[ensembl-dev] ids from older versions of Ensembl.

Andreas Kusalananda Kähäri ak4 at sanger.ac.uk
Fri Aug 16 23:14:15 BST 2013


I just want to point out that if a stable ID has changed it most likely
mean that the underlying sequence of the object (transcript, exon, etc.)
has changed or that its composition (number of exons for transcripts, or
its transcipts for genes) has changed, either as a result of a change in
the annotation (reannotated using different parameters, method etc.) or
as a result of a new assembly.

Therefore, the thing that previsouly had the stable ID "X", which now
is named "Y" (or "X.2" or whatever) is likely different from the thing
that you called "X" before.  It is possible that it's still a similar
sequence, but it *is* different.  If it was not different, it would
still be called "X".

If this matter to you, you need to look at the sequence (or the
supporting features) to make sure that you're still dealing with the
same or at least equivalent things as before.

This is true for at least the main Ensembl project.

Andreas (Ensembl Genebuild)

On Fri, Aug 16, 2013 at 05:34:05PM +0100, Adam Witney wrote:
> Thanks Nick,
> I would be looking to convert IDs for the whole genome. Do you not
> have a mapping file available?
> Thanks
> Adam
> On 15. 8. 2013 15:57, Nick Langridge wrote:
> >Hello again,
> >
> >After talking to my colleagues, I can give you an update on this. The ID
> >history converter tool is enabled for EG Bacteria, however not all
> >historical IDs are mapped:
> >"For protein coding genes, we use common identifiers (protein_ids) to do
> >the mapping from old to new. In this case, it appears to be an RNA gene
> >which was predicted in the old version by us running a third party
> >program. We no longer do this with the new system, where RNA genes come
> >from ENA annotation. This means there are no common identifiers we can
> >use, so we have not mapped these over. It might be possible to do this
> >mapping using sequence idenitiy or genome location overlap, but this
> >isn't something we've done."
> >
> >If you have other IDs you wish to try looking up, here are some brief
> >instructions for using the ID history converter in EG Bacteria (we plan
> >to make this a little easier in future versions):
> >
> >1. Visit a gene or location page for the species you are interested in,
> >e.g.
> >http://bacteria.ensembl.org/escherichia_coli_str_k_12_substr_mg1655/Location/View?r=Chromosome:1130661-1131065;time=1376564739066.066
> >
> >
> >2. Click the 'Add your data' button in the left-hand navigation to open
> >the configuration panel.
> >
> >3. Choose  'ID History Converter'
> >
> >4. Enter an ID (e.g. EBESCG00000000900), click Next, then choose a format.
> >
> >I hope this helps.
> >
> >Best regards,
> >Nick
> >
> >
> >
> >On 14/08/2013 15:32, Nick Langridge wrote:
> >>Hi Adam,
> >>
> >>This should be possible using the ID history converter tool, however
> >>the tool is not currently enabled for Ensembl Bacteria.
> >>I will look into this and get back to you.
> >>
> >>Best regards,
> >>Nick
> >>
> >>On 14/08/2013 14:07, Adam Witney wrote:
> >>>
> >>>Hi,
> >>>
> >>>Is there any way in Ensembl Bacteria to map older IDs to new IDs.
> >>>e.g. I have some genes labelled with IDs like EBSTRG00000063753, but
> >>>these don't find anything with the search field
> >>>
> >>>Thanks
> >>>
> >>>Adam
> >>>
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> >>
> >
> >
> >
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Andreas Kusalananda Kähäri
Ensembl Gene Annotation Team

That is all for now.

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