umlsCycles.pl

- UMLS-Similarity
- SYNOPSIS
- USAGE
- INPUT

- Optional Arguments:

- -username STRING
- -password STRING
- -hostname STRING
- -socket STRING
- -database STRING
- -file
- -unmark

- -help
- -version

- OUTPUT
- SYSTEM REQUIREMENTS
- AUTHOR
- COPYRIGHT

# UMLS-Similarity

umlsCycles

# 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) 2007,

     Bridget T. McInnes, University of Minnesota
     bthomson at cs.umn.edu

     Ted Pedersen, University of Minnesota Duluth
     tpederse at d.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.