/ 
UMLS-Similarity-0.35
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

Unless the --matrix option is chosen then it is just a list of CUIS: cui1 cui2 cui3 ...

--matrix

This option returns a matrix of similarity scores given a file containing a list of CUIs. The file is passed using the --infile option

--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.

--info

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.

--forcerun

This option will bypass any command prompts such as asking if you would like to continue with the index creation.

--debug

Sets the UMLS-Interface debug flag on for testing

--verbose

This option will print out the table information to the config file that you specified.

--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.