[ensembl-dev] Variant external references: MIM_MORBID

Will McLaren wm2 at ebi.ac.uk
Tue Apr 5 10:39:17 BST 2016


Hello,

It looks like we don't have the MIM number recorded for variant-phenotype
associations, only for gene-phenotype associations.

We can look into importing this data for Ensembl's next release.

Regards

Will

On 5 April 2016 at 10:13, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

> Hi Will,
>
> I had already tried that:
>
> for my $key (keys $pf->get_all_attributes) {
>     print "$key\t$pf->get_all_attributes{$key}\n";
> }
>
> associated_gene
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{associated_gene}
> variation_names
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{variation_names}
> risk_allele
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{risk_allele}
>
> associated_gene:ISG15    risk_allele:0003    variation_names:rs786201005
>
> I don't get why get_all_atributes() method only returns, associated_gene,
> variation_names and risk_allele. As I wrote on previous mail I'm able to
> retrieve the external_reference ($pf->external_id) that returns the MIM ID
> (gene) related to this phenotype and not the Phenotype MIM Number.
>
> Will could you please check if you only get this three attributes for this
> specific variant when using $pf->get_all_attributes? Could this be a
> problem related to API or my API local installation?
>
> Regards,
> Guillermo.
>
>
> On 05/04/16 10:45, Will McLaren wrote:
>
> Hi again,
>
> You can retrieve the MIM ID via fetching the attributes of the phenotype
> feature, use get_all_attributes()
>
>
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html#a7dfa8e10e74e9ede4d87257823ce564e
>
> Will
>
> On 5 April 2016 at 08:23, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>> Hi Will,
>>
>> Unfortunately I can't use the Phentoype.pm plugin since I can't support
>> VEP annotation in JSON format at this moment.
>> --check_existing and --check_alleles are enabled, for the feature types
>> I'm using Transcript (I don't know if this can be the cause of the problem
>> of not being able to retrieve phenotype ids):
>>
>> sub feature_types {
>>     return ['Transcript'];
>> }
>>
>> However with your previous answer and and old e-mail I've accomplished to
>> retrieve the phenotypes:
>>
>>     foreach my $known_var(@{$vf->{existing} || []}) {
>>         foreach my
>> $pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}){
>>             @phenotype_descriptions = ();
>>             if ($pf->source_name =~ /omim/i){
>>                 #do stuff with the omim phentoype
>>                 push(@phenotype_descriptions, $pf->phenotype->description)
>>                 #trying to retrieve the omim phenotype id however i can't
>> find a way to
>>                 print $pf->external_id,"\n";
>>                 #however i can get the external reference (OMIM gene id)
>>                 print $pf->external_reference,"\n";
>>                 }
>>             }
>>
>> Only problem left I've got is that I can't retrieve the phenotype id
>> itself (MIM morbid id) in this case it should be 616126
>> <http://www.omim.org/entry/616126>.
>> Phentoype description and external reference are working:
>>
>>    - The phentoype description: $pf->phenotype->description (ie:
>>    IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION)
>>    - The phentoype external reference (OMIM gene id) related to this
>>    phenotype: $pf->external_reference (ie: MIM:147571)
>>
>> For the ClinVar phentoypes I was able to get the ClinVar id with
>> $pf->external_id however I get always an *undef* value for OMIM
>> phenotypes.
>>
>> The VCF input record I'm using for testing is the following one extracted
>> from latest GRCh38:
>>
>>    - 1    1014143    rs786201005    C    T    .    .
>>    dbSNP_146;TSA=SNV;E_Phenotype_or_Disease;CLIN_pathogenic;AA=C
>>
>> Regards,
>> Guillermo.
>>
>>
>> On 04/04/16 17:43, Will McLaren wrote:
>>
>> Hi Guillermo,
>>
>> It may be that what you are trying to do is already encapsulated in our
>> (new to release 84) Phenotypes plugin:
>>
>> https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm
>>
>> It has the benefit of reducing DB lookups to a single download the first
>> time you run it. It's fully configurable to retrieve phenotypes associated
>> with whatever feature types (variants, genes etc) you like, as well as
>> limiting by source. One caveat is that to get rich data from it you must
>> currently use JSON output.
>>
>> If you wish to continue looking up by variant in your own plugin, you
>> should enable co-located variant lookup with --check_existing (add
>> --check_alleles to match alleles to your input variants), then you can use
>> fetch_all_by_object_id() [1] using the rsIDs in
>> $tva->variation_feature->{existing}, something like:
>>
>> sub run {
>>   my ($self, $tva) = @_;
>>
>>   ### get phenotype feature adaptor $pfa somehow
>>
>>   foreach my $id(map {$_->{variation_name}}
>> @{$tva->variation_feature->{existing} || []}) {
>>     my $pfs = $pfa->fetch_all_by_object_id($id);
>>
>>     ### do something with the phenotype features returned
>>   }
>> }
>>
>> Cheers
>>
>> Will
>>
>> [1]
>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c
>>
>> On 4 April 2016 at 16:12, Guillermo Marco Puche <
>> <guillermo.marco at sistemasgenomicos.com>
>> guillermo.marco at sistemasgenomicos.com> wrote:
>>
>>> 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  $self->{variant} but I'm getting always an "undef"
>>> value.
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
>>> On 04/04/16 14:50, Will McLaren wrote:
>>>
>>> Hi Guillermo,
>>>
>>> The data you refer to has been retracted from the Ensembl core database
>>> while we resolve some issues with external reference mapping between
>>> Ensembl and MIM.
>>>
>>> You should be able to access the same annotations via the variation API,
>>> using phenotype features. [1] shows an example fetching via a variation
>>> object, but you can also query by gene [2].
>>>
>>> Hope that helps
>>>
>>> Will McLaren
>>> Ensembl Variation
>>>
>>> [1]
>>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
>>> [2]
>>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72
>>>
>>> On 4 April 2016 at 11:46, Guillermo Marco Puche <
>>> <guillermo.marco at sistemasgenomicos.com>
>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>>> Dear devs,
>>>>
>>>> Up to VEP version 83 I was using the following code in a plugin to
>>>> retrieve gene OMIM related information.
>>>>
>>>>     my @db_entries = @{$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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>>>
>>>
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>>
>>
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