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Hello Will,<br>
<br>
Thank you for the information, I was going mad trying to retrieve
it! I think importing the MIM number could be a great new feature
for future Ensembl releases.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 05/04/16 11:39, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2DA1TKkxF9BPiDjEk0i5XdS8aNuks3iZTzOD1SJEJ+hQ@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a></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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a></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
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype"
target="_blank"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a></a></div>
<div>[2] <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72"
target="_blank"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72</a></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
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a></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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<div class="moz-signature">-- <br>
<title>Guillermo Marco Puche - Firma</title>
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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: +34 902 364 669 (Ext.777)<br>
Fax: +34 902 364 670</span><br>
<a href="www.sistemasgenomicos.com" target="_blank"><span
style="color:#000066;">www.sistemasgenomicos.com</span></a></span></span></p>
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<p><a
href="https://www.sistemasgenomicos.com/web_sg/web/areas-bioinformatica.php"><img
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