#!/usr/bin/perl
=head1 NAME
create-icfrequency.pl - This program sums the frequency counts
of the CUIs from a specified set of sources in plain text.
=head1 SYNOPSIS
This program sums the frequency counts of the CUIs from a specified
set of sources in plain text. The CUIs are determined by mapping
the words in the text to CUIs in the UMLS using the strings in
the MRCONSO table or MetaMap.
=head1 USAGE
Usage: create-icfrequency.pl.pl [OPTIONS] OUTPUTFILE INPUTFILE
=head2 OUTPUTFILE
The output file contains frequency counts for CUIs in the following
format:
SAB :: (include|exclude) <sources>
REL :: (include|exclude) <relations>
N :: NUMBER
CUI<>freq
CUI<>freq
...
=head2 INPUTFILE
File containing plain text.
=head2 Optional Arguments:
=head3 --st
Output the semantic type of the CUIs and their frequency counts.
The concepts are determined based on the source/relations in
the configuration file so I would recommend using UMLS_ALL with
the PAR/CHD/RB/RN relations unless you are certain of your
source.
=head3 --compoundify
The text contains compounds depicted by an underscore. For example,
the term blood_pressure would be counted as a single term rather
than blood and then pressure.
=head3 --term
Obtains the CUI counts using the term counts. This is the default.
=head3 --metamap TWO_DIGIT_YEAR
This option takes the two digit year of the version of metamap that
is being used. For example, --metamap 10 would use ./metamap10 to
call metamap to tag the text.
This obtains the CUI counts using MetaMap. This requires that you have
MetaMap installed on your system. You can obtain this package:
L<http://mmtx.nlm.nih.gov/>
These frequency counts are used to obtain the propagation counts.
The format is similar to the output of count.pl from Text::NSP
using the unigram option.
=head3 --config FILE
This is the configuration file. The format of the configuration
file is as follows:
SAB :: <include|exclude> <source1, source2, ... sourceN>
For example, if we wanted to include on those CUIs in the
MSH vocabulary:
SAB :: include MSH
REL :: include RB, RN
or maybe use all the CUIs except those in MSH:
SAB :: exclude MSH
If you go to the configuration file directory, there will
be example configuration files for the different runs that
you have performed.
=head3 --username STRING
Username is required to access the umls database on MySql
Note: if --username is specified the --password is also
required.
=head3 --password STRING
Password is required to access the umls database on MySql
Note: if --password is specified the --username is also
required.
=head3 --hostname STRING
Hostname where mysql is located. DEFAULT: localhost
=head3 --database STRING
Database contain UMLS DEFAULT: umls
=head3 --debug
Sets the UMLS-Interface debug flag on for testing
=head3 --help
Displays the quick summary of program options.
=head3 --version
Displays the version information.
=head1 PROPAGATION
The Information Content (IC) is defined as the negative log
of the probability of a concept. The probability of a concept,
c, is determine by summing the probability of the concept
ocurring in some text plus the probability its decendants
occuring in some text:
For more information on how this is calculated please see
the README file or the perldoc for create-icpropagation.pl
=head1 SYSTEM REQUIREMENTS
=over
=item * Perl (version 5.8.5 or better) - http://www.perl.org
=item * UMLS::Interface - http://search.cpan.org/dist/UMLS-Interface
=item * UMLS::Similarity - http://search.cpan.org/dist/UMLS-Similarity
=item * Text::NSP - http://search.cpan.org/dist/Text-NSP
=item * MetaMap - http://mmtx.nlm.nih.gov/
=back
=head1 CONTACT US
If you have any trouble installing and using CreatePropagationFile,
please contact us via the users mailing list :
umls-similarity@yahoogroups.com
You can join this group by going to:
http://tech.groups.yahoo.com/group/umls-similarity/
You may also contact us directly if you prefer :
Bridget T. McInnes: bthomson at cs.umn.edu
Ted Pedersen : tpederse at d.umn.edu
=head1 AUTHOR
Bridget T. McInnes, University of Minnesota
=head1 COPYRIGHT
Copyright (c) 2007-2011,
Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Siddharth Patwardhan, University of Utah, Salt Lake City
sidd@cs.utah.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002@umn.edu
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, write to:
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
=cut
###############################################################################
# THE CODE STARTS HERE
###############################################################################
# ================================
# COMMAND LINE OPTIONS AND USAGE
# ================================
use UMLS::Interface;
use Getopt::Long;
use File::Path;
eval(GetOptions( "version", "help", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "config=s", "debug", "t", "metamap=s", "term", "compoundify", "st")) or die ("Please check the above mentioned option(s).\n");
# if help is defined, print out help
if( defined $opt_help ) {
$opt_help = 1;
&showHelp();
exit;
}
# if version is requested, show version
if( defined $opt_version ) {
$opt_version = 1;
&showVersion();
exit;
}
# At least 2 terms should be given on the command line.
if( scalar(@ARGV) < 2) {
print STDERR "At least 2 files should be specified on the command line.\n";
&minimalUsageNotes();
exit;
}
# get the input and output files
my $outputfile = shift;
my $inputfile = shift;
# check to see if output file exists, and if so, if we should overwrite...
if ( -e $outputfile )
{
print "Output file $outputfile already exists! Overwrite (Y/N)? ";
$reply = <STDIN>;
chomp $reply;
$reply = uc $reply;
exit 0 if ($reply ne "Y");
}
# initialize variables
my $database = "";
my $hostname = "";
my $socket = "";
my $umls = "";
# initialize the total number of unigrams
my $N = 0;
# check the options
&checkOptions ();
&setOptions ();
# load the UMLS
&loadUMLS ();
my $sabstring = $umls->getSabString();
my $relstring = $umls->getRelString();
my $relastring = $umls->getRelaString();
# get the frequency counts
my $cuilist = $umls->getCuiList();
if(defined $opt_metamap) {
if(! ($opt_metamay=~/[0-9][0-9]/) ) {
print STDERR "The --metamap option requires a two digit year.\n";
&minimalUsageNotes();
exit;
}
&getMetaMapCounts($inputfile);
}
else {
&getTermCounts($inputfile);
}
if(defined $opt_st) {
&printStPropagationCounts();
}
else {
&printCuiPropagationCounts();
}
sub printStPropagationCounts {
my %stlist = (); my $N = 0;
foreach my $cui (sort keys %{$cuilist}) {
my $freq = ${$cuilist}{$cui};
my $sts = $umls->getSt($cui);
foreach my $st (@{$sts}) {
if(exists $stlist{$st}) { $stlist{$st} += $freq; }
else { $stlist{$st} = $freq; }
$N+= $freq;
}
}
open(OUTPUT, ">$outputfile") || die "Could not open $outputfile\n";
print OUTPUT "$sabstring\n";
print OUTPUT "$relstring\n";
if($relastring ne "") {
print OUTPUT "$relastring\n";
}
print OUTPUT "N :: $N\n";
foreach my $st (sort keys %stlist) {
my $freq = $stlist{$st};
print OUTPUT "$st<>$freq\n";
}
close OUTPUT;
}
sub printCuiPropagationCounts {
open(OUTPUT, ">$outputfile") || die "Could not open $outputfile\n";
print OUTPUT "$sabstring\n";
print OUTPUT "$relstring\n";
if($relastring ne "") {
print OUTPUT "$relastring\n";
}
print OUTPUT "N :: $N\n";
foreach my $cui (sort keys %{$cuilist}) {
my $freq = ${$cuilist}{$cui};
print OUTPUT "$cui<>$freq\n";
}
close OUTPUT;
}
sub getTermCounts {
my $text = shift;
my $countfile = "tmp.count";
system "count.pl --ngram 1 $countfile $text";
open(COUNT, $countfile) || die "Could not open the count file : $countfile\n";
my %hash = ();
my $header = <COUNT>;
while(<COUNT>) {
chomp;
my ($term, $freq) = split/<>/;
if(defined $opt_compoundify) {
$term=~s/_/ /g;
}
my $cuis = $umls->getConceptList($term);
foreach my $cui (@{$cuis}) {
if(exists ${$cuilist}{$cui}) {
${$cuilist}{$cui} += $freq;
$N += $freq;
}
}
}
close COUNT;
File::Path->remove_tree("tmp.count");
return \%hash;
}
sub getMetaMapCounts {
my $text = shift;
open(TEXT, $text) || die "Could not open $text for processing\n";
my %hash = ();
while(<TEXT>) {
chomp;
my $output = &callMetaMap($_);
my %temp = ();
while($output=~/\'(C[0-9]+)\'\,(.*?)\,(.*?)\,/g) {
my $cui = $1; my $str = $3;
$str=~s/[\'\"]//g;
$temp{$cui}++;
}
foreach my $cui (sort keys %temp) {
if(exists ${$cuilist}{$cui}) {
${$cuilist}{$cui}++;
$N++;
}
}
}
return \%hash;
}
sub callMetaMap
{
my $line = shift;
my $output = "";
my $timestamp = &timeStamp();
my $metamapInput = "tmp.metamap.input.$timestamp";
my $metamapOutput = "tmp.metamap.output.$timestamp";
open(METAMAP_INPUT, ">$metamapInput") || die "Could not open file: $metamapInput\n";
print METAMAP_INPUT "$line\n";
close METAMAP_INPUT;
my $metamap = "metamap" . $opt_metamap;
print "$metamap -q $metamapInput $metamapOutput\n";
system("$metamap -q $metamapInput $metamapOutput");
open(METAMAP_OUTPUT, $metamapOutput) || die "Could not open file: $metamapOutput\n";
while(<METAMAP_OUTPUT>) {
if($_=~/mappings\(/) {
$output .= $_;
}
}
close METAMAP_OUTPUT;
File::Path->remove_tree($metamapInput);
File::Path->remove_tree($metamapOutput);
return $output;
}
sub timeStamp {
my ($stamp);
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
$year += 1900;
$mon++;
$d = sprintf("%4d%2.2d%2.2d",$year,$mon,$mday);
$t = sprintf("%2.2d%2.2d%2.2d",$hour,$min,$sec);
$stamp = $d . $t;
return($stamp);
}
# checks the user input options
sub checkOptions {
if( (defined $opt_metamap) && (defined $opt_term) ) {
print STDERR "The --metamap and --term options can\n";
print STDERR "not both be specified at the same time.\n\n";
&minimalUsageNotes();
exit;
}
if( (defined $opt_username && !defined $opt_password) ||
(!defined $opt_username && defined $opt_password) ) {
print STDERR "The --username and --password options\n";
print STDERR "must both be specified if you are using\n";
print STDERR "one of them.\n\n";
&minimalUsageNotes();
exit;
}
}
# set user input and default options
sub setOptions {
if($debug) { print STDERR "In setOptions\n"; }
my $default = "";
my $set = "";
# check config file
if(defined $opt_config) {
$config = $opt_config;
$set .= " --config $config\n";
}
if(defined $opt_metamap) {
$set .= " --metamap $opt_metamap\n";
}
elsif(defined $opt_term) {
$set .= " --term\n";
}
else {
$default .= " --term\n";
}
if(defined $opt_compoundify) {
$set .= " --compoundify\n";
}
if(defined $opt_st) {
$set .= " --st\n";
}
# set database options
if(defined $opt_username) {
if(defined $opt_username) {
$set .= " --username $opt_username\n";
}
if(defined $opt_password) {
$set .= " --password XXXXXXX\n";
}
if(defined $opt_database) {
$database = $opt_database;
$set .= " --database $database\n";
}
else {
$database = "umls";
$default .= " --database $database\n";
}
if(defined $opt_hostname) {
$hostname = $opt_hostname;
$set .= " --hostname $hostname\n";
}
else {
$hostname = "localhost";
$default .= " --hostname $hostname\n";
}
if(defined $opt_socket) {
$socket = $opt_socket;
$set .= " --socket $socket\n";
}
else {
$socket = "/tmp/mysql.sock\n";
$default .= " --socket $socket\n";
}
}
if(defined $opt_debug) {
$set .= " --debug\n";
}
# check settings
if($default eq "") { $default = " No default settings\n"; }
if($set eq "") { $set = " No user defined settings\n"; }
# print options
print STDERR "Default Settings:\n";
print STDERR "$default\n";
print STDERR "User Settings:\n";
print STDERR "$set\n";
}
# load the UMLS
sub loadUMLS {
if(defined $opt_t) {
$option_hash{"t"} = 1;
}
if(defined $opt_config) {
$option_hash{"config"} = $opt_config;
}
if(defined $opt_debug) {
$option_hash{"debug"} = $opt_debug;
}
if(defined $opt_username and defined $opt_password) {
$option_hash{"driver"} = "mysql";
$option_hash{"database"} = $database;
$option_hash{"username"} = $opt_username;
$option_hash{"password"} = $opt_password;
$option_hash{"hostname"} = $hostname;
$option_hash{"socket"} = $socket;
}
$option_hash{"realtime"} = 1;
$umls = UMLS::Interface->new(\%option_hash);
die "Unable to create UMLS::Interface object.\n" if(!$umls);
}
##############################################################################
# function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
print "Usage: create-icfrequency.pl.pl [OPTIONS] OUTPUTFILE INPUTFILE\n";
&askHelp();
exit;
}
##############################################################################
# function to output help messages for this program
##############################################################################
sub showHelp() {
print "This is a utility that takes as input an output and input\n";
print "file and determines the frequency counts of the CUIs in\n";
print "a specified set of sources and relation using the frequency\n";
print "information from the inputfile\n\n";
print "Usage: create-icfrequency.pl.pl [OPTIONS] OUTPUTFILE INPUTFILE\n\n";
print "Options:\n\n";
print "--config FILE Configuration file\n\n";
print "--st Output the semantic type of the CUIs \n";
print " and their frequency counts.\n\n";
print "--compoundify The input text contains compounds\n";
print " depicted by an underscore. \n\n";
print "--term Calculates the frequency counts using\n";
print " the words in the input file. (DEFAULT)\n\n";
print "--metamap TWO_DIGIT_YEAR Calculates the frequency counts using\n";
print " the CUIs assigned to terms by MetaMap.\n\n";
print "--username STRING Username required to access mysql\n\n";
print "--password STRING Password required to access mysql\n\n";
print "--hostname STRING Hostname for mysql (DEFAULT: localhost)\n\n";
print "--database STRING Database contain UMLS (DEFAULT: umls)\n\n";
print "--debug Sets the UMLS-Interface debug flag on\n";
print " for testing purposes\n\n";
print "--version Prints the version number\n\n";
print "--help Prints this help message.\n\n";
}
##############################################################################
# function to output the version number
##############################################################################
sub showVersion {
print '$Id: create-icfrequency.pl,v 1.16 2011/05/04 18:39:25 btmcinnes Exp $';
print "\nCopyright (c) 2008-2011, Ted Pedersen & Bridget McInnes\n";
}
##############################################################################
# function to output "ask for help" message when user's goofed
##############################################################################
sub askHelp {
print STDERR "Type create-icfrequency.pl.pl --help for help.\n";
}