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

Michael Paulini mh6 at sanger.ac.uk
Thu Sep 2 16:29:06 BST 2010


  On 02/09/10 16:17, Liu, Mingyi wrote:
> 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.
>
> Thanks,
>
> Mingyi

problem with that is, that we use the stable_ids to create the links back to the wormbase database, and if I append 
letters, the links would break.

But you could use the connected xrefs as ids for your storage, as they got the proteinids. Sadly I connected them to 
translations/transcripts and genes, so it needs some kind of logic depending on the source of the table.

And to be fair, if you put in a logic to separate the xrefs, you could as well add a p to the molecule-type of your choice.

M

>> -----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.
>>
>> Michael
>>
>>
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