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# UMLS::Similarity::wup.pm
#
# Module implementing the semantic relatedness measure described 
# by Wu and Palmer (1994)
#
# Copyright (c) 2004-2010,
#
# Bridget T McInnes, University of Minnesota, Twin Cities
# bthomson at cs.umn.edu
#
# Siddharth Patwardhan, University of Utah, Salt Lake City
# sidd at cs.utah.edu
#
# Serguei Pakhomov, University of Minnesota, Twin Cities
# pakh002 at umn.edu
#
# Ted Pedersen, University of Minnesota, Duluth
# tpederse at d.umn.edu
#
# Ying Liu, University of Minnesota
# liux0935 at 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.
package UMLS::Similarity::wup;
use strict;
use warnings;
use UMLS::Similarity;
use UMLS::Similarity::ErrorHandler;
use vars qw($VERSION);
$VERSION = '0.07';
my $debug = 0;
sub new
{
    my $className = shift;
    return undef if(ref $className);
    if($debug) { print STDERR "In UMLS::Similarity::wup->new()\n"; }
    my $interface = shift;
    my $self = {};
      
    # Bless the object.
    bless($self, $className);
     
    # The backend interface object.
    $self->{'interface'} = $interface;
     
    #  check the configuration file if defined
    my $errorhandler = UMLS::Similarity::ErrorHandler->new("wup",  $interface);
    if(!$errorhandler) {
        print STDERR "The UMLS::Similarity::ErrorHandler did not load properly\n";
        exit;
    }
     
    return $self;
}
sub getRelatedness
{
    my $self = shift;
    return undef if(!defined $self || !ref $self);
    my $concept1 = shift;
    my $concept2 = shift;
    #  if concept 1 and 2 are the same just return 1
    if($concept1 eq $concept2) { return 1; }
    #  get the interface
    my $interface = $self->{'interface'};
     
    #  find the lcses of the two concepts
    my @lcses = $interface->findLeastCommonSubsumer($concept1, $concept2);
     
    #  if there aren't any return zero
    if($#lcses < 0) { return -1; }
     
    #  get the depth of the lowest lcs
    my $lcs_depth = 0; my $lcs = "";
    foreach my $l (@lcses) {
        my $depth  = $interface->findMaximumDepth($l);
        if(defined $depth and $lcs_depth < $depth) { 
            $lcs_depth = $depth; $lcs = $l;
        }
    }
     
    #  find the shortestpath between the concept and the lcses
    my $c1_length = $interface->findShortestPathLength($lcs, $concept1);
    my $c2_length = $interface->findShortestPathLength($lcs, $concept2);
     
    #  get the depth of the concepts taking that path
    my $c1_depth = $lcs_depth + $c1_length;
    my $c2_depth = $lcs_depth + $c2_length;
     
    #  if the depth of one of them is less than zero return zero
    if($c1_depth < 0 or $c2_depth < 0) { return -1; }
     
    #  otherwise calculate wup
    my $score = (2 * $lcs_depth) / ($c1_depth + $c2_depth);   
     
    return $score;
}
1;
__END__
HideShow 151 lines of Pod
=head1 NAME
UMLS::Similarity::wup - Perl module for computing semantic relatedness
of concepts in the Unified Medical Language System (UMLS) using the 
method described by Wu and Palmer (1994).
=head1 CITATION
 @article{WuP94,
  title={{Verbs semantics and lexical selection}},
  author={Wu, Z. and Palmer, M.},
  journal={Proceedings of the 32nd conference on Association 
           for Computational Linguistics},
  pages={133--138},
  year={1994},
  publisher={Association for Computational Linguistics 
             Morristown, NJ, USA}
 }
=head1 SYNOPSIS
  #!/usr/bin/perl
  use UMLS::Interface;
  use UMLS::Similarity::wup;
  my $umls = UMLS::Interface->new(); 
  die "Unable to create UMLS::Interface object.\n" if(!$umls);
  my $wup = UMLS::Similarity::wup->new($umls);
  die "Unable to create measure object.\n" if(!$wup);
  my $cui1 = "C0005767";
  my $cui2 = "C0007634";
  @ts1 = $umls->getTermList($cui1);
  my $term1 = pop @ts1;
  @ts2 = $umls->getTermList($cui2);
  my $term2 = pop @ts2;
  my $value = $wup->getRelatedness($cui1, $cui2);
  print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";
=head1 DESCRIPTION
The Wu & Palmer measure calculates relatedness by considering the 
depths of the two concepts in the UMLS, along with the depth of the 
LCS.  The formula is S<score = 2*depth(lcs) / (depth(s1) + depth(s2))>.
This means that S<0 < score <= 1>.  The score can never be zero because 
the depth of the LCS is never zero (the depth of the root of a taxonomy 
is one). The score is one if the two input concepts are the same.
=head1 USAGE
The semantic relatedness modules in this distribution are built as classes
that expose the following methods:
  new()
  getRelatedness()
=head1 TYPICAL USAGE EXAMPLES
To create an object of the wup measure, we would have the following
lines of code in the perl program. 
   use UMLS::Similarity::wup;
   $measure = UMLS::Similarity::wup->new($interface);
The reference of the initialized object is stored in the scalar
variable '$measure'. '$interface' contains an interface object that
should have been created earlier in the program (UMLS-Interface). 
If the 'new' method is unable to create the object, '$measure' would 
be undefined. 
To find the semantic relatedness of the concept 'blood' (C0005767) and
the concept 'cell' (C0007634) using the measure, we would write
the following piece of code:
   $relatedness = $measure->getRelatedness('C0005767', 'C0007634');
=head1 CONFIGURATION OPTION
The UMLS-Interface package takes a configuration file to determine 
which sources and relations to use when obtaining the path information.
The format of the configuration file is as follows:
SAB :: <include|exclude> <source1, source2, ... sourceN>
REL :: <include|exclude> <relation1, relation2, ... relationN>
For example, if we wanted to use the MSH vocabulary with only 
the RB/RN relations, the configuration file would be:
SAB :: include MSH
REL :: include RB, RN
or 
SAB :: include MSH
REL :: exclude PAR, CHD
If you go to the configuration file directory, there will 
be example configuration files for the different runs that 
you have performed.
For more information about the configuration options please 
see the README.
=head1 SEE ALSO
perl(1), UMLS::Interface
perl(1), UMLS::Similarity(3)
=head1 CONTACT US
  If you have any trouble installing and using UMLS-Similarity, 
  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 AUTHORS
  Bridget T McInnes <bthomson at cs.umn.edu>
  Siddharth Patwardhan <sidd at cs.utah.edu>
  Serguei Pakhomov <pakh0002 at umn.edu>
  Ted Pedersen <tpederse at d.umn.edu>
=head1 COPYRIGHT AND LICENSE
Copyright 2004-2010 by Bridget T McInnes, Siddharth Patwardhan, 
Serguei Pakhomov, Ying Liu and Ted Pedersen
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. 
=cut