=head1 NAME

Bio::KEGG::API - Perl interface to KEGG API.

=head1 VERSION

Version 0.01

=head1 SYNOPSIS

    use Bio::KEGG::API;

    my $api = Bio::KEGG::API->new();
    say $api->database_info(database => 'hsa');

    ...

=head1 DESCRIPTION

This is a simple Perl interface to KEGG API system, please verify which databases are available before using the API.

=head1 METHODS

=head2 Database information

Displays the current statistics of a given database

options: database, oganism.

<database> = pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ | genomes | genes | ligand | kegg

<org> = KEGG organism code or T number

Examples:

	my @result = $api->database_info(database => 'kegg');
	my @result = $api->database_info(database => 'pathway');
	my @result = $api->database_info(database => 'hsa');



=head2 Entry list

Returns a list of entry identifiers and associated definition for a given database or a given set of database entries

options: database, oganism.

<database> = pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ | organism

<org> = KEGG organism code or T number

Examples:

	my @result = $api->entry_list(database => 'pathway');
	my @result = $api->entry_list(database => 'pathway', organism => 'hsa');
	my @result = $api->entry_list(organism => 'hsa');

=head2 Data Search

Finds entries with matching query keywords or other query data in a given database.

options: database, oganism, query.

<database> = pathway | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ | genes | ligand

<org> = KEGG organism code or T number

Example:

	my @result = $api->data_search(database => 'genes', query => 'kinase');
	my @result = $api->data_search(database => 'reaction', query => 'kinase');
	my @result = $api->data_search(database => 'pathway', organism => 'hsa', query => 'kinase');

=head2 ID Convertion

Convert KEGG identifiers to/from outside identifiers.

options: target, source.

For gene identifiers:
<kegg_db> = <org>
<org> = KEGG organism code or T number
<outside_db> = ncbi-gi | ncbi-geneid | uniprot

For chemical substance identifiers:
<kegg_db> = drug | compound | glycan
<outside_db> = pubchem | chebi

Examples:

	my @result = $api->id_convertion(target => 'eco', source => 'ncbi-geneid');
	my @result = $api->id_convertion(target => 'ncbi-geneid', source => 'eco');


=head2 Linked Entries

Find related entries by using database cross-references.

options: target, source.

<target_db> = <database>
<source_db> = <database>

<database> = pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ

Examples:

	my @result = $api->linked_entries(target => 'pathway', source => 'hsa');
	my @result = $api->linked_entries(target => 'genes', source => 'K00500');

=head1 AUTHOR

Felipe da Veiga Leprevost, C<< <leprevost at cpan.org> >>

=head1 BUGS

Please report any bugs or feature requests to C<bug-bio-kegg-api at rt.cpan.org>, or through
the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-KEGG-API>.  I will be notified, and then you'll
automatically be notified of progress on your bug as I make changes.




=head1 SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Bio::KEGG::API


You can also look for information at:

=over 4

=item * RT: CPAN's request tracker (report bugs here)

L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-KEGG-API>

=item * AnnoCPAN: Annotated CPAN documentation

L<http://annocpan.org/dist/Bio-KEGG-API>

=item * CPAN Ratings

L<http://cpanratings.perl.org/d/Bio-KEGG-API>

=item * Search CPAN

L<http://search.cpan.org/dist/Bio-KEGG-API/>

=back


=head1 ACKNOWLEDGEMENTS


=head1 LICENSE AND COPYRIGHT

Copyright 2014 Felipe da Veiga Leprevost.

This program is free software; you can redistribute it and/or modify it
under the terms of the the Artistic License (2.0). You may obtain a
copy of the full license at:

L<http://www.perlfoundation.org/artistic_license_2_0>

Any use, modification, and distribution of the Standard or Modified
Versions is governed by this Artistic License. By using, modifying or
distributing the Package, you accept this license. Do not use, modify,
or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made
by someone other than you, you are nevertheless required to ensure that
your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service
mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge
patent license to make, have made, use, offer to sell, sell, import and
otherwise transfer the Package with respect to any patent claims
licensable by the Copyright Holder that are necessarily infringed by the
Package. If you institute patent litigation (including a cross-claim or
counterclaim) against any party alleging that the Package constitutes
direct or contributory patent infringement, then this Artistic License
to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER
AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES.
THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY
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CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
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EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


