umls-association.pl This program calculates the assocation between two concepts or sets of concepts
This utility takes two sets of concepts and returns their assocation score
Usage: umls-assocation.pl [OPTIONS] CUI_set1 CUI_set2 --matrix Matrix_File --measure Assoc_Measure
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. Frequency 2. Random 3. Dice Coefficient 4. Fishers exact test - left sided 5. Fishers exact test - right sided 6. Fishers twotailed test - right sided 7. Jaccard Coefficient 8. Log-likelihood ratio 9. Mutual Information 10. Odds Ratio 11. Pointwise Mutual Information 12. Phi Coefficient 13. Pearson's Chi Squared Test 14. Poisson Stirling Measure 15. T-score
Optional command line arguements
Displays the quick summary of program options.
If selected, the order in which CUIs appear will be disregarded when the association score is calculated.
Linking Term Association - Calculates the association scores using implicit or intermediate relationships between the specified CUIs, and the count of unique shared co-occurrences.
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.
Linking Set Association - Calculates the association scores using the association between the sets of co-occurring terms of the original terms
Shared B to C association - Calculates the association scores using the association between the set of A co-occuring terms, and the term C.
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)
Indicates that the weights in WSA will NOT be normalized between 0 and 1 and instrad the direct association score will be used
Displays values up to N places of decimal. (DEFAULT: 4)
Displays the version information.
The association between the two concepts (or terms)
Perl (version 5.8.5 or better) - http://www.perl.org
Text::NSP - http://search.cpan.org/dist/Text-NSP
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
Bridget T. McInnes, Virginia Commonwealth University Alexander D. McQuilkin, Virginia Commonwealth University Sam Henry, Virginia Commonwealth University
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.
To install UMLS::Association, copy and paste the appropriate command in to your terminal.
cpanm
cpanm UMLS::Association
CPAN shell
perl -MCPAN -e shell install UMLS::Association
For more information on module installation, please visit the detailed CPAN module installation guide.