[ensembl-dev] empty compara database in ensemblgenomes

Dan Staines dstaines at ebi.ac.uk
Thu Feb 21 11:45:37 GMT 2013

On 02/21/2013 11:38 AM, PATERSON Trevor wrote:
> however this database is empty
> (select TABLE_NAME, TABLE_ROWS from TABLES where
> INFORMATION_SCHEMA.TABLE_SCHEMA='ensembl_compara_pan_homology_17_70';)

Hmm, it looks like something has gone badly wrong with the data loading 
pipeline for some databases on the public SQL site this time round. I'll 
look into resyncing these dbs but it might take some time for this one 
as its a big database to transfer.

> Also, alas, I don’t really understand the provision of family-based
> compara data he alluded to  - where is this information stored?

family, family_member and member in ensembl_compara_bacteria_17_70. 
However, note that this is generated and handled in a completely 
different way to the family data in other Ensembl databases so you 
probably can't generalise.

Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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