[ensembl-dev] VEP ClinVar information

[Guillermo Marco Puche]

Hi Will,

Indeed I'm looking to retrieve this information from VEP plugin.

Regards,
Guillermo.

On 02/03/15 15:25, Will McLaren wrote:
> Hi Guillermo,
>
> The detailed ClinVar information is stored against PhenotypeFeature 
> objects (each SNP/disease pairing gets its own entry in ClinVar, e.g. 
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2, 
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/, 
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/ for rs699).
>
> 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.
>
> See 
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html 
> and 
> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype 
> for more info.
>
> Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() is an internal 
> method that you should not use.
>
> 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).
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 2 March 2015 at 14:06, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Dear devs,
>
>     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".
>
>     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().
>
>     What about ClinVar rating? Is it possible to retrieve it from API?
>
>     Thanks!
>
>     Regards,
>     Guillermo.
>
>
>
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-- 
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>

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