[ensembl-dev] Missing data in public mysql database

[Will McLaren]

Hello,

The 1000 Genomes project genotype and allele frequency data is too large to
store efficiently in our MySQL schema, so our APIs use a custom VCF backend
to retrieve these data and return them on the web, REST and Perl API
interfaces.

Therefore to retrieve them you must use one of our APIs or access the VCF
files directly yourself.

There's a blog post about this that you can read here:
http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/

Regards

Will McLaren
Ensembl Variation

On 14 September 2015 at 09:53, Fin Swimmer <ensembl at need-login.de> wrote:

> Hello,
> i'm conncecting to the public mysql database via mysql workbench with
> the following login informations:
>
> server: ensembldb.ensembl.org
> port: 3306
> user: anonymous
>
> I was trying to fetch the allel frequencys for a SNP but could not get
> all informations I need. So further investigations shows that some data
> are missing.
>
> I looked up the population table to find the id for 1000Genomes:
>
> SELECT * FROM homo_sapiens_variation_81_38.population WHERE name LIKE
> "%1000GENOMES%";
>
> This give me for example the id 373417 for "1000GENOMES:phase_3:CEU".
>
> With the id I went to the allele table:
>
> SELECT * FROM homo_sapiens_variation_81_38.allele WHERE
> population_id=373417;
>
> This ended up in 0 rows returned.
>
>
> I know I could fetch frequency information via the REST-API. But I would
> like to use mysql.
>
> So, am I doing something wrong?
>
> fin swimmer
>
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