[ensembl-dev] Querying E. Coli strains from Ensembl Bacteria Release 12

Dan Staines dstaines at ebi.ac.uk
Thu Jul 26 22:18:04 BST 2012


Hi Harold,

I'd strongly recommend the API as this takes care of everything for you 
in a multispecies database. We can help if you need any advice on this.

If you cannot use the API, you need to use the meta table to identify 
the entries with the correct species_id (for K12, I recall this is 
species_id 1), and from there find the coordinate system for that 
species. You can do this in a join across meta to coord_region to 
seq_region thence to gene e.g.
select g.* from gene g join seq_region s using (seq_region_id) join 
coord_system cs using (coord_system_id) where species_id=1;

or indeed join on species_id to meta and query by meta_key/meta_value 
e.g. species.production_name/e_coli_k12 e.g.
select g.* from gene g join seq_region s using (seq_region_id) join 
coord_system cs using (coord_system_id) join meta using (species_id) 
where meta_key='species.production_name' and meta_value='e_coli_k12';

Hope this helps!

Dan.






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