[ensembl-dev] versioned Ensembl identifiers in HGVS tags reported by VEP

[Kieron Taylor]

It is true that versioned identifiers are not really intended for 
external use. They exist to show a history of revised data, but are 
generally not used directly. It is not possible to search for an old 
version of an ID in the present release, because the underlying data has 
changed somewhat.

If a change is too dramatic, then a new stable ID is assigned and the 
old one retired. Essentially, the versioning exists for allowing users 
to find the closest up-to-date equivalent to data from an old release, 
and to provide some extra information if a feature should require 
further investigation.

I cannot comment on the function of the VEP, perhaps one of the 
Variation team will comment on the presence of versioned identifiers.

Regards,

Kieron

On 14/01/12 08:20, Reece Hart wrote:
> Hi-
>
> VEP reports versioned ENST and ENSP identifiers when using the --hgvs
> switch. The hgvs_coding and hgvs_protein columns in the
> transcript_variation table also contain versioned identifiers.
>
> This is the first time I've come across versioned identifiers in
> Ensembl. I'm unable to find much information on them. Searching for a
> versioned identifier on the Ensembl website fails, but using the
> corresponding version-less identifier works. Similarly in the API,
> Bio::EnsEMBL::Transcript::fetch_by_stable_id does't support versioned
> identifiers and there's no corresponding method for versioned
> identifiers. So, as far as I can tell, versioned identifiers are stored
> and reported by VEP, but there's no way to use them as-is for transcript
> lookup.
>
> Do I have this right or am I missing something?
>
> Thanks,
> Reece
>
>
>
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