[ensembl-dev] Accessing a. thaliana data with the Compara API

[Andy Yates]

Hi James,

Homology between plants & non-plants is only available from the Ensembl Genomes websites and is provided by their pan-taxonomic compara resource. You can access this by modifying your script like so:

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_multiple_dbs(
  {
    -HOST => 'mysql.ebi.ac.uk',
    -PORT => 4157,
    -USER => 'anonymous',
  },
  {
    -HOST => 'ensembldb.ensembl.org',
    -USER => 'anonymous', 
  }
);

my $pan_compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('pan_homology', 'compara');

This command loads the databases from Ensembl Genomes' public sql server as well as Ensembl's server. It also allows the registry to resolve species clashes by using a first seen first used policy. Everything else should work as you currently expect it to do so

Hope this helps,

Andy

P.S. The list of species compared is available from http://plants.ensembl.org/info/docs/compara/homology_method.html#species

On 17 Nov 2011, at 17:18, James Blackshaw wrote:

> Hi,
> 
> I've been trying to access the database fro A. thaliana using the Compara API, but I can't get it to work using any of:
> fetch_by_name_assembly("arabidopsis _thaliana");
> fetch_by_registry_name("Arabidopsis thaliana");
> fetch_by_taxon_id("3702");
> 
> I can see it's possible to compare homology between non-plants and plants using the website, so I'm wondering why I can't do so with the API. I can confirm the script works comparing S.cerevisiae and H. sapiens homologs and S. cerevis and M. musculus ones.
> Script is attached.
> 
> Regards,
> James
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---
Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/