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

Will McLaren wm2 at ebi.ac.uk
Mon Jan 16 11:12:34 GMT 2012


Hello,

I think (although I'm not sure as I didn't personally code the HGVS
part of the API) that we are required by HGVS standards to provide a
version number with any transcript or protein identifier that we list
as part of HGVS notation.

Cheers

Will

On 16 January 2012 11:04, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:
> 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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>
>
>
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