[ensembl-dev] Variant external references: MIM_MORBID
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Apr 5 08:23:01 BST 2016
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
> <mailto: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 $self->{variant} but I'm getting always an
> "undef" value.
>
> Regards,
> Guillermo.
>
>
> On 04/04/16 14:50, Will McLaren wrote:
>> Hi Guillermo,
>>
>> The data you refer to has been retracted from the Ensembl core
>> database while we resolve some issues with external reference
>> mapping between Ensembl and MIM.
>>
>> You should be able to access the same annotations via the
>> variation API, using phenotype features. [1] shows an example
>> fetching via a variation object, but you can also query by gene [2].
>>
>> Hope that helps
>>
>> Will McLaren
>> Ensembl Variation
>>
>> [1]
>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
>> [2]
>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72
>>
>> On 4 April 2016 at 11:46, Guillermo Marco Puche
>> <guillermo.marco at sistemasgenomicos.com
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>> Dear devs,
>>
>> Up to VEP version 83 I was using the following code in a
>> plugin to retrieve gene OMIM related information.
>>
>> my @db_entries = @{$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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