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).
use UMLS::Interface;
use UMLS::Similarity::wup;
my $umls = UMLS::Interface->new();
die "Unable to create UMLS::Interface object.\n" if(!$umls);
($errCode, $errString) = $umls->getError();
die "$errString\n" if($errCode);
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";
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 score = 2*depth(lcs) / (depth(s1) + depth(s2)). This means that 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.
The semantic relatedness modules in this distribution are built as classes that expose the following methods: new() getRelatedness() getError() getTraceString()
See the UMLS::Similarity(3) documentation for details of these methods.
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. This, as well as any other error/warning may be tested.
die "Unable to create object.\n" if(!defined $measure); ($err, $errString) = $measure->getError(); die $errString."\n" if($err);
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');
To get traces for the above computation:
print $measure->getTraceString();
However, traces must be enabled using configuration files. By default traces are turned off.
perl(1), UMLS::Interface
perl(1), UMLS::Similarity(3)
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
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>
Copyright 2004-2009 by Bridget T McInnes, Siddharth Patwardhan, Serguei Pakhomov and Ted Pedersen
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
