[ensembl-dev] How are variations stored?
lgil at ebi.ac.uk
Mon Apr 23 10:48:54 BST 2012
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
- structural_variation_feature stores the location information about the
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
- 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:
> I've been reading this:
> but I don't see info on how different types of variation  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 , 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!
>  http://www.ensembl.org/info/docs/variation/data_description.html#datatypes
>  http://www.ensembl.org/info/docs/variation/variation_schema.html#structural_variation
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
More information about the Dev