PomBase-Chobo

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

https://github.com/pombase/chobo

Build status

Features

• Fast

• Few dependencies

• Single command for loading (chobo_load)

Current problems

• 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"

  • a CV named "cvterm_property_type" containing terms named "replaced_by" and "consider"

  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

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

Example usage

chobo_load test-db my_username my_password *.obo

Support

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

License and Copyright

Copyright (C) 2013-2022 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.