[Gmod-help] CHADO Ontologies Install

[Scott Cain]

Hi Todd,

The files for the 0.003 release of Chado have been removed from the
SourceForge site because they are very out of date, and cause people
more problems that they help; you've just run into the first one.  Other
problems include a lack of support for OBO formatted ontology files
(what the sequence, gene and plant ontologies all use), as well as very
finicky requirements about BioPerl.

I am furiously at work getting a Chado 1.0 release ready, but in the
meantime, I would suggest that you use the Chado schema and related
tools that are in the development code repository.  See

  http://www.gmod.org/wiki/index.php/Chado_-_Getting_Started#Chado_From_CVS

for more information.

Scott

On Fri, 2008-02-08 at 17:25 -0500, todd.moughamer at syngenta.com wrote:
> I am running into a error during the manual ontology installation that
> manifests pretty much identical to the error described in #1 on the
> chado 0.003 FAQ
> (http://gmod.sourceforge.net/schema/gmod-0.003-faq.shtml). The fix
> being to apply a patch to Class::DB::Pg. I could not find the patch in
> the source tree or on sourceforge as described in
> http://sourceforge.net/project/shownotes.php?release_id=340674 . Is
> the patch still necessary and if so is it available?
> 
> The specific command and error follow:
> 
> gmod_load_ontology.pl ./tmp/manual_dwnld/ro.obo 
> DBD::Pg::st execute failed: ERROR:  more than one row returned by a
> subquery used as an expression 
>  [for Statement "SELECT indkey FROM pg_catalog.pg_index 
> WHERE indisprimary=true AND indrelid=( 
> SELECT oid FROM pg_catalog.pg_class 
> WHERE relname = ?) 
> " with ParamValues: 1='db']
> at /usr/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52. 
> Compilation failed in require at lib/Chado/LoadDBI.pm line 5. 
> BEGIN failed--compilation aborted at lib/Chado/LoadDBI.pm line 5. 
> Compilation failed in require at /usr/bin/gmod_load_ontology.pl line
> 10. 
> BEGIN failed--compilation aborted at /usr/bin/gmod_load_ontology.pl
> line 10.
> 
> Thanks,
> 
> Todd
> 
> 
> Todd Moughamer 
> 
> Bioinformatics Consultancy & Training Group
> 
> Syngenta Biotechnology, Inc.
> 
> 3054 Cornwallis Road, 1243.E
> 
> Research Triangle Park, NC 27709-2257
> 
> Tel: 919-597-3078
> 
> Email: todd.moughamer at syngenta.com 
> www.syngenta.com
> 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory