/ 
UMLS-Association-0.01
River stage one • 1 direct dependent • 1 total dependent
/ calculate-association.pl

NAME

calculate-association.pl This program calculates the assocation between two concepts (or terms)

SYNOPSIS

This utility takes two concepts (or terms) and returns their assocation score

USAGE

Usage: calculate-assocation.pl [OPTIONS] CUI1|TERM CUI2|TERM

INPUT

[CUI1|TERM1] [CUI2|TERM2]

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

OPTIONS

Optional command line arguements

General Options:

Displays the quick summary of program options.

--measure

The measure used to calculate the assocation. Default = tscore.

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 (DEFAULT)

--help

Displays the quick summary of program options.

--version

Displays the version information.

Input Options:

--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 ...

General Database Options:

--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

--socket STRING

Socket where the mysql.sock or mysqld.sock is located. DEFAULT: mysql.sock

UMLS::Interface Database Options:

--umlsdatabase STRING

Database contain UMLS DEFAULT: umls

UMLS::Association Database Options:

--assocdatabase STRING

The UMLS-Association database containing the CUI bigrams and their associated frequency information. DEFAULT: CUI_BIGRAMS

OUTPUT

The association between the two concepts (or terms)

SYSTEM REQUIREMENTS

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

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

  • 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 :
  
    Bridget T. McInnes: btmcinnes at vcu.edu

AUTHOR

Bridget T. McInnes, 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.