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. 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(); 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). umls-association-runDataSet.pl -- outputs the association scores of an entire dataset (such as minimayo UMNSRS, etc.) CUICollector.pl -- script to create the CUI_BIGRAM database from the Metamapped Medline Baseline The package also contains a Apache Hadoop MapReduce java implementation of CUICollector.pl named CUICollectorMapReduce in the '/Hadoop' directory. Refer to the README file in the '/Hadoop' directory for installation and running instructions. 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 : Sam Henry: henryst at vcu.edu Bridget T. McInnes: btmcinnes at vcu.edu SOFTWARE COPYRIGHT AND LICENSE Copyright (C) 2018 Sam Henry 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.