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 <reference 1>
2 <reference 2> s
SEE ALSO
CONTACT US
If you have any trouble installing and using SemMed-Interface, please
contact us via the users mailing list :
<mailing list email>
You can join this group by going to:
<mailing list website>
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.