NAME
create-icfrequency.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.
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:
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.
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 ocurring in some text plus the probability its decendants occuring in some text:
For more information on how this is calculated please see the README file.
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.eduAUTHOR
Bridget T. McInnes, University of MinnesotaCOPYRIGHT
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.eduThis 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.