NAME

getAssociatedTerms.pl - This program returns all associated terms of a concept.

SYNOPSIS

This program takes in a CUI and returns all of its associated terms either given the sources and relations specified in the config file or in the entire UMLS.

USAGE

Usage: getAssociatedTerms.pl [OPTIONS] CUI

INPUT

Required Arguments:

CUI

Concept Unique Identifier (CUI) from the Unified Medical Language System (UMLS)

Optional Arguments:

--infile FILE

FILE is the name of a file containing a list of CUIs. The expected format is one CUI per line for example:

--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>

RELA :: <include|exclude> <rela1, rela2, ... relaN> (optional)

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 RELA :: include inverse_isa, isa

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.

Return only the preferred term of the CUI. When used with --config option the preferred term must be in the sources specified in the configuration file otherwise it will not return anything. Without the --config option the preferred term will be returned.

To be clear, here are the options:

1. --config FILE returns the cuis associated terms from the sources specified in the configuration file

2. --preferred --config FILE returns the cuis preferred term from the sources specified in the configuration file

3. --preferred returns the cuis preferred term

4. no config and no preferred option returns the cuis associated terms from the entire UMLS

--debug

Sets the debug flag for testing

--username STRING

Username is required to access the umls database on MySql unless it was specified in the my.cnf file at installation

--password STRING

Password is required to access the umls database on MySql unless it was specified in the my.cnf file at installation

--hostname STRING

Hostname where mysql is located. DEFAULT: localhost

--socket STRING

The socket your mysql is using. DEFAULT: /tmp/mysql.sock

--database STRING

Database contain UMLS DEFAULT: umls

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

List of CUIs that are associated with the input term

SYSTEM REQUIREMENTS

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

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

 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.

CPAN RT