The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
UMLS-Interface-0.89
River stage one • 3 direct dependents • 3 total dependents
/ umlsCycles.pl

NAME

umlsCycles.pl - This program marks problematic relations defined by the user.

SYNOPSIS

This is a utility that takes as input a list of problematic relations in the MRREL file. The relations cause cycles in structure. This programs marks the problematic relations in the MRREL file by inserting a '1' into the CVF column. It does not physicall remove a relation from the table only tags it. The bad-relations.txt file is found in the default_options directory. This file is used as the default unless one is specified on the command line.

Documentation on how the badrelation files was compiled, please refer to:

          Bodenreider O. An object-oriented model for representing 
          semantic locality in the UMLS. Medinfo 2001;10(Pt 1):161-5.
          http://mor.nlm.nih.gov/pubs/pdf/2001-medinfo-ob.pdf

USAGE

Usage: umlsCycles.pl --username STRING --password STRING [OPTIONS]

INPUT

Optional Arguments:

--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

--file

File containing the bad relations. The assumption is that you are running umlsCycles from the utils directory.

DEFAULT: ../default_options/2008AA-badpairs

--unmark

It removes the marks of the the problematic relations in the MRREL file by inserting a NULL into the CVF column.

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

disambiguate.pl creates two directories. One containing the arff files and the other containing the weka files. In the weka directory, the overall averages are stored in the OverallAverage file.

SYSTEM REQUIREMENTS

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

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 200 - 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.