=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.