[ensembl-dev] getting exons from database directly

Bert Overduin bert at ebi.ac.uk
Fri May 6 15:50:49 BST 2011

Hi Andrea,

I suspect that your BioMart results are truncated because the query is too

However, that doesn't explain your API results .... How does your API code
look like?


On Fri, May 6, 2011 at 3:45 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>wrote:

> Hello
> I'm sorry for the basic question but I was looking at the ensembl core
> schema and trying to retrieve just the exons on chromosomes and couldn't
> work out why i am getting such different figures than with biomart and the
> perl api
> For example for cow there are 25670 exons in genes with biomart and the api
> but with this sql  ~210k exons. This code is just looking for exons on
> chromosomes 1-30 and X
> select count(distinct stable_id) from exon e inner join exon_stable_id es
> using(exon_id) inner join seq_region sr using(seq_region_id) where
> sr.coord_system_id = 2 and sr.name REGEXP '^[1-9]|^X'  and e.is_current=1
> I get 8k just on chromosome 1
> I'm sure this is simple and perhaps its because its Friday afternoon but
> I'm just not seeing it!!
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Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom


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