/ 
UMLS-Association-0.11
River stage one • 1 direct dependent • 1 total dependent
/ umls-association.pl

NAME

umls-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: umls-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 
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.