<div dir="ltr">Hi Guillermo,<div><br></div><div>To get the rest of that data in the table you need to access the additional attributes of the PhenotypeFeature object, something like:</div><div><br></div><div>my $attr = $pfs->[0]->get_all_attributes;<br></div><div>print "$_:".$attr->{$_}."\t" for keys %$attr;</div><div>print "\n;</div><div><br></div><div>Regards</div><div><br></div><div>Will</div><div><br></div><div>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.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 13 March 2015 at 12:03, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Hi,<br>
<br>
I'm trying to retrieve ClinVar information with the code example you
provided.<span class=""><br>
<br>
my $self = shift;<br>
my $tva = shift;<br>
my $vf = $tva->variation_feature;<br>
my $pfa =
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');<br>
<br>
foreach my $known_var(@{$vf->{existing} || []}) {<br>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{<br></span>
if ($pf->{'source'} eq "dbSNP_ClinVar"){<br>
print
"$pf->{'source'}\t$pf->{'external_id'}\t$pf->{'is_significant'}\t$pf->{'phenotype'}\n",
;<br>
}<br>
}<br>
}<br>
<br>
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".<br>
<br>
On the other hand I'm trying to retrieve Disease, Source and
Clinical Significance from this example table:
<a href="http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266</a><br>
<br>
I think I'm doing something wrong I got totally lost in
Phenotypefeature.<br>
<br>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 02/03/15 16:05, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">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:
<div><br>
</div>
<div>sub run {</div>
my $self = shift;
<div> my $tva = shift;</div>
<div> my $vf = $tva->variation_feature;</div>
<div><br>
</div>
<div> foreach my $known_var(@{$vf->{existing} || []}) {</div>
<div> # do stuff</div>
<div> }</div>
<div>}</div>
<div><br>
</div>
<div>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}</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>
<div>sub run {</div>
<div> my $self = shift;</div>
<div> my $tva = shift;</div>
<div> my $vf = $tva->variation_feature;</div>
<div> my $pfa =
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');</div>
<div><br>
</div>
<div> foreach my $known_var(@{$vf->{existing} || []}) {</div>
<div> foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{</div>
<div> # do stuff</div>
<div> }</div>
<div> }</div>
<div>}</div>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 2 March 2015 at 14:47, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Hi Will,<br>
<br>
Indeed I'm looking to retrieve this information from VEP
plugin.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On 02/03/15 15:25, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The detailed ClinVar information is stored
against PhenotypeFeature objects (each
SNP/disease pairing gets its own entry in
ClinVar, e.g. <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2</a>, <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/</a>, <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/</a>
for rs699).</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>See <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html</a>
and <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype" target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a>
for more info.</div>
<div><br>
</div>
<div><span style="font-size:12.8000001907349px">Bio::EnsEMBL::Variation::</span><span style="font-size:12.8000001907349px">Utils::VEP::get_clin_sig()
is an internal method that you should not use.</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">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).</span><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 2 March 2015 at 14:06,
Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear
devs,<br>
<br>
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".<br>
<br>
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().<br>
<br>
What about ClinVar rating? Is it possible to
retrieve it from API?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
</div>
<br>
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<p><span style="font-size:12px"><span style="font-family:arial,helvetica,sans-serif"><span style="color:#000066"><strong>Guillermo
Marco Puche</strong><br>
<br>
Bioinformatician, Computer Science
Engineer<br>
Sistemas Genómicos S.L.<br>
Phone: <a href="tel:%2B34%20902%20364%20669" value="+34902364669" target="_blank">+34
902 364 669</a> (Ext.777)<br>
Fax: <a href="tel:%2B34%20902%20364%20670" value="+34902364670" target="_blank">+34
902 364 670</a></span><br>
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<p><span style="font-size:12px"><span style="font-family:arial,helvetica,sans-serif"><span style="color:#000066"><strong>Guillermo Marco
Puche</strong><br>
<br>
Bioinformatician, Computer Science Engineer<br>
Sistemas Genómicos S.L.<br>
Phone: <a href="tel:%2B34%20902%20364%20669" value="+34902364669" target="_blank">+34 902 364 669</a> (Ext.777)<br>
Fax: <a href="tel:%2B34%20902%20364%20670" value="+34902364670" target="_blank">+34 902 364 670</a></span><br>
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