[ensembl-dev] How are variations stored?

Laurent Gil lgil at ebi.ac.uk
Mon Apr 23 10:48:54 BST 2012

Hi Dan,

For SNP, indels, ... and variation locations you have to look at the 
tables variation and variation_features.
The phenotypes are stored in the phenotype table and linked to the 
variations into the variation_annotation table.

You are right for the structural variation tables:
- structural_variation like the variation tables stores the general 
information about the structural variations and copy number variations 
(CNV probes).
- structural_variation_feature stores the location information about the 
structural variations.

The other structural variation tables are "optional": I mean they are 
not populated for each structural variation.
- structural_variation_association links the structural variations to 
their supporting evidences (stored in structural variation with the 
value is_evidence=1).
- structural_variation_annotation links the structural variations to 
phenotype and/or sample data.

For the rest of the data types, you can find them by the table names..

I hope this helps.


On 23/04/2012 10:16, Dan Bolser wrote:
> Hi,
> I've been reading this:
> http://www.ensembl.org/info/docs/variation/database.html
> but I don't see info on how different types of variation [1] are
> mapped into the database. In particular, how are structural variations
> stored in the database? i.e. in the simplest case, which tables get
> populated when describing one SV?
> Looking at the table descriptions [2], I can guess that, at a minimum,
> there should be one row in structural_variation and one row in
> structural_variation_feature for every SV, but I'm not sure about the
> other structural_variation_* tables.
> Sorry for the basic questions!
> Cheers,
> Dan.
> [1] http://www.ensembl.org/info/docs/variation/data_description.html#datatypes
> [2] http://www.ensembl.org/info/docs/variation/variation_schema.html#structural_variation
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