Bridget McInnes

NAME

umls-senserelate-evaluation.pl - This program evaluates the umls-senserelate algorithm using the semeval scorer program

SYNOPSIS

This program evaluates the senses assigned by the UMLS-SenseRelate algorithm using the semeval scorer program

USAGE

Usage: umls-senserelate-evaluation.pl LOG_DIRECTORY

OUTPUT

Required Options

LOG_DIRECTORY

This is the directory outputted by the umls-targetword-senserelate.pl program which contains the key and answer files for each of the target words.

General Options:

--info FILE

Prints out accuracy information to FILE

--senses DIR|File

Sometimes of the senses in the key file do not map directly to the senses in the answer file. This will happen when using the NLM-WSD dataset which uses tags to indicate the sense of the ambiguous word and then those tags are mapped to concepts in the UMLS. The key file would contain the CUIs while the answer file contains the tags. Therefore, we need the sense (sometimes called choice) files to evaluate the mappings.

So this options takes the directory that contains the the sense file for each target word you are going to disambiguate or just the file itself.

The files for the target word contains the possible senses of the target word.

This may be temporary but right now this is who I have it because often times the possible senses change depending on the version of the UMLS that you are using. I felt this allowed the most flexibility with it.

The naming convention for this is a file called: <target word>.choices

The format for this file is:

    <tag>|<target word name>|semantic type|CUI

This format is based on the choice files in the NLM-WSD dataset which we use for our experiments. If you are using the NLM-WSD dataset you can download these choice files from NLM's site. There are the 1999 tagset and the 2007 tagset available. You can find them here:

  http://wsd.nlm.nih.gov/collaboration.shtml

--verbose

Prints out accuracy information to STDOUT.

--version

Displays the version information.

--help

Displays the help information

SYSTEM REQUIREMENTS

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

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 umn.edu 

      Ted Pedersen : tpederse at d.umn.edu

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2010-2012,

 Bridget T. McInnes, University of Minnesota Twin Cities
 bthomson at umn.edu
    
 Ted Pedersen, University of Minnesota Duluth
 tpederse at d.umn.edu
 
 Serguei Pakhomov, University of Minnesota Twin Cities
 pakh0002 at umn.edu

 Ying Liu, University of Minnesota Twin Cities
 liux0395 at 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.



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