Sam Henry
and 1 contributors

NAME

UMLS::Association - A suite of Perl modules that implement a number of semantic association measures in order to calculate the semantic association between two concepts in the UMLS.

SYNOPSIS

INSTALL

To install the module, run the following magic commands:

  perl Makefile.PL
  make
  make test
  make install

This will install the module in the standard location. You will, most probably, require root privileges to install in standard system directories. To install in a non-standard directory, specify a prefix during the 'perl Makefile.PL' stage as:

  perl Makefile.PL PREFIX=/home/sid

It is possible to modify other parameters during installation. The details of these can be found in the ExtUtils::MakeMaker documentation. However, it is highly recommended not messing around with other parameters, unless you know what you're doing.

DESCRIPTION

This package provides a Perl interface to

DATABASE SETUP

The interface assumes that the CUI network extracted from the MetaMapped Medline Baseline is present in a mysql database. The name of the database can be passed as configuration options at initialization. However, if the names of the databases are not provided at initialization, then default value is used -- the database is called 'CUI_BIGRAMS'.

The CUI_BIGRAMS database must contain four? tables: 1. N11 2. N1P 3. NP1 4. NPP

All other tables in the databases will be ignored, and any of these tables missing would raise an error.

A script explaining how to create the CUI network and the mysql database are in the INSTALL file.

INITIALIZING THE MODULE

To create an instance of the interface object, using default values for all configuration options:

  use UMLS::Association;
  my $associaton = UMLS::Association->new();

Database connection options can be passed through the my.cnf file. For example: [client] user = <username> password = <password> port = 3306 socket = /tmp/mysql.sock database = mmb

Or through the by passing the connection information when first instantiating an instance. For example:

    $associaton = UMLS::Association->new({"driver" => "mysql", 
                                  "database" => "$database", 
                                  "username" => "$username",  
                                  "password" => "$password", 
                                  "hostname" => "$hostname", 
                                  "socket"   => "$socket"}); 

  'driver'       -> Default value 'mysql'. This option specifies the Perl 
                    DBD driver that should be used to access the
                    database. This implies that the some other DBMS
                    system (such as PostgresSQL) could also be used,
                    as long as there exist Perl DBD drivers to
                    access the database.
  'database'     -> Default value 'CUI_BIGRAM'. This option specifies the name
                    of the database.
  'hostname'     -> Default value 'localhost'. The name or the IP address
                    of the machine on which the database server is
                    running.
  'socket'       -> Default value '/tmp/mysql.sock'. The socket on which 
                    the database server is using.
  'port'         -> The port number on which the database server accepts
                    connections.
  'username'     -> Username to use to connect to the database server. If
                    not provided, the module attempts to connect as an
                    anonymous user.
  'password'     -> Password for access to the database server. If not
                    provided, the module attempts to access the server
                    without a password.

More information is provided in the INSTALL file.

PARAMETERS

You can also pass other parameters which controls the functionality of the Association.pm module.

    $assoc = UMLS::Association->new({"measure"     => "lch"});

   'measure'    -> This modifies the association measure 

FUNCTION DESCRIPTIONS

exists

description:

 function to check if a concept ID exists in the database.

input:

 $concept <- string containing a cui

output:

 1 | 0    <- integers indicating if the cui exists

example:

 use UMLS::Association;
 my $umls = UMLS::Association->new(); 
         
 my $concept = "C0018563";      
 if($umls->exists($concept)) { 
    print "$concept exists\n";
 }

getFrequency

description:

 function returns the frequency of a given concept pair

input:

 $concept1 <- cui
 $concept2 <- cui

output:

$frequency <- number

example:

 use UMLS::Association;
 my $associator = UMLS::Association->new(); 
 my $freq = $mmb->getFrequency($concept1, $concept2)

calculateStatistic

description:

 function returns the given statistical score of a given concept pair

input:

 $concept1 <- cui
 $concept2 <- cui 
 $measure <- statistical measure
output:

$score <- float

example:

 use UMLS::Association;
 my $associator = UMLS::Association->new(); 
 my $stat = $associator->calculateStatistic($concept1, $concept2, $measure)

getParents

description:

 returns the parents of a concept - the relations that are considered parents 
 are predefined by the user in the configuration file. The default is the PAR 
 relation.

input:

 $concept <- string containing cui

output:

 $array   <- reference to an array containing a list of cuis

example:

 use UMLS::Association;
 my $umls = UMLS::Association->new(); 
 my $concept  = "C0018563";     
 my $parents  = $umls->getParents($concept);
 print "The parents of $concept are:\n";
 foreach my $parent (@{$parents}) { print "  $parent\n"; }

getChildren

description:

 returns the children of a concept - the relations that are considered children 
 are predefined by the user in the configuration file. The default is the CHD 
 relation.

input:

 $concept <- string containing cui

output:

 $array   <- reference to an array containing a list of cuis

example:

 use UMLS::Association;
 my $umls = UMLS::Association->new(); 
 my $concept  = "C0018563";     
 my $children = $umls->getChildren($concept);
 print "The children of $concept are:\n";
 foreach my $child (@{$children}) { print "  $child\n"; }

REFERENCING

If you write a paper that has used UMLS-Association in some way, we'd certainly be grateful if you sent us a copy. Currently we have no paper referrencing the package hopefully we will soon.

SEE ALSO

http://search.cpan.org/dist/UMLS-Association

AUTHOR

Bridget T McInnes <btmcinnes@vcu.edu>

COPYRIGHT

 Copyright (c) 2015
 Bridget T. McInnes, Virginia Commonwealth University
 btmcinnes at vcu.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.