[Gmod-help] Alternatives to DBIx::DBStag for loading ontologies

[Scott Cain]

Hi James,

There was a report of this just a few days ago on the schema mailing
list.  It appears that a new release of DBIx::DBSchema breaks
DBIx::DBStag.  Try going to cpan and getting an older version to see
if it fixes it.

Scott

On Thursday, January 21, 2010, James Estill <jestill at plantbio.uga.edu> wrote:
> I am to the point where I am attempting to load ontologies into my CHADO installation.
>
> Using 'make ontologies' gives
>
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 2
>
> I can download the ontologies and convert to xml manually, but it looks like DBIx::DBStag is broken in some way, when I do
>
> stag-storenode.pl -d 'dbi:Pg:dbname=chado_test;host=localhost;port=5432' --user myname --password mypassword ro.oboxml
>
> I get the error message
>
> Cannot quote a reference at /Library/Perl/5.8.8/DBIx/DBStag.pm line 3736.
>
> Is there an alternative way to load ontologies into the database that do not rely on DBIx::DBStag? I installed DBIx::DBStag the "manual" way and it is apparently not doing its job.
>
> -- Jamie Estill
> -- jestill at uga.edu
> -- http://jestill.myweb.uga.edu
> -- http://www.epernicus.com/people/jestill
>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research