[ensembl-dev] is SQL access available for Ensembl Species List and Table of assemblies?
mchakiachvili at ebi.ac.uk
Tue Jun 8 16:49:02 BST 2021
You'll need to access our metadata databases in order to retrieve these
information, you can find the `ensembl_metadata_104` database on our
`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
More info about our PERL software stack available
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:
> [Table of
> 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
> Dev mailing list Dev at ensembl.org
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Ensembl Production Project Leader - Genomics Technology Infrastructure
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
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