[ensembl-dev] plants.ensembl.org questions

[Dan Bolser]

Hi Wolf,

As Andrew points out, with genotype data being hosted in VCF files instead
of the database, there is no easy way to get MAFs into BioMart. I
appreciate that a 'one stop shop' is better than hitting multiple APIs, but
in this case the data more correctly 'belongs' in EVA than in the Ensembl
API.

The data that you're seeing in human is actually imported from dbSNP. i.e.
these are 'official MAFs' rather than MAFs calculated 'on the fly', so to
speak. It's possible that we could look at developing a similar import
mechanism from EVA so that MAFs appear in the BioMart API.

Until then, sorry for the inconvenience.


Cheers,
Dan.

On 10 October 2017 at 07:44, Wolf Beat <Beat.Wolf at hefr.ch> wrote:

> Thank you for that information.
>
>
> That said, is there a reason that the information is not in biomart? The
> query field is present, its just empty.
>
> One reason to use biomart is also that its no longer necessary to combine
> dozens of different APIs to get a certain result, which here does not seem
> to be the case.
>
> Considering the normal ensembl release contains this information for
> example for humans, could this also be added to the next plants.ensembl
> release?
>
>
> Thank you very much
>
>
> Beat Wolf
>
> ________________________________
> From: Dev <dev-bounces at ensembl.org> on behalf of Olson, Andrew <
> olson at cshl.edu>
> Sent: Monday, October 9, 2017 8:10:08 PM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] plants.ensembl.org questions
>
> Sample genotypes are accessed by the web server to a remotely hosted index
> vcf file instead of in the ensembl variation database. The MAF for a
> variant obtained from this remote file. As far as I know, the biomart
> database build does not gather sample alleles from these remotely hosted
> vcf files. However, one way to get it programmatically is from the EVA rest
> API:
> https://www.ebi.ac.uk/eva/webservices/rest/swagger-ui.html
> It didn’t work for me given the variant ID ENSVATH02373908, but id did
> work with a segments query
> https://www.ebi.ac.uk/eva/webservices/rest/v1/segments/
> 3%3A15142729-15142729/variants?species=athaliana_tair10
>
> Andrew
>
> On Oct 9, 2017, at 10:10 AM, Wolf Beat <Beat.Wolf at hefr.ch<mailto:Beat
> .Wolf at hefr.ch>> wrote:
>
> Hello,
>
>
> i have 2 questions about plants.ensembl.org<http://plants.ensembl.org>
>
>
> First, is there a rest interface similar to the main ensembl release?
>
>
> Second, is there a way to find the minor allele frequence through the
> biomart interface?
>
>
> For example this variant:
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__plants.
> ensembl.org_Arabidopsis-5Fthaliana_Variation_Explore-
> 3Fr-3D3-3A15142229-2D15143229-3Bv-3DENSVATH02373908-3Bvdb-
> 3Dvariation-3Bvf-3D7087020&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe
> 4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=Sk5LhgZF6Gtx39HDqDIDUmZyOA2hs0
> elnvr8Vbrx0Lw&s=kOstIMPNzVgL6yRgjn5wk0lG6cc27m0-DvJpJJ_o_aY&e=
>
>
> States that the MAF is < 0.01. Yet the biomart interface returns nothing
> when retrieving the minor_allele_freq for this variant. Is there a
> different way to get it?
>
>
> Kind regards
>
>
> Beat Wolf
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