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use of Uniprot accession Vs GenBank Accession in With column

Karen Christie kchris at genome.Stanford.EDU
Tue Jan 30 13:42:21 PST 2007

Hi Pankaj,

GenBank IDs are already allowed in the with column. The main requirement 
is that the abbreviation (or namespace) for the source of the ID be 
included in the GO.xrf_abbs file. There is already an entry for IDs coming 
from GenBank/DDBJ/EMBL, so these IDs are already permissable.


abbreviation: EMBL
database: International Nucleotide Sequence Database Collaboration, 
comprising EMBL-EBI International Nucleotide Sequence Data Library 
(EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
object: Sequence accession number
example_id: EMBL:AA816246
example_id: DDBJ:AA816246
example_id: GB:AA816246
synonym: DDBJ
synonym: GB
synonym: GenBank

On Tue, 30 Jan 2007, Pankaj Jaiswal wrote:

> Hi Everyone,
> I know it is an accepted SOP to include either the Uniprot accession number 
> or the individual database's own gene/protein ID in the WITH column of the 
> association tables.
> However while doing it it seems that it is too much of the work to find out 
> what is the Uniprot entry, because often the DDBJ and GenBank do not Xref 
> each other using the Uniprot accession. However the best alternative is to 
> use the GenBank's Accession number. Which I see that almost all the databases 
> including Uniprot, DDBJ, EMBL, PIR etc. use it to cross refer. It is also the 
> most suitable ID used to find the particular nucleotide/protein accession 
> that we are looking for using the same query, no matter which db is queried.
> I hope you would consider my request by adopting the GenBank's accession 
> number, unless there is a better option.
> Thanks
> Pankaj
> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683

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