SemMed-Interface SYNOPSIS The SemMed-Interface is a suite of Perl modules that utilize path information present in the Semantic Medline Database in order to calculate the semantic association between two concepts in the UMLS. INSTALL To install these modules run: perl Makefile.PL make make test make install This will install the modules in the standard locations. 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 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. CONTENTS All the modules that will be installed in the Perl system directory are present in the '/lib' directory tree of the package. These include the semantic relatedness modules -- SemMed/Interface.pm SemMed/Interface/CUI.pm SemMed/Interface/Predicate.pm SemMed/Interface/GraphTraversal.pm SemMed/Interface/DataAccess.pm -- present in the lib/ subdirectory. All these modules, once installed in the Perl system directory, can be directly used by Perl programs. The package contains a utils/ directory that contain Perl utility programs. These utilities use the modules or provide some supporting functionality. nanob2b-example.pl -- simple example of using the module CONFIGURATION The SemMed-Interface requires access to the Semantic Medline Database. Please install this database onto your MySQL server and follow the set-up steps found in the INSTALL file. SOFTWARE COPYRIGHT AND LICENSE Copyright (C) 2016 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. REFERENCING This is where you would add the paper referencing the packge. For example: If you write a paper that has used SemMed-Interface in some way, we'd certainly be grateful if you sent us a copy and referenced: @inproceedings{McInnesPP09, title={{UMLS-Interface and NanoB2B-Example : Open Source Software for Measuring Paths and Semantic Similarity}}, author={McInnes, B.T. and Pedersen, T. and Pakhomov, S.V.}, booktitle={Proceedings of the American Medical Informatics Association (AMIA) Symposium}, year={2009}, month={November}, address={San Fransisco, CA} } This paper is also found in or REFERENCES 1 2 s SEE ALSO CONTACT US If you have any trouble installing and using SemMed-Interface, please contact us via the users mailing list : You can join this group by going to: You may also contact us directly if you prefer : Bridget T. McInnes: btmcinnes at vcu.edu AUTHORS Bridget T McInnes, University of Minnesota Twin Cities bthomson at cs.umn.edu Andriy Y. Mulyar DOCUMENTATION COPYRIGHT AND LICENSE Copyright (C) 2016 Bridget T. McInnes Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. Note: a copy of the GNU Free Documentation License is available on the web at: and is included in this distribution as FDL.txt.