/ 
UMLS-Similarity-0.51
River stage one • 1 direct dependent • 1 total dependent
/ UMLS::Similarity::res

NAME

UMLS::Similarity::res - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Resnik (1995).

CITATION

@article{Resnik95,
 title={{Using information content to evaluate semantic 
         similarity in a taxonomy}},
 author={Resnik, P.},
 journal={Proceedings of the 14th International Joint 
          Conference on Artificial Intelligence},
 volume={1},
 pages={448--453},
 year={1995}
}

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::res;

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

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

  my $value = $res->getRelatedness($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 Resnik (1995). The relatedness measure proposed by Resnik is the information content (IC) of the least common subsumer of the two concepts.

The IC of a concept is defined as the negative log of the probabilty of the concept.

To use this measure, a propagation file containing the probability of a CUI for each of the CUIs from the source(s) specified in the configuration file. The format for this file is as follows:

C0000039<>0.00003951
C0000052<>0.00003951
C0000084<>0.00003951
C0000096<>0.00003951

A larger of example of this file can be found in the icpropagation file in the samples/ directory. In order to create a propagation file given

A propagation file can be created using the create-propagation-file.pl program in the utils/ directory. This file will take either a list of CUIs with their frequency counts or a raw text file and compute the probability of each of the CUIs using the set of source(s) and relations specified in the configuration file.

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 res measure, we would have the following lines of code in the perl program.

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