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UMLS-Similarity-0.17
River stage one • 1 direct dependent • 1 total dependent
/ umls-similarity.pl

NAME

umls-similarity.pl - This program returns a semantic similarity score between two concepts.

SYNOPSIS

This is a utility that takes as input either two terms (DEFAULT) or two CUIs and returns the similarity between the two.

USAGE

Usage: umls-similarity.pl [OPTIONS] [CUI1|TERM1] [CUI2|TERM2]

INPUT

[CUI1|TERM1] [CUI2|TERM2]

The input are two terms or two CUIs associated to concepts in the UMLS.

Optional Arguments:

--infile FILE

A file containing pairs of concepts or terms in the following format:

    term1<>term2 
    
    or 

    cui1<>cui2

    or 

    cui1<>term2

    or 

    term1<>cui2

--username STRING

Username is required to access the umls database on MySql

--password STRING

Password is required to access the umls database on MySql

--hostname STRING

Hostname where mysql is located. DEFAULT: localhost

--database STRING

Database contain UMLS DEFAULT: umls

--measure MEASURE

Use the MEASURE module to calculate the semantic similarity. The available measure are: 1. Leacock and Chodorow (1998) refered to as lch 2. Wu and Palmer (1994) refered to as wup 3. The basic path measure refered to as path 4. Rada, et. al. (1989) refered to as cdist 5. Nguyan and Al-Mubaid (2006) refered to as nam

--precision N

Displays values upto N places of decimal.

--verbose

Displays information about the concept if it doesn't exist in the source.

--dbfile FILE

This is the Berkley DB file that contains the vector information to use with the vector measure. This is required if you specify vector with the --measure option.

--allsenses

This option prints out all the possible CUIs pairs and their semantic similarity score if one of the inputs is a term that maps to more than one CUI. Right now we just return the CUIs that are the most similar.

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

disambiguate.pl creates two directories. One containing the arff files and the other containing the weka files. In the weka directory, the overall averages are stored in the OverallAverage file.

SYSTEM REQUIREMENTS

  • Perl (version 5.8.5 or better) - http://www.perl.org

  • UMLS::Interface - http://search.cpan.org/dist/UMLS-Interface

  • UMLS::Similarity - http://search.cpan.org/dist/UMLS-Similarity

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

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2007-2009,

 Bridget T. McInnes, University of Minnesota
 bthomson at cs.umn.edu
    
 Ted Pedersen, University of Minnesota Duluth
 tpederse at d.umn.edu


 Siddharth Patwardhan, University of Utah, Salt Lake City
 sidd@cs.utah.edu
 
 Serguei Pakhomov, University of Minnesota Twin Cities
 pakh0002@umn.edu

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to:

 The Free Software Foundation, Inc.,
 59 Temple Place - Suite 330,
 Boston, MA  02111-1307, USA.