Re: [GUSDEV] how do I load GO terms

[Isabelle P. <isa...@sb...>]

I rejoiced too soon....

There is a problem with the GO plugin, after the GO terms have been
loaded, I am getting:

Transitive closure (length 4000418): added 0 edges
DBD::Pg::st execute failed: ERROR:  prepared statement "dbdpg_2" does
not exist

Isabelle


> -----Original Message-----
> From: Isabelle Phan 
> Sent: Monday, December 15, 2008 10:29 AM
> To: 'Elisabetta Manduchi'; Jian Lu
> Cc: gus...@li...
> Subject: RE: [GUSDEV] how do I load GO terms
> 
> > This command will no longer work with the new updates to the plugin 
> > applied 2 days ago and reflected in the plugin John 
> Brestelli sent to 
> > Isabelle (also available in the gus svn trunk). The new 
> > version takes in just one .obo file.
> 
> Thanks Elisabetta.
> 
> The new plugin works great. There is an minor issue with a 
> very long GO synonym that required a change in the 
> SRes.GOSynonym table. The problem might be specific for 
> Postgres, where the SRes.GOSynonym.TEXT column type is set by 
> default to varchar(255).
> 
> This needs to be increased to accommodate the GO synonym to 
> avoid this error:
> 
> DBD::Pg::st execute failed: ERROR:  value too long for type 
> character varying(255)
> 
> ERROR:
> 
>  SQL ERROR!! involving
> 
>     INSERT INTO SRes.GOSynonym (  
> external_database_release_id, source_id, go_term_id, 
> group_write, other_read, group_read, go_synonym_id, 
> user_read, row_user_id, modification_date, other_write, 
> row_alg_invocation_id, row_project_id, text, row_group_id, 
> user_write )
>     VALUES   (  ?, null, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, 
> ?, ?, ? )
>  Values: 170, 3222, 1, 1, 1, 4048, 1, 1, 0, 16, 1, 
> UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted 
> mannose of 
> N4-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3
)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]->
beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-a
> cetyl-beta-D-glucosaminyl}asparagine) 
> 2-beta-D-xylosyltransferase activity, 1, 1 at 
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbH
andle.pm line 166
> 
> Increasing the column size solves this issue, e.g. for Postgres:
> 
> alter table GOSynonym alter column text type varchar(1000);
> 
> Thanks,
> 
> Isabelle
> 
> --
> Isabelle Phan, DPhil
> Seattle Biomedical Research Institute
> +1(206)256 7113
>  
>