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use of Uniprot accession Vs GenBank Accession in With column

Valerie Wood val at sanger.ac.uk
Wed Jan 31 06:26:33 PST 2007




Hi Pankaj,

This is not always the case. This cannot happen if your EMBL entry 
contains multiple proteins.

Val

Pankaj Jaiswal wrote:

> Hi,
>
> PID is the same as GB/EMBL/DDBJ accession number
> e.g.
> /protein_id="AAT37941.1"
> referred in nucleotide entry
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=47717898
> is the same as accession number in
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AAT37941
> ACCESSION AAT37941
> VERSION AAT37941.1 GI:47717899
>
> The version is fine, that refers to any new updates in the entry and 
> they are all tracked. However, in most cases it is not that significant.
>
> The problem I raised is also because it is a rare occurrence a 
> citation refers to Uniprot accessions. Almost always they refer to 
> GB/EMBL/DDBJ accessions. In that case a curator has to go and find out 
> the possible Uniprot accession as Emily has suggested. This I think is 
> extra curational load. There are other problems as well cited in this 
> mail tread as well. So my suggestion is to adopt a universal system to 
> always refer by an EMBL/GB/DDBJ accession number in the association 
> files and some magic script should be able to link back to all the 
> respective dbs and not just one source.
>
> On the other hand we should encourage the GB to provide Xrefs to the 
> Uniprot accessions also. I have seen them in unigenes/genes/genomes 
> but not always in protein and nucleotide dbs.
>
> -Pankaj
>
> Michael Ashburner (Genetics) wrote:
>
>> All
>>
>> Am I being thick or not ? It seems as if the obvious object to refer
>> to, if Uniprot ID is not available, is the PID contained within GenBank
>> EMBL records. This is shared between GB, EMBL and DDBJ. It is versioned
>> and gets over the problem that Val points to:
>> 'it may be a problem to refer to the Genbank/EMBL accession number as 
>> this will often be a cosmid or contig and contain multiple CDS- in 
>> these cases you can't refer to the gene/protein uniquely with an EMBL 
>> ID.'
>>
>> Michael
>>
>>
>
>


-- 
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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe 
Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe




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