[ensembl-dev] Mouse genes discrepancies

[Dan Sheppard]

Hi,

Thanks for your queries, and sorry for the delay getting back to you.

Concerning your first query, -- on the name 'B930076A02' in e!75 mouse, 
-- the synonym actually being matched is B930076A02Rik. Search considers 
this a plausible match to your query.

If you wish, you can use %-wildcards with fetch_all_by_external_name(), 
which instructs the API to return records by prefix. For example:

my $genes = $gene_adaptor->fetch_all_by_external_name('B930076A02%');

Concerning your second query, -- on LOC232400 and LOC241525, -- we do 
have some LOC% synonyms from a number of sources (EntrezGene, Uniprot, 
RFAM, RGD, ...). In this case the NCBI URLs are not overly informative, 
so it's hard to say whether they should be present or not, but most 
likely either we don't have the associated gene or the synonym is 
deprecated.

Hope this helps. Do let us know if you have any further queries about this.

All the best,
Dan.

On 19/06/14 12:58, Genomeo Dev wrote:
> Hi,
>
> I wanted to dig out some mouse genes from Ensembl using old symbols of
> which I don't know the source. I am getting this discrepancy:
>
> 1) Between Ensembl website and API (75):
>
> B930076A02
>
> The website found this:
>
> http://www.ensembl.org/Multi/Search/Results?q=B930076A02;site=ensembl
>
>
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
> -host => 'ensembldb.ensembl.org <http://ensembldb.ensembl.org>',
> -user => 'anonymous'
> );
>
> my $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor( "mouse", "core",
> "gene" );
> my $genes = $gene_adaptor->fetch_all_by_external_name('B930076A02');
>
> This code found nothing.
>
> 2) Ensmebl does not recognise these names while NCBI does:
>
> LOC232400
> LOC241525
>
> http://www.ncbi.nlm.nih.gov/gene/?term=LOC232400
> http://www.ncbi.nlm.nih.gov/gene/?term=LOC241525
>
> Thanks,
>
> --
> G.