Sam Henry
and 1 contributors

NAME

umls-association.pl This program calculates the assocation between two concepts or sets of concepts

SYNOPSIS

This utility takes two sets of concepts and returns their assocation score

USAGE

Usage: umls-assocation.pl [OPTIONS] CUI_set1 CUI_set2 --matrix Matrix_File --measure Assoc_Measure

INPUT

[CUI_set1] [CUI_set2]

Two sets of CUIs in the UMLS. Each CUI in the CUI set is comma seperated

[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

General Options:

Displays the quick summary of program options.

--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.

--lsa

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

--sbc

Shared B to C association - Calculates the association scores using the association between the set of A co-occuring terms, and the term C.

--wsa

Weighted Set Association - Same as linking set association, but weights the members of the linking set based on their association with the original term. The association measure used for weighting is the same as specified for quantifying association overall (--measure)

--nonorm

Indicates that the weights in WSA will NOT be normalized between 0 and 1 and instrad the direct association score will be used

--precision N

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

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

The association between the two concepts (or terms)

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

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

COPYRIGHT

Copyright (c) 2015

 Sam Henry, Virginia Commonwealth University 
 henryst 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.