[ensembl-dev] [EnsemblGenomes] $NCBI_taxon_adaptor->fetch_node_by_name() not working for some divisions

[Andy Yates]

Hi Giuseppe,

Looks like the population of the taxonomy tables slipped through the cracks in release 5 & since fungi's compara 6 run was a patch of 5 the problem has persisted. I'm populating those tables will be populated on our public MySQL server.

I'm very sorry that this happened as it is an error on my part.

As to getting the scientific name of a species in Ensembl Genomes you can always ask the meta container from a core DBAdaptor for it e.g.

Bio::EnsEMBL::Registry->load_registry_from_database(-HOST => 'mysql.ebi.ac.uk', -PORT=>4157, -USER=>'anonymous');
my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('plants','compara');

my $genome_db = $compara_dba->get_GenomeDBAdaptor()->fetch_by_name_assembly('aspergillus_fumigatus');
# You can also use taxon id
# my $genome_db = $compara_dba->get_GenomeDBAdaptor()->fetch_by_taxon_id(330879);
$genome_db->db_adaptor()->get_MetaContainer()->get_scientific_name();

You can also request the NCBITaxon object from the GenomeDB object e.g.

$genome_db->get_taxon()->get_tagvalue('scientific name');

But to answer you original query you should see a marked improvement. These files will also be updated on the FTP site within the next 10 minutes

Regards,

Andy

On 25 Sep 2010, at 23:35, Giuseppe Gallone wrote:

> Hi thanks for your reply. Unfortunately the inconsistency is there when
> I use the pan taxonomic db as well. If a taxon object is not returned
> for a scientific name in its db, it won't be returned if the pan
> homology db is set instead.
> 
> Regards
> G.
> 
> On 25/09/10 14:21, Daniel Hughes wrote:
>> Perhaps use pan compara and not division specific DBs:
>> 
>> mysql> use ensembl_compara_pan_homology_6_59
>> Database changed
>> mysql> select * from ncbi_taxa_name where name like 'Aspergillus
>> nidulans' \G
>> *************************** 1. row ***************************
>>   taxon_id: 162425
>>       name: Aspergillus nidulans
>> name_class: genbank anamorph
>> 1 row in set (0.30 sec)
>> 
>> mysql> use ensembl_compara_fungi_6_59
>> Database changed
>> mysql> select * from ncbi_taxa_node;
>> Empty set (0.04 sec)
>> 
>> dan.
>> 
>> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>> -------------------------------------------------------------------------------------
>> dsth at cantab.net <mailto:dsth at cantab.net>
>> dsth at cpan.org <mailto:dsth at cpan.org>
>> 
>> 
>> 2010/9/25 Daniel Hughes <dsth at ebi.ac.uk <mailto:dsth at ebi.ac.uk>>
>> 
>>    Not very familiar with Compara, but perhaps:
>> 
>>    mysql> use aspergillus_nidulans_core_6_59_6e
>>    Database changed
>>    mysql> select meta_value from meta where meta_key =
>>    'species.taxonomy_id' \G
>>    *************************** 1. row ***************************
>>    meta_value: 162425
>>    1 row in set (0.09 sec)
>> 
>>    mysql> use ensembl_compara_metazoa_6_59
>>    Database changed
>>    mysql> select * from ncbi_taxa_name where name like 'Aspergillus
>>    nidulans' \G
>>    *************************** 1. row ***************************
>>       taxon_id: 162425
>>           name: Aspergillus nidulans
>>    name_class: genbank anamorph
>>    1 row in set (0.10 sec)
>> 
>>    mysql> use ensembl_compara_fungi_6_59
>>    Database changed
>>    mysql> select * from ncbi_taxa_name where name like 'Aspergillus
>>    nidulans' \G
>>    Empty set (0.12 sec)
>> 
>>    Dan
>> 
>>    Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>>    -------------------------------------------------------------------------------------
>>    dsth at cantab.net <mailto:dsth at cantab.net>
>>    dsth at cpan.org <mailto:dsth at cpan.org>
>> 
>> 
> 
> -- 
> 
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-- 
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/