[ensembl-dev] VEP ClinVar information
Will McLaren
wm2 at ebi.ac.uk
Mon Mar 16 16:50:44 GMT 2015
The "is_significant" field is an internal flag that doesn't necessarily
have the meaning you expect; it is used to distinguish between genuine
reported associations and e.g. non-significant associations reported from
genome-wide studies.
You should not see undef for phenotype; I suspect you are accessing the
hashref directly ($pf->{phenotype}) rather than making the method call
($pf->phenotype()).
You could try
ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_clinically_associated.vcf.gz
as a test input set.
Will
On 16 March 2015 at 16:39, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:
> Hi Will,
>
> Thank you for your quick response! Very clarifying.
>
> I guess that the way to retrieve ClinVar data I posted is correct. With my
> test dataset I've only seen "is_significant" values of "1" and undef
> 'phenotype' values. I think I need a synthetic vcf with ClinVar annotation
> variants to very that the plugin is working.
>
> I've been looking on Ensembl website for a test dataset. I think you don't
> provide any right? Correct me if I'm wrong.
>
> Thanks!
>
> Regards,
> Guillermo.
>
>
> On 16/03/15 16:16, Will McLaren wrote:
>
> Hi Guillermo,
>
> To get the rest of that data in the table you need to access the
> additional attributes of the PhenotypeFeature object, something like:
>
> my $attr = $pfs->[0]->get_all_attributes;
> print "$_:".$attr->{$_}."\t" for keys %$attr;
> print "\n;
>
> Regards
>
> Will
>
> More info: the reason these data are stored as attributes is due to the
> diverse data sources and types that we import into our phenotype schema; to
> create a database column and corresponding API method for each data type
> (p-value, review status, risk allele, external ID etc etc) would be
> cumbersome and inefficient. To this end we provide a few methods that
> shortcut the attribute approach for the most common data types; everything
> else must be accessed through the attributes method. This is a common theme
> across the Ensembl API.
>
> On 13 March 2015 at 12:03, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>> Hi,
>>
>> I'm trying to retrieve ClinVar information with the code example you
>> provided.
>>
>> my $self = shift;
>> my $tva = shift;
>> my $vf = $tva->variation_feature;
>> my $pfa =
>> $self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');
>>
>> foreach my $known_var(@{$vf->{existing} || []}) {
>> foreach my
>> $pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}) {
>> if ($pf->{'source'} eq "dbSNP_ClinVar"){
>> print
>> "$pf->{'source'}\t$pf->{'external_id'}\t$pf->{'is_significant'}\t$pf->{'phenotype'}\n",
>> ;
>> }
>> }
>> }
>>
>> As you can see I'm "filtering" the results to only output phenotype
>> feature when source is dbSNP_ClinVar. I don't know why but I guess
>> filtering should be done when doing the "fetch_all".
>>
>> On the other hand I'm trying to retrieve Disease, Source and Clinical
>> Significance from this example table:
>> http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266
>>
>> I think I'm doing something wrong I got totally lost in Phenotypefeature.
>>
>> Regards,
>> Guillermo.
>>
>>
>> On 02/03/15 16:05, Will McLaren wrote:
>>
>> If you enable the --check_existing flag when you run the VEP, you'll be
>> able to see any known co-located variants attached to the VariationFeature
>> object in your plugin:
>>
>> sub run {
>> my $self = shift;
>> my $tva = shift;
>> my $vf = $tva->variation_feature;
>>
>> foreach my $known_var(@{$vf->{existing} || []}) {
>> # do stuff
>> }
>> }
>>
>> The $known_var is not an API object but a simple hashref with a number
>> of fields; you're probably interested in $known_var->{clin_sig}
>>
>> However, as I mentioned, this is the only data that is stored in the
>> cache. To access the rating and the specific disease association, you'll
>> need to make calls to the database by getting an adaptor, something like:
>>
>> sub run {
>> my $self = shift;
>> my $tva = shift;
>> my $vf = $tva->variation_feature;
>> my $pfa =
>> $self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');
>>
>> foreach my $known_var(@{$vf->{existing} || []}) {
>> foreach my
>> $pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}) {
>> # do stuff
>> }
>> }
>> }
>>
>> Be aware that this will access the database, so unless you have a local
>> copy please don't run this sort of code on genome-wide VCFs using our
>> public DB server.
>>
>> Regards
>>
>> Will
>>
>> On 2 March 2015 at 14:47, Guillermo Marco Puche <
>> guillermo.marco at sistemasgenomicos.com> wrote:
>>
>>> Hi Will,
>>>
>>> Indeed I'm looking to retrieve this information from VEP plugin.
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
>>> On 02/03/15 15:25, Will McLaren wrote:
>>>
>>> Hi Guillermo,
>>>
>>> The detailed ClinVar information is stored against PhenotypeFeature
>>> objects (each SNP/disease pairing gets its own entry in ClinVar, e.g.
>>> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2,
>>> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/,
>>> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/ for rs699).
>>>
>>> The rating (and indeed the clinical significance) is stored as an
>>> attribute on the PhenotypeFeature object; you can retrieve this with the
>>> get_all_attributes() method.
>>>
>>> See
>>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html
>>> and
>>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
>>> for more info.
>>>
>>> Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() is an internal
>>> method that you should not use.
>>>
>>> The VEP cache contains the list of clinical significance states for
>>> each variant, but neither the disease association or the rating. If you
>>> want help getting access to this data via a plugin, let me know as it's a
>>> little more involved than the API methods above (though it is faster as no
>>> database access is required).
>>>
>>> Regards
>>>
>>> Will McLaren
>>> Ensembl Variation
>>>
>>> On 2 March 2015 at 14:06, Guillermo Marco Puche <
>>> guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>>> Dear devs,
>>>>
>>>> I'm looking forward to retrieve ClinVar information and add it to VEP
>>>> annotation. From my understanding I should be able to retrieve "Clinical
>>>> significance" and "ClinVar Rating".
>>>>
>>>> I've been looking the Varation API, and I'm confused. I guess for
>>>> significance I should use
>>>> Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() or
>>>> Bio::EnsEMBL::Variation::VariationFeature::get_all_clinical_significance_states().
>>>>
>>>> What about ClinVar rating? Is it possible to retrieve it from API?
>>>>
>>>> Thanks!
>>>>
>>>> Regards,
>>>> Guillermo.
>>>>
>>>>
>>>>
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>>>>
>>>
>>>
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