/ 
UMLS-Similarity-0.05
River stage one • 1 direct dependent • 1 total dependent
/ UMLS::Similarity::path

NAME

UMLS::Similarity::path - Perl module for computing semantic relatedness of concepts in the UMLS by simple edge counting.

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::path;

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

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

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

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

DESCRIPTION

This module computes the semantic relatedness of two concepts by simple edge counitng in a specified view of the UMLS.

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

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

AUTHORS

Bridget T McInnes <bthomson@cs.umn.edu>
Siddharth Patwardhan <sidd@cs.utah.edu>
Serguei Pakhomov <pakhomov.serguei@mayo.edu>
Ted Pedersen <tpederse@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.