/ 
UMLS-Similarity-0.47
River stage one • 1 direct dependent • 1 total dependent
/ UMLS::Similarity::lin

NAME

UMLS::Similarity::lin - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Lin (1998).

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::lin;

  my $propagation_file = "samples/icpropagation";

  my %option_hash = ();
  $option_hash{"propagation"} = $propagation_file;

  my $umls = UMLS::Interface->new(\%option_hash); 
  die "Unable to create UMLS::Interface object.\n" if(!$umls);
  ($errCode, $errString) = $umls->getError();
  die "$errString\n" if($errCode);

  my $lin = UMLS::Similarity::lin->new($umls);
  die "Unable to create measure object.\n" if(!$lin);
  
  my $cui1 = "C0005767";
  my $cui2 = "C0007634";
	
  @ts1 = $umls->getTermList($cui1);
  my $term1 = pop @ts1;

  @ts2 = $umls->getTermList($cui2);
  my $term2 = pop @ts2;

  my $value = $lin->getRelatedness($cui1, $cui2);

  print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";

DESCRIPTION

This module computes the semantic relatedness of two concepts in the UMLS according to a method described by Lin (1998). The relatedness measure proposed by Lin is the IC(lcs) / IC(concept1) + IC(concept2). One can observe, then, that the realtedness value will be greater-than or equal-to zero and less-than or equal-to one.

If the information content of any of either concept1 or concept2 is zero, then zero is returned as the relatedness score, due to lack of data. Ideally, the information content of a synset would be zero only if that synset were the root node, but when the frequency of a synset is zero, we use the value of zero as the information content because of a lack of better alternatives.

USAGE

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

TYPICAL USAGE EXAMPLES

To create an object of the lin measure, we would have the following lines of code in the perl program.

use UMLS::Similarity::lin;
$measure = UMLS::Similarity::lin->new($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');

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 2004-2010 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.