Megan Charity
and 1 contributors

NAME

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

DESCRIPTION

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.

SYNOPSIS

add synopsis

ABSTRACT

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.

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/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.

FUNCTION DESCRIPTIONS

NAME

NanoB2B-NNER-PM::NER - The main file that runs all of the processes for NER

DESCRIPTION

This package turns nanoparticle texts into ARFF files and WEKA accuracy files based on the nanoparticle characteristics found from pre-annotated articles

VERSION

Version 0.08

INITIALIZING THE MODULE

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);

nerByFile

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();

nerByMethod

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 method until all the files have been processed

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->nerByMethod();

metaSet

description:

  Runs a set of files through metamap

input:

 None

output:

 Metamap files for every file found in the directory specified in the constructor parameters

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->metaSet();

arffSet

description:

  Turns a set of files into ARFF files based on the features specificied in the constructor parameters

input:

 None

output:

 ARFF file sets for every file found in the directory specified in the constructor parameters

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->arffSet();

wekaSet

description:

  Runs a set of ARFF files through WEKA

input:

 None

output:

 WEKA files for every file found in the directory specified in the constructor parameters

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->wekaSet();

avgSet

description:

  Averages together a set of WEKA files

input:

 None

output:

 Average accuracy files for every file found in the directory specified in the constructor parameters

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->avgSet();

SEE ALSO

AUTHOR

Megan Charity <charityml@vcu.edu> Bridget T McInnes <btmcinnes@vcu.edu>

COPYRIGHT

 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

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Around line 60:

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