[ensembl-dev] $NCBI_taxon_adaptor->fetch_node_by_name() broken in EnsemblGenomes 7

[Giuseppe G.]

Hi Andy, thanks for that. I checked and the data is there now.

Thanks for the suggestion related to name/taxon_id mapping.

As a general rule for fetch_node_by_name(), what is the most correct way 
to deal with ensembl genome strains having complex names?

eg:

  $NCBI_taxon_adaptor->fetch_node_by_name('Caenorhabditis japonica DF5081')

is this correct?


Giuseppe


On 14/12/10 13:39, Andy Yates wrote:
> Hi Giuseppe,
>
> It seems that the taxonomy tables were missed out of the load for some unknown reason. I have gone&  populated the servers and am updating the MySQL dumps we provide so for anyone who is providing mirrors of this data you will have to update ncbi_taxa_name and ncbi_taxa_node.
>
> Your method should now work. However as an aside if you are looking for homologies linked to Plasmodium falciparum please watch out for the naming used in the Taxonomy as well as the taxonomy identifier linked to the genome db. In this situation our falciparum is linked to taxon 36329 which has the name Plasmodium falciparum 3D7. Using Plasmodium falciparum will return back 5833&  will not link to any valid GenomeDB.
>
> Reagrds,
>
> Andy
>
> On 14 Dec 2010, at 13:16, Giuseppe G. wrote:
>
>> Hi,
>>
>> There is a problem with $NCBI_taxon_adaptor->fetch_node_by_name() in release 60.
>>
>>
>> STEPS TO REPRODUCE THE BUG
>> --------------------------
>>
>> 1) get a registry by doing
>>           $registry->load_registry_from_multiple_dbs(
>>           {    #VERTEBRATES
>>                   -host       =>  'ensembldb.ensembl.org',
>>                   -user       =>  'anonymous',
>>                   -verbose    =>  1
>>               },
>>           {     #EnsemblGenomes
>>                      -host    =>  'mysql.ebi.ac.uk',
>>                      -user    =>  'anonymous',
>>                      -port    =>  4157,
>>                      -verbose =>  1
>>               }
>>           );
>>
>> -this step is successful
>>
>> 2) get a taxon adaptor using pan_homology by doing
>>
>> my $NCBI_taxon_adaptor = $registry->get_adaptor('pan_homology', 'compara', "NCBITaxon");
>>
>> -this step is successful
>>
>> 3) get a taxon id from the species name by using fetch_node_by_name()
>>
>> my $source_taxon = $NCBI_taxon_adaptor->fetch_node_by_name($source_organism);
>>
>> where for $source_organism I tried 'Plasmodium falciparum', 'plasmodium_falciparum', 'drosophila_melanogaster', ecc ecc
>>
>> -source_taxon is undefined
>> -----------------------------
>>
>>
>> ADDITIONAL INFORMATION
>> ----------------------
>> -This worked  in release 59/6
>> -The method still works when the registry is connecting to vertebrate compara
>>
>>
>> Any help is particularly appreciated because a core feature of my scripts relies on this adaptor and its seamless functionality (as per API docs) across Multi, ensemblgenomes and pan compara.
>>
>>
>> Thanks a lot in advance.
>>
>> Giuseppe
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
>>
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>

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The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336.