NAME

UMLS::Similarity::nam - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Nguyen and Al-Mubaid (2006)

CITATION

 @inproceedings{NguyenA06,
  title={{New ontology-based semantic similarity measure 
          for the biomedical domain}},
  author={Nguyen, H.A. and Al-Mubaid, H.},
  booktitle={Proceedings of the IEEE International Conference 
             on Granular Computing},
  pages={623--628},
  year={2006}
 }

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::nam;

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

  my $nam = UMLS::Similarity::nam->new($umls);
  die "Unable to create measure object.\n" if(!$nam);

  my $cui1 = "C0005767";
  my $cui2 = "C0007634";

  $ts1 = $umls->getTermList($cui1);
  my $term1 = pop @{$ts1};

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

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

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

DESCRIPTION

The Nguyen and Al-Mubaid measure calculates similarity by calculating the log of two plus the product of the shortest distance between the two concepts minus one and the depth of the taxonomy minus the depth of the LCS. Concepts that are more similar with have a lower similarity score than concepts that are less similar with this measure.

USAGE

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

TYPICAL USAGE EXAMPLES

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

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

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');

CONFIGURATION OPTION

The UMLS-Interface package takes a configuration file to determine which sources and relations to use when obtaining the path information.

The format of the configuration file is as follows:

SAB :: <include|exclude> <source1, source2, ... sourceN>

REL :: <include|exclude> <relation1, relation2, ... relationN>

For example, if we wanted to use the MSH vocabulary with only the RB/RN relations, the configuration file would be:

SAB :: include MSH REL :: include RB, RN

or

SAB :: include MSH REL :: exclude PAR, CHD

If you go to the configuration file directory, there will be example configuration files for the different runs that you have performed.

For more information about the configuration options please see the README.

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 2004-2011 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.

cpanm UMLS::Similarity

perl -MCPAN -e shell
install UMLS::Similarity