<div dir="ltr">Hi again,<div><br></div><div>You can retrieve the MIM ID via fetching the attributes of the phenotype feature, use get_all_attributes()</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html#a7dfa8e10e74e9ede4d87257823ce564e">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html#a7dfa8e10e74e9ede4d87257823ce564e</a><br></div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 5 April 2016 at 08:23, 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>
Unfortunately I can't use the Phentoype.pm plugin since I can't
support VEP annotation in JSON format at this moment. <br>
--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):<br>
<br>
sub feature_types {<br>
return ['Transcript'];<br>
}<br>
<br>
However with your previous answer and and old e-mail I've
accomplished to retrieve the phenotypes:<br>
<br>
foreach my $known_var(@{$vf->{existing} || []}) {<br>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}){<br>
@phenotype_descriptions = ();<br>
if ($pf->source_name =~ /omim/i){<br>
#do stuff with the omim phentoype<br>
push(@phenotype_descriptions,
$pf->phenotype->description)<br>
#trying to retrieve the omim phenotype id however i
can't find a way to<br>
print $pf->external_id,"\n";<br>
#however i can get the external reference (OMIM gene
id)<br>
print $pf->external_reference,"\n";<br>
}<br>
}<br>
<br>
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
<a href="http://www.omim.org/entry/616126" target="_blank">616126</a>.<br>
Phentoype description and external reference are working:<br>
<ul>
<li>The phentoype description: $pf->phenotype->description
(ie: IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION)<br>
</li>
<li>The phentoype external reference (OMIM gene id) related to
this phenotype: $pf->external_reference (ie: MIM:147571)<br>
</li>
</ul>
<p>For the ClinVar phentoypes I was able to get the ClinVar id with
$pf->external_id however I get always an <i>undef</i> value
for OMIM phenotypes.<br>
</p>
<p>The VCF input record I'm using for testing is the following one
extracted from latest GRCh38: <br>
</p>
<ul>
<li>1 1014143 rs786201005 C T . .
dbSNP_146;TSA=SNV;E_Phenotype_or_Disease;CLIN_pathogenic;AA=C</li>
</ul>
<p>
</p>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 04/04/16 17:43, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>It may be that what you are trying to do is already
encapsulated in our (new to release 84) Phenotypes plugin:</div>
<div><br>
</div>
<div><a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm" target="_blank">https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm</a><br>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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 $tva->variation_feature->{existing},
something like:</div>
<div><br>
</div>
<div>sub run {</div>
<div> my ($self, $tva) = @_;</div>
<div> </div>
<div> ### get phenotype feature adaptor $pfa somehow</div>
<div> </div>
<div> foreach my $id(map {$_->{variation_name}}
@{$tva->variation_feature->{existing} || []}) {</div>
<div> my $pfs = $pfa->fetch_all_by_object_id($id);</div>
<div><br>
</div>
<div> ### do something with the phenotype features returned</div>
<div> }</div>
<div>}</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Will</div>
<div><br>
</div>
<div>[1] <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c</a></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 4 April 2016 at 16:12, 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"> Hello Will,<br>
<br>
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 ( <span>Variation::Variation</span>)
from inside VEP plugin.<br>
I'm trying with $self->{variant} but I'm getting
always an "undef" value.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On 04/04/16 14:50, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The data you refer to has been retracted from
the Ensembl core database while we resolve some
issues with external reference mapping between
Ensembl and MIM.</div>
<div><br>
</div>
<div>You should be able to access the same
annotations via the variation API, using
phenotype features. [1] shows an example
fetching via a variation object, but you can
also query by gene [2].</div>
<div><br>
</div>
<div>Hope that helps</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
<div>[1] <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype" target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a></div>
<div>[2] <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72</a></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 4 April 2016 at 11:46,
Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank"></a><a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear
devs,<br>
<br>
Up to VEP version 83 I was using the
following code in a plugin to retrieve gene
OMIM related information.<br>
<br>
my @db_entries =
@{$gene->get_all_DBEntries()};<br>
foreach my $db_entry(@db_entries){<br>
if ($db_entry->dbname eq
"MIM_GENE"){<br>
$mim_id =
$db_entry->primary_id;<br>
}<br>
if ($db_entry->dbname eq
"MIM_MORBID"){<br>
push(@mim_morbid_ids,
$db_entry->primary_id);<br>
}<br>
}<br>
<br>
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?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</div>
<br>
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