[ensembl-dev] Variant external references: MIM_MORBID

[Guillermo Marco Puche]

Hello Will,

Code in example [1] is working perfectly for me since I would like to 
get the phenotype features related to the variant and not to the gene. 
However I don't how to get $var ( Variation::Variation) from inside VEP 
plugin.
I'm trying with $self->{variant} but I'm getting always an "undef" value.

Regards,
Guillermo.

On 04/04/16 14:50, Will McLaren wrote:
> Hi Guillermo,
>
> The data you refer to has been retracted from the Ensembl core 
> database while we resolve some issues with external reference mapping 
> between Ensembl and MIM.
>
> You should be able to access the same annotations via the variation 
> API, using phenotype features. [1] shows an example fetching via a 
> variation object, but you can also query by gene [2].
>
> Hope that helps
>
> Will McLaren
> Ensembl Variation
>
> [1] 
> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
> [2] 
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72
>
> On 4 April 2016 at 11:46, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Dear devs,
>
>     Up to VEP version 83 I was using the following code in a plugin to
>     retrieve gene OMIM related information.
>
>         my @db_entries = @{$gene->get_all_DBEntries()};
>         foreach my $db_entry(@db_entries){
>             if ($db_entry->dbname eq "MIM_GENE"){
>                 $mim_id = $db_entry->primary_id;
>             }
>             if ($db_entry->dbname eq "MIM_MORBID"){
>                 push(@mim_morbid_ids, $db_entry->primary_id);
>             }
>         }
>
>     However since I've updated to VEP 84 I don't get any MIM_MORBID
>     db_entry associated to any gene. Has this been removed or changed
>     location?
>
>     Best regards,
>     Guillermo.
>
>
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