/ 
UMLS-Similarity-0.55
River stage one • 1 direct dependent • 1 total dependent
/ create-icfrequency.pl.pl

NAME

create-icfrequency.pl.pl - This program sums the frequency counts of the CUIs from a specified set of sources in plain text.

SYNOPSIS

This program sums the frequency counts of the CUIs from a specified set of sources in plain text. The CUIs are determined by mapping the words in the text to CUIs in the UMLS using the strings in the MRCONSO table or MetaMap.

PROPAGATION

The Information Content (IC) is defined as the negative log of the probability of a concept. The probability of a concept, c, is determine by summing the probability of the concept (P(c)) ocurring in some text plus the probability its decendants (P(d)) occuring in some text:

P(c*) = P(c) + \sum_{d\exists decendant(c)} P(d)

The initial probability of a concept (P(c)) and its decendants (P(d)) is obtained by dividing the number of times a concept is seen in the corpus (freq(d)) by the total number of concepts (N):

P(d) = freq(d) / N

Not all of the concepts in the taxonomy will be seen in the corpus. We have the option to use Laplace smoothing, where the frequency count of each of the concepts in the taxonomy is incremented by one. The advantage of doing this is that it avoides having a concept that has a probability of zero. The disadvantage is that it can shift the overall probability mass of the concepts from what is actually seen in the corpus.

USAGE

Usage: create-icfrequency.pl.pl [OPTIONS] OUTPUTFILE INPUTFILE

OUTPUTFILE

The output file contains frequency counts for CUIs in the following format:

SAB :: <sources>
CUI<>freq
CUI<>freq
...

INPUTFILE

File containing plain text.

Optional Arguments:

--term

Obtains the CUI counts using the term counts. This is the default.

--metamap

Obtain the CUI counts using MetaMap. This requires that you have MetaMap installed on your system. You can obtain this package:

http://mmtx.nlm.nih.gov/

These frequency counts are used to obtain the propagation counts. The format is similar to the output of count.pl from Text::NSP using the unigram option.

--config FILE

This is the configuration file. The format of the configuration file is as follows:

SAB :: <include|exclude> <source1, source2, ... sourceN>

For example, if we wanted to include on those CUIs in the MSH vocabulary:

SAB :: include MSH REL :: include RB, RN

or maybe use all the CUIs except those in MSH:

SAB :: exclude MSH

If you go to the configuration file directory, there will be example configuration files for the different runs that you have performed.

--username STRING

Username is required to access the umls database on MySql Note: if --username is specified the --password is also required.

--password STRING

Password is required to access the umls database on MySql Note: if --password is specified the --username is also required.

--hostname STRING

Hostname where mysql is located. DEFAULT: localhost

--database STRING

Database contain UMLS DEFAULT: umls

--debug

Sets the UMLS-Interface debug flag on for testing

--help

Displays the quick summary of program options.

--version

Displays the version information.

SYSTEM REQUIREMENTS

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

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

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

  • Text::NSP - http://search.cpan.org/dist/Text-NSP

  • MetaMap - http://mmtx.nlm.nih.gov/

CONTACT US

If you have any trouble installing and using CreatePropagationFile, 
please contact us via the users mailing list :
  
    umls-similarity@yahoogroups.com
   
You can join this group by going to:
  
    http://tech.groups.yahoo.com/group/umls-similarity/
   
You may also contact us directly if you prefer :
  
    Bridget T. McInnes: bthomson at cs.umn.edu 

    Ted Pedersen : tpederse at d.umn.edu

AUTHOR

Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2007-2009,

Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
   
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu


Siddharth Patwardhan, University of Utah, Salt Lake City
sidd@cs.utah.edu

Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002@umn.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.