($pfline = <PF>) {
chomp $pfline;
if ($pfline =~ /((.)+)\|\|\|\|((.)+)\|\|\|\|((.)+)/ig) {
my $pid = $1;
$known_first_names = $3;
$known_last_names = $5;
$pidPtNames{$pid}[0] = $known_first_names;
$pidPtNames{$pid}[1] = $known_last_names;
}# end if pfline = ~ /((.)+)\|\|\|\|((.)+)\|\|\|\|((.)+)/ig)
} # end while $pfline = <PF>
} #end if pid_patient_name_list ~= y
###End loading the patient names
while ($line = <DF>) {
#If this is a new record, set PID, Note ID
#we assume all notes for the same patient go together
if ( $line =~ /\ASTART_OF_RECORD=(([0-9]+)(\|)+([0-9]+)(\|)+(\d\d\/\d\d\/\d{4})?)/) {
# $currentNote = $2;
# $thePT = $4;
# $noteDate =$6; #noteDate is empty in gold std
#print "pt $thePT, currentNote $currentNote\n";
#if it's gold standard, the header contains PID then NID
$currentNote = $4;
$thePT = $2;
$noteDate =$6; #noteDate is empty in gold std
my $label = "Patient $thePT\tNote $currentNote";
open DEST, ">>".$debug_file or die "Cannot open $debug_file";
print DEST "$label\n";
close DEST;
#Gold Standard corpus does not specify note date, so assign a default
#If you would like deid to date shift the notes on a per note basis, make sure you
#specify the record date in the header!
if (length($noteDate) ==0){
#$noteDate="01/01/2020";
$noteDate = $DEFAULT_DATE;
}
#if this is a new patient, set the PID, and lookup patient name
if ($thePT != $currentID) { #This is a new patient!
$currentID = $thePT;
%phiTerms = (); #clear the phiTerms on new pt
# Find the patient name for the current PID
#lookup first and last name of this patient
if ($pid_patientname_list =~ /y/ && exists $pidPtNames{$currentID} ) {
$known_first_names = $pidPtNames{$currentID}[0];
$known_last_names = $pidPtNames{$currentID}[1];
#print "Found patient names, first = $known_first_names last = $known_last_names\n";
if ($known_first_names =~ /([a-z][a-z]+)[\s\-]([a-z][a-z]+)/ig) {
@known_first_name = ($1, $2);}
else {
if ($known_first_names =~ /\b([a-z])(\.?)\s([a-z]+)/ig) {
@known_first_name = ($3);
}
elsif ($known_first_names =~ /\b([a-z][a-z]+)\s([a-z])(\.?)/ig) {
@known_first_name = ($1);
}
else {
@known_first_name = ($known_first_names);
}
}
if ($known_last_names =~ /([a-z][a-z]+)[\s\-]([a-z][a-z]+)/ig) {
@known_last_name = ($1, $2);}
else {
if ($known_last_names =~ /\b([a-z])(\.?)\s([a-z]+)/ig) {
@known_last_name = ($3);
}
elsif ($known_last_names =~ /\b([a-z][a-z]+)\s([a-z])(\.?)/ig) {
@known_last_name = ($1);
}
else {
@known_last_name = ($known_last_names);
}
}
} else { #if no pid/patient name file, just set the first name and last name to null
@known_first_name = ();
@known_last_name = ();
}
} # end if this is a new patient
#output the header to output file
$allText = ""; #reset,
$allallText = ""; #reset
$stpos = 0;
$para = "";
#if output mode, output the header line (with patient and note ID) to .res file
if ($comparison == 0) {
open TF, ">>$deid_text_file" or die "Cannot open $deid_text_file"; #now open in append mode
print TF "\n$line";
close TF;
}
next; #skip to next line
} #end if this is start of a record
else { #else this is not the start of a record, just append the line to the end of the current text
chomp $line;
$allText .= $line."\n";
$allallText .= $line."\n";
#$myline = $line;
#chomp $myline;
#$allText .= $myline."\n";
#$allallText .= $myline."\n";
}
#Look for paragraph separator: if this is a line is entirely non-alphanumeric or
#if it starts with spaces, or if it is an empty line, or if this line marks the end of record,
#then call findPHI() for the current paragraph we have so far.
#If end of record is encoutnered, output the de-id text; else if
#it's not end of record yet, append the line to the paragraph.
# if ( (!($line =~ /[a-zA-Z\d]+/)) || $line =~ /^ +/ || $line eq "" || ($line =~ /\|\|\|\|END_OF_RECORD/) ) {
if ( (!($line =~ /[a-zA-Z\d]+/)) || ($line eq "") || ($line =~ /\|\|\|\|END_OF_RECORD/) ) {
if ($para =~ /\w/ ){ #if para contains alphanumeric
# Calls findPHI() with current paragraph; resulting PHI locations are stored in %phiT
#%phiT = findPHI("Para $paraCount", $date, $stpos, $para);
%phiT = findPHI("Para $paraCount", $noteDate, $stpos, $para);
$paraCount++;
# %phiT is copied over to %phiTT
foreach $x (sort numerically keys %phiT) {
@{$phiTT{$x}} = @{$phiT{$x}};
}
#Sorts keys in %phiT; outputs text accordingly
foreach $k (keys %phiT) {
my ($start, $end) = split '-', $k;
# $deids_end = ${@{$deids{$start}}}[0]; #does not work with perl v5.10
my @deidsval = ${@{$deids{$start}}};
$deids_end = $deidsval[0];
$found = $phiT{$k};
foreach $t (@{$phiT{$k}}) {
}
my $word = lc(substr $allallText, $start, ($end - $start));
#print "Key in PhiT = $k, word = $word\n"; #DEBUG
# if ($end > ${@{$deids{$start}}}[0]) {
if ($end > $deidsval[0]) {
$deids{$start}[0] = $end;
$deids{$start}[1] = $currentID;
$deids{$start}[2] = $noteDate;
}
#############################################################################
#Now remember the PHI terms that are important names for checking for repeated occurrences of PHIs
#PHI Name Tags
#(NI) Name indicators