[ensembl-dev] Variant external references: MIM_MORBID
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Apr 5 10:48:26 BST 2016
Hello Will,
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.
Regards,
Guillermo.
On 05/04/16 11:39, Will McLaren wrote:
> Hello,
>
> It looks like we don't have the MIM number recorded for
> variant-phenotype associations, only for gene-phenotype associations.
>
> We can look into importing this data for Ensembl's next release.
>
> Regards
>
> Will
>
> On 5 April 2016 at 10:13, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> Hi Will,
>
> I had already tried that:
>
> for my $key (keys $pf->get_all_attributes) {
> print "$key\t$pf->get_all_attributes{$key}\n";
> }
>
> associated_gene
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{associated_gene}
> variation_names
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{variation_names}
> risk_allele
> Bio::EnsEMBL::Variation::PhenotypeFeature=HASH(0x73c0840)->get_all_attributes{risk_allele}
>
> associated_gene:ISG15 risk_allele:0003 variation_names:rs786201005
>
> 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.
>
> 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?
>
> Regards,
> Guillermo.
>
>
> On 05/04/16 10:45, Will McLaren wrote:
>> Hi again,
>>
>> You can retrieve the MIM ID via fetching the attributes of the
>> phenotype feature, use get_all_attributes()
>>
>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html#a7dfa8e10e74e9ede4d87257823ce564e
>>
>> Will
>>
>> On 5 April 2016 at 08:23, Guillermo Marco Puche
>> <guillermo.marco at sistemasgenomicos.com
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>> Hi Will,
>>
>> Unfortunately I can't use the Phentoype.pm plugin since I
>> can't support VEP annotation in JSON format at this moment.
>> --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):
>>
>> sub feature_types {
>> return ['Transcript'];
>> }
>>
>> However with your previous answer and and old e-mail I've
>> accomplished to retrieve the phenotypes:
>>
>> foreach my $known_var(@{$vf->{existing} || []}) {
>> foreach my
>> $pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}){
>> @phenotype_descriptions = ();
>> if ($pf->source_name =~ /omim/i){
>> #do stuff with the omim phentoype
>> push(@phenotype_descriptions, $pf->phenotype->description)
>> #trying to retrieve the omim phenotype id
>> however i can't find a way to
>> print $pf->external_id,"\n";
>> #however i can get the external reference
>> (OMIM gene id)
>> print $pf->external_reference,"\n";
>> }
>> }
>>
>> 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
>> 616126 <http://www.omim.org/entry/616126>.
>> Phentoype description and external reference are working:
>>
>> * The phentoype description: $pf->phenotype->description
>> (ie: IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION)
>> * The phentoype external reference (OMIM gene id) related
>> to this phenotype: $pf->external_reference (ie: MIM:147571)
>>
>> For the ClinVar phentoypes I was able to get the ClinVar id
>> with $pf->external_id however I get always an /undef/ value
>> for OMIM phenotypes.
>>
>> The VCF input record I'm using for testing is the following
>> one extracted from latest GRCh38:
>>
>> * 1 1014143 rs786201005 C T . .
>> dbSNP_146;TSA=SNV;E_Phenotype_or_Disease;CLIN_pathogenic;AA=C
>>
>> Regards,
>> Guillermo.
>>
>>
>> On 04/04/16 17:43, Will McLaren wrote:
>>> Hi Guillermo,
>>>
>>> It may be that what you are trying to do is already
>>> encapsulated in our (new to release 84) Phenotypes plugin:
>>>
>>> https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm
>>>
>>> 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.
>>>
>>> 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
>>> $tva->variation_feature->{existing}, something like:
>>>
>>> sub run {
>>> my ($self, $tva) = @_;
>>> ### get phenotype feature adaptor $pfa somehow
>>> foreach my $id(map {$_->{variation_name}}
>>> @{$tva->variation_feature->{existing} || []}) {
>>> my $pfs = $pfa->fetch_all_by_object_id($id);
>>>
>>> ### do something with the phenotype features returned
>>> }
>>> }
>>>
>>> Cheers
>>>
>>> Will
>>>
>>> [1]
>>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c
>>>
>>> On 4 April 2016 at 16:12, Guillermo Marco Puche
>>> <guillermo.marco at sistemasgenomicos.com
>>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>
>>> Hello Will,
>>>
>>> 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 ( Variation::Variation) from inside VEP plugin.
>>> I'm trying with $self->{variant} but I'm getting always
>>> an "undef" value.
>>>
>>> Regards,
>>> Guillermo.
>>>
>>>
>>> On 04/04/16 14:50, Will McLaren wrote:
>>>> Hi Guillermo,
>>>>
>>>> The data you refer to has been retracted from the
>>>> Ensembl core database while we resolve some issues with
>>>> external reference mapping between Ensembl and MIM.
>>>>
>>>> You should be able to access the same annotations via
>>>> the variation API, using phenotype features. [1] shows
>>>> an example fetching via a variation object, but you can
>>>> also query by gene [2].
>>>>
>>>> Hope that helps
>>>>
>>>> Will McLaren
>>>> Ensembl Variation
>>>>
>>>> [1]
>>>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
>>>> [2]
>>>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72
>>>>
>>>> On 4 April 2016 at 11:46, Guillermo Marco Puche
>>>> <guillermo.marco at sistemasgenomicos.com
>>>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>
>>>> Dear devs,
>>>>
>>>> Up to VEP version 83 I was using the following code
>>>> in a plugin to retrieve gene OMIM related information.
>>>>
>>>> my @db_entries = @{$gene->get_all_DBEntries()};
>>>> foreach my $db_entry(@db_entries){
>>>> if ($db_entry->dbname eq "MIM_GENE"){
>>>> $mim_id = $db_entry->primary_id;
>>>> }
>>>> if ($db_entry->dbname eq "MIM_MORBID"){
>>>> push(@mim_morbid_ids, $db_entry->primary_id);
>>>> }
>>>> }
>>>>
>>>> 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?
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
>>>> <mailto:Dev at ensembl.org>
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog:http://www.ensembl.info/
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>>
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog:http://www.ensembl.info/
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
--
Guillermo Marco Puche - Firma
------------------------------------------------------------------------
*Guillermo Marco Puche*
Bioinformatician, Computer Science Engineer
Sistemas Genómicos S.L.
Phone: +34 902 364 669 (Ext.777)
Fax: +34 902 364 670
www.sistemasgenomicos.com
<https://www.sistemasgenomicos.com/web_sg/web/areas-bioinformatica.php>
------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160405/cb2e3d88/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bioinfo.png
Type: image/png
Size: 27377 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160405/cb2e3d88/attachment.png>
More information about the Dev
mailing list