NAME UMLS-Association README SYNOPSIS This package consists of Perl modules along with supporting Perl programs that calculate the association between CUI pairs using frequency information from the Metamapped Medline baseline. UMLS::Association requires the Text::NSP module to calculate the association measures. Text::NSP currently implements the following measures for bigrams: UMLS::Association requires the UMLS::Interface module to access the Unified Medical Language System (UMLS) to map input terms to Concept Unique Identifiers (CUIs) and provide additional information. The following sections describe the organization of this software package and how to use it. A few typical examples are given to help clearly understand the usage of the modules and the supporting utilities. 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/programs 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. DATABASE SETUP UMLS-Association assumes that the CUI bigrams extracted from the Metamapped Medline baseline is present as a mysql database. The names of these databases can be passed as configuration options at initialization. However, if the names of the database is not provided at initialization, then default values are used -- the database is called CUI_BIGRAMS and contains four tables: 1. N_11 2. N_1P 3. N_P1 4. N_PP Direction on installing the CUI_BIGRAMS database is in the INSTALL file. All other tables in the databases will be ignored, and any of these tables missing would raise an error. The mysql server can be on the same machine as the module or could be on a remotely accessible machine. The location of the server can be provided during initialization of the module. INITIALIZING THE MODULE To create an instance of the UMLS-Association object, using default values for all configuration options: use UMLS::Association; my $association = UMLS::Association->new(); The following configuration options are also provided though: '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_BIGRAMS'. This option specifies the name UMLS-Association 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. These are passed through a hash. For example: my %options = (); $options{'config'} = $config; $options{'database'} = 'CUI_BIGRAM_V1'; my $association = UMLS::Association->new(\%options); Keep in mind that the database configuration options can be included in the MySQL my.cnf file. This is preferable. The directions for this are in the INSTALL file. CONTENTS All the modules that will be installed in the Perl system directory are present in the '/lib' directory tree of the package. The package contains a utils/ directory that contain Perl utility programs. These utilities use the modules or provide some supporting functionality. umls-association.pl -- returns the association score of two terms or UMLS CUIs given a specified measure (and view of the UMLS). CUICollector.pl -- script to create the CUI_BIGRAM database from the Metamapped Medline Baseline 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. CONTACT US If you have any trouble installing and using UMLS-Interface, please contact us via the users mailing list : umls-association@yahoogroups.com You can join this group by going to: You may also contact us directly if you prefer : Bridget T. McInnes: btmcinnes at vcu.edu SOFTWARE COPYRIGHT AND LICENSE Copyright (C) 2015 Bridget T McInnes This suite of programs 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. Note: The text of the GNU General Public License is provided in the file 'GPL.txt' that you should have received with this distribution.