Bridget McInnes
and 1 contributors

NAME

findNumberOfCloserConcepts.pl - This program finds the number of concepts closer to the first concept than the second.

SYNOPSIS

This program takes two terms or CUIs and returns the number of concepts closer to the first concept than the second.

USAGE

Usage: findNumberOfCloserConcepts.pl [OPTIONS] [CUI1|TERM1] [CUI2|TERM2]

INPUT

Required Arguments:

[CUI1|TERM1] [CUI2|TERM2]

A TERM or CUI (or some combination) from the Unified Medical Language System

Optional Arguments:

--config FILE

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.

--infile FILE

   A file containing pairs of concepts or terms in the following format:

    term1<>term2 
    
    or 

    cui1<>cui2
 
    or 
    
    cui1<>term2

    or 

    term1<>cui2

--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

--verbose

This option will print out the table information to the config directory that you specified.

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

The path(s) between the two given CUIs or terms

SYSTEM REQUIREMENTS

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

AUTHOR

 Bridget T. McInnes, University of Minnesota

COPYRIGHT

Copyright (c) 2007-2009,

 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.