[ensembl-dev] Can't get GO adapter with latest ensembl plants release

[Andy Yates]

Hi Simon,

We're investigating the reason behind this now. I believe it has something to do with the naming of the ontology database in this release. In previous releases we had called it ensembl_ontology_release e.g. ensembl_ontology_59. In this release we changed it to ensemblgenomes_ontology_60 which will mean the registry will not pick up on the name. For the moment you can code around this with an explicit link to that databases:

use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;

my $ontology_dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
-SPECIES => 'Multi',
-GROUP => 'ontology',
-HOST => 'mysql.ebi.ac.uk',
-PORT => 4157,
-USER => 'anonymous',
-DBNAME => 'ensemblgenomes_ontology_60'
);

The by-product of this creation is that the DBAdaptor will go into the Registry under the multi with the group ontology so your original code post will still work.

We will have a proper fix for it soon though

Andy

On 2 Dec 2010, at 10:31, simon andrews (BI) wrote:

> I'm trying to get some information out of the new TAIR10 release in ensembl plants.  Having just updated my ensembl plants API code today (to ensembl-genomes-7-60), I now can't get a GO adapter using:
> 
> $registry -> get_adaptor('Multi','Ontology','GOTerm')
> 
> This same call worked fine with the previous release (6-59)
> 
> was there a change to the syntax, or are there some parts of the new release which haven't transferred over yet?
> 
> Thanks
> 
> Simon.
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/