[ensembl-dev] Variant external references: MIM_MORBID

[Will McLaren]

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The data you refer to has been retracted from the Ensembl core database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> 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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