view release on metacpan or  search on metacpan

lib/AIIA/GMT.pm  view on Meta::CPAN

our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );

our @EXPORT = qw(pmid2entity text2entity);

our $VERSION = '0.05';

require XSLoader;
XSLoader::load('AIIA::GMT', $VERSION);

# Preloaded methods go here.

# Autoload methods go after =cut, and are processed by the autosplit program.
my $SERVER_URL = 'http://bcsp1.iis.sinica.edu.tw:8080/aiiagmt/XmlRpcServlet';

sub pmid2entity {
    my $id = shift;
    die "Usage: &pmid2entity(\'PubMed Article ID\');\n" if ($id !~ /^\d+$/);
    return &submit($id);
}

sub text2entity {
    my $txt = shift;
    $txt =~ s/\n//g;
    my $num;
    map {$num++;} split(/\s/, $txt);
    die "Usage: &text2entity(\'less than 3000 words\');\n" if ($num > 3000);
    return &submit($txt);
}

sub submit {
    my @args = (shift);
    my $client = Frontier::Client->new(url => $SERVER_URL, debug => 0);
    my $ret = $client->call('Annotator.getAnnotation', @args);
    my @rep;
    map {push @rep, $_->{'offset'} . "\t" . $_->{'mention'};} @{$ret->{'mentions'}};
    @rep = sort @rep;
    return \@rep;
}

1;
__END__
# Below is stub documentation for your module. You'd better edit it!

=head1 NAME

AIIA::GMT - a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles

=head1 SYNOPSIS

 use YAML;
 use AIIA::GMT;

 $result = &text2entity('less than 3000 words');
 print Dump $result;


=head1 DESCRIPTION

AIIA::GMT is a XML-RPC client of a web-service server, AIIA gene mention tagger, which provides the service to recognize named entities in the biomedical articles. 

AIIA gene mention tagger, developed by Adaptive Internet Intelligent Agents Lab, Institute of Information Science, Academia Sinica, Taiwan and I-Fang Chung's Lab, Institute of Bioinformatics, National Yang-Ming University, Taiwan, is a named entity r...

This module is developed to help those who want to use this remote service with XML-RPC, rather than with its web interface. Finally, this module and service is released under a GPLv3 License. You're free to use it for both academic or personal use.

=head1 METHODS

=over 4

=item text2entity('less than 3000 words');

Return a ARRAY reference which contains all of the entities recognized from your input with its position information, for example: '20 seperated-by-tab human protein-tyrosine-phosphatase'.

=back

=item pmid2entity('PubMed Article ID');

Return a ARRAY reference which contains all of the entities recognized from your input with its position information, for example: '20 seperated-by-tab human protein-tyrosine-phosphatase'.

=back

=head1 REQUIREMENT

Frontier::Client

=head1 BUGS

Hopefully none.


=head1 SEE ALSO

http://aiia.iis.sinca.edu.tw/biocreative2.htm

=head1 AUTHOR

Cheng-Ju Kuo
cju.kuo@gmail.com

=head1 COPYRIGHT AND LICENSE


Copyright (c) 2008 by Cheng-Ju Kuo and the Institute of Information
Science, Academia Sinica, Taipei, Taiwan.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.8 or,
at your option, any later version of Perl 5 you may have available.


=cut