Bridget McInnes
and 1 contributors

NAME

getCuiList.pl - This program returns a list of CUIs based on the configuration file.

SYNOPSIS

This program returns a list of CUIs based on the sources and relations specified in the configuration file.

USAGE

Usage: getCuiList.pl [OPTIONS] CONFIGFILE

INPUT

CONFIGFILE

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

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.

OUTPUT

List of CUIs that are associated with the input term

OPTIONAL ARGUMENTS:

--children

Returns the number of children of a given CUI. The format for just using --children is:

 CUI children

--parents

Returns the number of children of a given CUI. The format for just using --parents is:

 CUI parents

The format for using both --parents and --children is:

 CUI children|parents

--relations REL

Returns the number of relations of a given CUI. The REL input can be a list of comma seperated relations. For example:

  --relation "SIB,RO"

This would return the number of SIB and RO relations for a given concept in the format : CUI sib|ro

This option current can not be used with the --children and --parent option because if you want them just add them to the list. For example: --relation "SIB,PAR,CHD"

--term

Returns the terms associated with the CUI in the following format:

 CUI term1|term2|term3|...

If used with the --parents and/or --children options or the --relation options, the following format is returned:

 CUI children|parents|term1|term2|...

Remember children and parents is a number!

--st <semantic type abbreviation>

Returns only those CUIs with the specified semantic type

--sg <semantic group name>

Returns only those CUIs with the specified semantic group

--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.

SYSTEM REQUIREMENTS

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

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2007-2011,

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