Sam Henry
and 1 contributors

NAME

umls-association-runDataSet.pl This program calculates the assocation a dataset of term pairs

SYNOPSIS

This utility takes a file of line seperated term pairs as input. The file is of the form: "cui1<>cui2\n" with each line containing a new cui pair. It outputs a line seperated list of association score and term pair of the form: "score<>cui1<>cui2". Each line contains a different cui pair and their score

USAGE

Usage: umls-assocation-runDataSet.pl [OPTIONS] CUI_LIST_FILE OUTPUT_FILE --measure Assoc_Measure --matrix Matrix_FileName

INPUT

CUI_LIST_FILE

the input file containing line seperated cui pairs of the form: "cui1<>cui2"

OUTPUT_FILE

the output file, where each score and cui pair are output of the form: score<>cui1<>cui2

[Matrix_File]

File name containing co-occurrence data in sparse matrix format

[Assoc_Measure]

A string specifying the association measure to use The measure used to calculate the assocation. Recommended = x2

The package uses the Text::NSP package to do the calculation. The measure included within this package are: 1. Dice Coefficient 2. Fishers exact test - left sided 3. Fishers exact test - right sided 4. Fishers twotailed test - right sided 5. Jaccard Coefficient 6. Log-likelihood ratio 7. Mutual Information 8. Odds Ratio 9. Pointwise Mutual Information 10. Phi Coefficient 11. Pearson's Chi Squared Test 12. Poisson Stirling Measure 13. T-score

OPTIONS

Optional command line arguements. These options are identical to umls-association.pl. Please see umls-associaton.pl for descriptions.

OUTPUT

The association between the each concept pair of the input file written to a new line of the output file.

SYSTEM REQUIREMENTS

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

  • Text::NSP - http://search.cpan.org/dist/Text-NSP

CONTACT US

  If you have any trouble installing and using UMLS-Assocation, 
  please contact us via the users mailing list :
    
      umls-association@yahoogroups.com
     
  You can join this group by going to:
    
      http://tech.groups.yahoo.com/group/umls-assocation/
     
  You may also contact us directly if you prefer :
    
      Sam Henry: henryst at vcu.edu 

AUTHOR

 Sam Henry, Virginia Commonwealth University
 Bridget T. McInnes, Virginia Commonwealth University 
 Alexander D. McQuilkin, Virginia Commonwealth University

COPYRIGHT

Copyright (c) 2015

 Bridget T. McInnes, Virginia Commonwealth University 
 btmcinnes at vcu.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.