UMLS::Similarity::lch - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Leacock and Chodorow (1998).
use UMLS::Interface;
use UMLS::Similarity::lch;
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 $lch = UMLS::Similarity::lch->new($umls);
die "Unable to create measure object.\n" if(!$lch);
my $cui1 = "C0005767";
my $cui2 = "C0007634";
@ts1 = $umls->getTermList($cui1);
my $term1 = pop @ts1;
@ts2 = $umls->getTermList($cui2);
my $term2 = pop @ts2;
my $value = $lch->getRelatedness($cui1, $cui2);
print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";
This module computes the semantic relatedness of two concepts in the UMLS according to a method described by Leacock and Chodorow (1998). The relatedness measure proposed by Leacock and Chodorow is -log (length / (2 * D)), where length is the length of the shortest path between the two synsets (using node-counting) and D is the maximum depth of the taxonomy.
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 lch measure, we would have the following lines of code in the perl program.
use UMLS::Similarity::lch; $measure = UMLS::Similarity::lch->new($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.
