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

Liu, Mingyi Mingyi.Liu at bms.com
Thu Sep 2 16:17:38 BST 2010

Hi, Michael,

Thanks for the quick response!  That makes sense, but is it possible/if there's any plan to maybe just attach a 'p' to the end of the transcript id to make unique protein ids?  This way the transcript IDs would be different from protein IDs, making sure a mixed storage facility would not be confused (especially since Ensembl traditionally do give transcripts and proteins different IDs, e.g. not using ENST000... for both protein/dna).  We would probably do that internally but it'd makes it harder to x-check with ensembl.org if we keep our own internal protein IDs different.



>-----Original Message-----
>From: Michael Paulini [mailto:mh6 at sanger.ac.uk]
>Sent: Thursday, September 02, 2010 11:10 AM
>To: Liu, Mingyi
>Cc: dev at ensembl.org
>Subject: Re: [ensembl-dev] C.elegans protein/transcripts share same IDs
>  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.
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