=encoding utf8

=head1 PomBase-Chobo

Prototype code from PomBase for reading OBO files into a Chado
database using PostgreSQL COPY.

L<https://github.com/pombase/chobo>

=head2 Build status

=for html <a href="https://travis-ci.org/pombase/chobo"><img src="https://travis-ci.org/pombase/chobo.svg?branch=master"></a>

=head1 Features

=over

=item * Fast

=item * Few dependencies

=item * Single command for loading (chobo_load)

=back

=head1 Current problems

=over

=item * Some OBO files aren't supported because not all edge cases are handled

=item * Uses a lot of memory (500MB to read and store GO)

=item * Currently ignores stanza tags that PomBase doesn't use (eg. "xref:")

=item * The destination Chado database must contain:

=over

=item * an is_a relation

=item * a CV named "synonym_type" containing all synonym types from the input OBO files

=item * a CV named "cv_property_type" containing a term named "cv_version"

=back

An example Chado DB containing these is here:
L<https://github.com/pombase/pombase-legacy/blob/master/pombase-chado-base.dump?raw=true>

=item * Ontologies can't be re-loaded

=back


=head2 Installation

From CPAN:

 cpan PomBase::Chobo

or

 cpanm PomBase::Chobo

To install from Git:

 cpanm Dist::Zilla
 git clone https://github.com/pombase/chobo.git
 cd chobo
 dzil install


=head2 Example usage

C<chobo_load test-db my_username my_password *.obo>


=head2 Support

Please report problems at: L<https://github.com/pombase/chobo/issues>


=head2 License and Copyright

Copyright (C) 2016 Kim Rutherford

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.
