<div dir="ltr">Hello,<div><br></div><div>It looks like we don't have the MIM number recorded for variant-phenotype associations, only for gene-phenotype associations.</div><div><br></div><div>We can look into importing this data for Ensembl's next release.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 5 April 2016 at 10:13, 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>
I had already tried that:<br>
<br>
for my $key (keys $pf->get_all_attributes) {<br>
print "$key\t$pf->get_all_attributes{$key}\n";<br>
}<br>
<br>
associated_gene
Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{associated_gene}<br>
variation_names
Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{variation_names}<br>
risk_allele
Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{risk_allele}<br>
<br>
associated_gene:ISG15 risk_allele:0003
variation_names:rs786201005<br>
<br>
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_id) that returns the MIM ID (gene) related to this
phenotype and not the Phenotype MIM Number.<br>
<br>
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?<br>
<br>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 05/04/16 10:45, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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><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"></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"> 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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