/ 
UMLS-Similarity-0.35
River stage one • 1 direct dependent • 1 total dependent
/ UMLS::Similarity::jnc

NAME

UMLS::Similarity::jnc - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Jiang and Conrath 1997.

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::jnc;

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

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

  my $value = $jnc->getRelatedness($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 Jiang and Conrath (1997). This measure is based on a combination of using edge counts in the UMLS 'is-a' hierarchy and using the information content values of the concepts, as describedin the paper by Jiang and Conrath. Their measure, however, computes values that indicate the semantic distance between words (as opposed to theirsemantic relatedness). In this implementation of the measure we invert the value so as to obtain a measure of semantic relatedness. Other issues that arise due to this inversion (such as handling of zero values in the denominator) have been taken care of as special cases.

USAGE

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.

TYPICAL USAGE EXAMPLES

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

use UMLS::Similarity::jnc;
$measure = UMLS::Similarity::jnc->new($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.

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 2004-2009 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.