[ensembl-dev] C.elegans protein/transcripts share same IDs

[Michael Paulini]

  On 02/09/10 15:52, Liu, Mingyi wrote:
> Hi,
>
> Sorry if it's answered before (googled and didn't find answer) - We just noticed that in Ensembl C.elegans transcripts share the same IDs as proteins, while annotating Wormbase protein IDs as a xref.  Is there any particular reason why it was done this way?  The same IDs present an issue for our sequence storage.  We could work around it but it'd be messy.  It seems best if Ensembl could use Wormbase's protein IDs in addition to the transcript IDs too?
>
> Thanks,
>
> Mingyi
>
Hi Mingyi,

I used the WormBase-TranscriptIDs as stable_ids for the translations (knowing that people expect unique translation 
IDs), therefore they should be unique.

The protein xrefs in contrast are not unique to a single transcript, as WormBase-ProteinIDs are unique to the protein 
sequence, so more than one transcript/translation/gene can share the same WormBase-proteinID as xref.

Michael