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NAME ^ - This program finds the shoretest path between two concepts.


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




Required Arguments:


A TERM or CUI (or some combination), or two semantic types (with the --st option) from the Unified Medical Language System

Optional Arguments:


The input is two seamntic types and the shortest path between them comes from the semantic network. This can either be a TUI or the Abbreviation of the semantic type.

--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


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.


The path between the concepts is not required to be directed such that an LCS can be obtained. This means that we can obtain a path from CUI1 to CUI2 by meandering through the graph rather than finding the CUI that subsumes both of them and then finding the shortest path between those points.


This prints out the relation and source information between the CUIs in the path

--icpropagation FILE

Takes in a propagation file and then outputs the information content of the CUIs in the shortest path


Prints out the length of the shortest path for ease of counting

--infile FILE

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






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


This option will not create a database of the path information for all of concepts in the specified set of sources and relations in the config file but obtain the information for just the input concept


This option will bypass any command prompts such as asking if you would like to continue with the index creation.

--debugpath FILE

This option prints out the path information for debugging purposes. This option is only really available with the --reatime option because otherwise the path information is stored in the database. You can get this information in a file if you use the --verbose option while creating the index.


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

--cuilist FILE

This option takes in a file containing a list of CUIs (one CUI per line) and stores only the path information for those CUIs rather than for all of the CUIs given the specified set of sources and relations


Displays the quick summary of program options.


Displays the version information.


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



 Bridget T. McInnes, University of Minnesota


Copyright (c) 2007-2009,

 Bridget T. McInnes, University of Minnesota
 bthomson at
 Ted Pedersen, University of Minnesota Duluth
 tpederse at

 Siddharth Patwardhan, University of Utah, Salt Lake City
 Serguei Pakhomov, University of Minnesota Twin Cities

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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