[ensembl-dev] database model and API versions

Thomas Juettemann juettemann at ebi.ac.uk
Mon May 11 16:50:03 BST 2015

Hi Duarte,

I can’t see a reply yet, my apologies either if this is a duplicate or for the late reply. 

We are aware that many people are still using GRCh37, therefore we are applying MySQL schema patches regularly, which then allows you to use API versions higher than the original v75. 

You can find an overview about the connection settings here:

To use either homo_sapiens_xxx_78_37 or  homo_sapiens_xxx_79_37 use these settings (I assume you only need to change the port in your scripts):
host: ensembldb.ensembl.org 
port: 3337  
user: anonymous

Please let us know if you have anymore questions.

Best wishes,

On 27 Apr 2015, at 16:56, Duarte Molha <duartemolha at gmail.com> wrote:

Dear developers

On your GRCh37 archive site you say this:


About this archive

This archive is based on Ensembl Release 75 data, and gives continuing access to human assembly GRCh37, as well as all our other release 75 species (data freeze March 2014) for comparative purposes. Human variation and regulation data has since been updated in March 2015.

The API and website will be updated in tandem with the release of the main Ensembl website (currently version 79), and we will also periodically update this site with new data human, which will be announced in this panel.

MySQL dumps of human databases on the most recent schema version are available on our FTP site.


It was my understanding that an API version was directly linked to a specific assembly. So I thought that if I wanted to query the latest GRCh37 assembly I would need to use the api v75 and if I wanted to use a local database, I would download the corresponding sql tables for that version.

However, according to this announcement, I can now use the V79 api and query the old assembly... How is this accomplished ?
What you I have to do on my scripts to make sure I am querying the 37 version even though I am using the latest API?

Sorry, I hope this is not a stupid question but I am a bit confused.

Best regards


     Duarte Miguel Paulo Molha      
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Thomas Juettemann, PhD
Senior Technical Officer - Ensembl DNA Regulation

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
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