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NAME ^

findAncestors.pl - This program returns the ancestors of a given CUI based on the configuration file.

SYNOPSIS ^

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

USAGE ^

Usage: findAncestors.pl [OPTIONS] CUI

INPUT ^

CUI

A CUI from the UMLS sources specified in the configuration file (or default source)

OUTPUT ^

List of CUIs that are the ancestors of the given term

OPTIONAL ARGUMENTS: ^

--config

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.

--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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