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).

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}
}

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";

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 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.

USAGE

The semantic relatedness modules in this distribution are built as classes that expose the following methods: new() getRelatedness()

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');

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.

SEE ALSO

perl(1), UMLS::Interface

perl(1), UMLS::Similarity(3)

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

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>

COPYRIGHT AND LICENSE

Copyright 2004-2011 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.

cpanm UMLS::Similarity

perl -MCPAN -e shell
install UMLS::Similarity