/ 
UMLS-Similarity-1.47
River stage one • 1 direct dependent • 1 total dependent
/ sim2r.pl

NAME

sim2r.pl - This program converts a series of umls-similarity output to R format in order to run the SignificanceTesting.r program.

SYNOPSIS

This program converts output generated by umls-similarity.pl to R format in order to run the SignificanceTesting.r program

USAGE

Usage: sim2r.pl GOLD_FILE [FILE1 FILE2 ...]

INPUT

Required:

GOLD_FILE

This is the gold standard. Usually this is the data that has manually been score by human annotaters. This is what the SignificanceTesting.r program is going to use to determine the correlation against for the other files.

The format of this file is the same as output format of the umls-similarity.pl program.

score<>cui1<>cui2 score<>term1<>term2 ...

FILE1 FILE2 ...

These are the output files generated by the umls-similarity.pl program. The header information in R will be the name of the file.

Options:

--word

The format of hte input files contains words rather than CUIs or is not a umls-simmilarity.pl output file.

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

A cvs file that can be read by the SignificanceTesting.r program

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 cs.umn.edu 

    Ted Pedersen : tpederse at d.umn.edu

AUTHOR

Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2007-2011,

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.