[ensembl-dev] VEP ClinVar information

[Will McLaren]

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> 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.
>
>
>
> _______________________________________________
> 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/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150302/29817b7e/attachment.html>