/ 
UMLS-Similarity-0.49
River stage one • 1 direct dependent • 1 total dependent
/ create-propagation-file.pl

NAME

create-propagation-file.pl - This program determines the propagation counts of the CUIs in a specified set of sources and relations given a dataset.

SYNOPSIS

This program determines the propagation counts of the CUIs in a specified set of sources and relations given a dataset.

USAGE

Usage: create-propagation-file.pl [OPTIONS] OUTPUTFILE INPUTFILE

INPUT

OUTPUTFILE

File in which the propagation counts for the CUIs will be stored

INPUTFILE

File containing plain text. One record per line.

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/

--icfrequency

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

These frequency counts are used to obtain the propagation counts

--config FILE

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

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

REL :: <include|exclude> <relation1, relation2, ... relationN>

For example, if we wanted to use the MSH vocabulary with only the RB/RN relations, the configuration file would be:

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

or

SAB :: include MSH REL :: exclude PAR, CHD

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

--password STRING

Password is required to access the umls database on MySql

--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.

OUTPUT

File containing the propagation counts for the information content measures in the create-propagation-file.pl program

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.