[ensembl-dev] is SQL access available for Ensembl Species List and Table of assemblies?

mchakiachvili mchakiachvili at ebi.ac.uk
Tue Jun 8 16:49:02 BST 2021

Hi Malcom, 

You'll need to access our metadata databases in order to retrieve these
information, you can find the `ensembl_metadata_104` database on our
public server:

`mysql --host=ensembldb.ensembl.org --port=3306 --user=anonymous`

Database hold a organism <-> genome (s) association per release, where
you'll find your information. 

To access programmatically I would invite you to use our dedicated
 PERL API available here https://github.com/Ensembl/ensembl-metadata 
If you only need to retrieve information for a particular release,
please have a look at our set of useful script to retrieve
data https://github.com/Ensembl/ensembl-metadata/tree/release/104/misc_scripts

More info about our PERL software stack available
here https://www.ensembl.org/info/docs/index.html

Hope that will help you to sort things out. 


On Sun, 2021-06-06 at 20:47 +0000, Cook, Malcolm wrote:
> Dear Ensembl Devs,
> I am looking for programmatic way to access in tabular form the data
> behind these two pages:
>         [Species
> List](https://www.ensembl.org/info/about/species.html)
>         [Table of
> assemblies](https://www.ensembl.org/info/website/archives/assembly.html
> )
> Preferably a SQL query on remotely accessible mysql server.
> Additionally, if it were possible to include the name used by UCSC
> for the assembly, if available.... (perhaps this is the same as
> asking for NCBI's alternate name)
> Thanks for any tips and suggestions.
> Malcolm Cook
> Database Applications Manager
> Stowers Institute for Medical Research
> Kansas City, MO  USA    I
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Marc Chakiachvili

Ensembl Production Project Leader - Genomics Technology Infrastructure

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