NanoB2B::NER - turns labeled text lines into ARFF files based on specified features that are extracted using MetaMap and runs through WEKA to average the results
This package turns labeled text lines into ARFF files based on specified features that are extracted using MetaMap and runs through WEKA to average the results
For more information please see the NanoB2B::NER.pm documentation.
add synopsis
There is a critical need to automatically extract and synthesize knowledge and trends in nanotechnology research from an exponentially increasing body of literature. Engineered nanomaterials (ENMs), such as nanomedicines, are continuously being discovered and Natural Language Processing approaches can semi‐automate the cataloging of ENMs and their unique physico‐chemical properties; automatically aggregate studies on their exposure and hazards; and link the physicochemical properties to the measured effects. The goal of this project is to develop a nanomedicine entity extraction system to automatically identify nanomedicine physico-characteristics, exposure and biological effects.
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/milk
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.
NanoB2B-NNER-PM::NER - The main file that runs all of the processes for NER
This package turns nanoparticle texts into ARFF files and WEKA accuracy files based on the nanoparticle characteristics found from pre-annotated articles
Version 1.01
To create an instance of the ner module, using default values for all configuration options:
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params);
description:
Runs the files specified in the parameters program_dir metamaps all the files, arffs all the files, wekas all the files, and averages all the files This NER method doesn't move on to the next file until all the methods have been used
input:
None
output:
Metamap files, ARFF file sets, Weka file sets, and Averaged Accuracy files
example:
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->nerByFile();
Runs the files specified in the parameters program_dir metamaps all the files, arffs all the files, wekas all the files, and averages all the files This NER method doesn't move on to the next method until all the files have been processed
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->nerByMethod();
Runs a set of files through metamap
Metamap files for every file found in the directory specified in the constructor parameters
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->metaSet();
Turns a set of files into ARFF files based on the features specificied in the constructor parameters
ARFF file sets for every file found in the directory specified in the constructor parameters
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->arffSet();
Runs a set of ARFF files through WEKA
WEKA files for every file found in the directory specified in the constructor parameters
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->wekaSet();
Creates WEKA models from the training ARFF files
WEKA model files for every file with training ARFF files
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->modelSet();
Averages together a set of WEKA files
Average accuracy files for every file found in the directory specified in the constructor parameters
use NanoB2B::NER; my %params = (); $params{'dir'} = "my_directory"; $params{'features'} = "ortho morph text pos cui sem"; my $nner = new NanoB2B::NER(\%params); $nner->avgSet();
Megan Charity <charityml@vcu.edu> Bridget T McInnes <btmcinnes@vcu.edu>
Copyright (c) 2017 Megan Charity, Virginia Commonwealth University charityml at vcu.edu 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.
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'semi‐automate'. Assuming UTF-8
To install NanoB2B::NER, copy and paste the appropriate command in to your terminal.
cpanm
cpanm NanoB2B::NER
CPAN shell
perl -MCPAN -e shell install NanoB2B::NER
For more information on module installation, please visit the detailed CPAN module installation guide.