Bridget McInnes > UMLS-Interface > getCuiList.pl

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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 ^

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.
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