/ 
UMLS-Association-0.15
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.

--conceptexpansion

Calculates the association score taking into account the occurrences of descendants of the specified CUIs.

--noorder

If selected, the order in which CUIs appear will be disregarded when the association score is calculated.

--lta

Linking Term Association - Calculates the association scores using implicit or intermediate relationships between the specified CUIs, and the count of unique shared co-occurrences.

--mwa

Minimum Weight Association - Calculates the association scores using implicit or intermediate relationships between the specified CUIs, and the minimum co-occurrence count between shared co-occurrences.

--vsa

Vector Set Association - Calculates the association scores using the association between the sets of co-occurring terms of the original terms

--precision N

Displays values up to N places of decimal. (DEFAULT: 4)

--measure STRING

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:

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

--matrix FILE

File name containing co-occurrence data in sparse matrix format This is an alternative to storing in a database, but will be slower for single queries, but much faster for multiple queries File should should be sparse format of the form CUI1\tCUI2\tvalue\\n \n\n";

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
Sam Henry, 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.