Prototype code from PomBase for reading OBO files into a Chado database using PostgreSQL COPY.
Single command for loading (chobo_load)
Some OBO files aren't supported because not all edge cases are handled
Uses a lot of memory (500MB to read and store GO)
Currently ignores stanza tags that PomBase doesn't use (eg. "xref:")
The destination Chado database must contain:
an is_a relation
a CV named "synonym_type" containing all synonym types from the input OBO files
a CV named "cv_property_type" containing a term named "cv_version"
An example Chado DB containing these is here: https://github.com/pombase/pombase-legacy/blob/master/pombase-chado-base.dump?raw=true
Ontologies can't be re-loaded
To install from Git:
cpanm Dist::Zilla git clone https://github.com/pombase/chobo.git cd chobo dzil install
chobo_load test-db my_username my_password *.obo
Please report problems at: https://github.com/pombase/chobo/issues
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.