[ensembl-dev] database versions and genome builds

[Andreas Kahari]

On Thu, Nov 18, 2010 at 04:33:58PM +0000, Bronwen Aken wrote:
> Hi Andrea,
[cut]
> Gene IDs (ENSBTAG*) are stable and are versioned: 
> http://www.ensembl.org/Bos_taurus/Gene/Idhistory?g=ENSBTAG00000003925;r=9:107457744-107460348;t=ENSBTAT00000005121
> As far as I know, if a gene moves position then its stable_id will change. We don't explicitly add documentation for each gene by recording where it was in the last build compared to the current build.

The stable ID may still be the same even if a gene moves, but...

A gene stable ID will have its version incremented if any of the gene's
transcripts changes.

A transcript stable ID will have its version incremented if the spliced
exon sequence changes.

A translation stable ID will have its version incremented if its
transcript changes.

An exon stable ID will have its version incremented if its sequence
changes.


A new stable ID will be created for any object that does not map
perfectly (start to end location) to an object of the same type in the
previous release and that additionally fails a number of similarity
comparisons (etc. etc.).

Stable IDs that can not be mapped are retired and will not be re-used
again.


Andreas

-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom