[ensembl-dev] MySQL MANUAL

Emily Perry emily at ebi.ac.uk
Tue Nov 19 09:18:40 GMT 2019

Hi Yossi

The schema for the MySQL databases can all be accessed from here:
http://www.ensembl.org/info/docs/api/index.html <http://www.ensembl.org/info/docs/api/index.html>

We provide BioMart, REST and the Perl APIs in order for people to query the database. If you want an easy way to query the database, that is the way to do it.
All the best


> On 19 Nov 2019, at 05:50, Joseph Steinberger <joseph.steinberger at weizmann.ac.il> wrote:
> Hello Development team,
> I made a local MySQL database of the entire Ensembl database. I would like to use regular MySQL commands to interface with the local MySQL data - as opposed to the Perl API.
> Do you have printed material - pdfs - relating MySQL commands for the core, compara, regulation,variation, etc. databases?
> I see the schema description which has specific SQL examples for compara but not for core. However, I am looking for something more pedagogically written, that illustrates how to do the more common BioMART and REST queries, using instead MySQL commands.
> Sincerely,
> Yossi
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Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader 

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory 
Wellcome Genome Campus
CB10 1SD

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