NAME

UMLS::Similarity::lesk - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Banerjee and Pedersen (2002).

CITATION

 @article{BanerjeeP03,
  title={An Adapted Lesk Algorithm for Word Sense Disambiguation using WordNet}, 
  author={Banerjee and Pedersen},
  journal={Proceedings of the Third International Conference on Intelligent Text Processiong 
                   and Computational Linguistics},  
  pages={136-145},
  year={2002}
  month={February}
  address={Mexico City}
 }

SYNOPSIS

  use UMLS::Interface;
  use UMLS::Similarity::lesk;

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

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

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

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

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

  my $value = $lesk->getRelatedness($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 Banerjee and Pedersen(2002). The relatedness measure proposed by Banerjee and Pedersen is and adaptation of Lesk's dictionary-based word sense disambiguation algorithm.

--defraw option is a flag for the lesk measure. The definitions used are 'cleaned'. If the --defraw flag is set they will not be cleaned, and it will leave the definitions in their "raw" form.

--dictfile option is a dictionary file for the lesk measure. It contains the 'definitions' of a concept which would be used rather than the definitions from the UMLS.

--stoplist option is a word list file for the lesk measure. The words in the file should be removed from the definition. In the stop list file, each word is in the regular expression format. A stop word sample file is under the samples folder which is called toplist-nsp.regex.

--stem option is a flag for the lesk measure. If we the --stem flag is set, the words of the definition are stemmed by the the Porter Stemming algorithm.

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

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

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>
  Ying Liu <liux0395 at 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.

cpanm UMLS::Similarity

perl -MCPAN -e shell
install UMLS::Similarity