Re: [GUSDEV] how do I load GO terms

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

> 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-acety
l-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1
->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}as
paragine) 2-beta-D-xylosyltransferase activity, 1, 1 at
/core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.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