UMLS::Similarity::lch - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Leacock and Chodorow (1998).
@article{LeacockC98, title={{Combining local context and WordNet similarity for word sense identification}}, author={Leacock, C. and Chodorow, M.}, journal={WordNet: An Electronic Lexical Database}, pages={265--283}, year={1998} }
use UMLS::Interface; use UMLS::Similarity::lch; my $umls = UMLS::Interface->new(); die "Unable to create UMLS::Interface object.\n" if(!$umls); my $lch = UMLS::Similarity::lch->new($umls); die "Unable to create measure object.\n" if(!$lch); my $cui1 = "C0005767"; my $cui2 = "C0007634"; $ts1 = $umls->getTermList($cui1); my $term1 = pop @{$ts1}; $ts2 = $umls->getTermList($cui2); my $term2 = pop @{$ts2}; my $value = $lch->getRelatedness($cui1, $cui2); print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";
This module computes the semantic relatedness of two concepts in the UMLS according to a method described by Leacock and Chodorow (1998). The relatedness measure proposed by Leacock and Chodorow is -log (length / (2 * D)), where length is the length of the shortest path between the two synsets (using node-counting) and D is the maximum depth of the taxonomy.
The semantic relatedness modules in this distribution are built as classes that expose the following methods: new() getRelatedness()
To create an object of the lch measure, we would have the following lines of code in the perl program.
use UMLS::Similarity::lch; $measure = UMLS::Similarity::lch->new($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');
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.
perl(1), UMLS::Interface
perl(1), UMLS::Similarity(3)
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
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 2004-2011 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.
To install UMLS::Similarity, copy and paste the appropriate command in to your terminal.
cpanm
cpanm UMLS::Similarity
CPAN shell
perl -MCPAN -e shell install UMLS::Similarity
For more information on module installation, please visit the detailed CPAN module installation guide.