/ 
UMLS-Interface-0.21
River stage one • 3 direct dependents • 3 total dependents
/ findShortestPath.pl

NAME

findShortestPath.pl - This program finds the shoretest path between two concepts.

SYNOPSIS

This program takes two terms or CUIs and returns the shortest path between them.

USAGE

Usage: findShortestPath.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:

--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

--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.

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.