[ensembl-dev] plants.ensembl.org questions

[Wolf Beat]

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=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=Sk5LhgZF6Gtx39HDqDIDUmZyOA2hs0elnvr8Vbrx0Lw&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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