[ensembl-dev] Variant external references: MIM_MORBID
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Apr 5 10:18:13 BST 2016
Sorry fixed mistake in my previous mail:
> 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_reference*) 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
>> <mailto: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> 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 $self->{variant} but I'm getting always an
>>> "undef" value.
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
>>> On 04/04/16 14:50, Will McLaren wrote:
>>>> Hi Guillermo,
>>>>
>>>> The data you refer to has been retracted from the Ensembl
>>>> core database while we resolve some issues with external
>>>> reference mapping between Ensembl and MIM.
>>>>
>>>> You should be able to access the same annotations via the
>>>> variation API, using phenotype features. [1] shows an
>>>> example fetching via a variation object, but you can also
>>>> query by gene [2].
>>>>
>>>> Hope that helps
>>>>
>>>> Will McLaren
>>>> Ensembl Variation
>>>>
>>>> [1]
>>>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
>>>> [2]
>>>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72
>>>>
>>>> On 4 April 2016 at 11:46, Guillermo Marco Puche
>>>> <guillermo.marco at sistemasgenomicos.com> wrote:
>>>>
>>>> Dear devs,
>>>>
>>>> Up to VEP version 83 I was using the following code in
>>>> a plugin to retrieve gene OMIM related information.
>>>>
>>>> my @db_entries = @{$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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