Code for loading OBO files into a Chado database using COPY (prototype)
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README.pod

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"

    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

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.