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use of Uniprot accession Vs GenBank Accession in With column

Midori Harris midori at ebi.ac.uk
Wed Jan 31 01:49:52 PST 2007


Actually, GB or GenBank would also be acceptable, because they're listed 
as synonyms in GO.xrf_abbs (tthe filtering script allows anything in the 
'aabbreviation' or 'synonym' fields).

m

On Tue, 30 Jan 2007, Karen Christie wrote:

> Note that the abbreviation selected by GO for the IDs for GenBank, DDBJ, and 
> EMBL is EMBL, so that's the namespace that needs to be used in the 
> gene_association files for GO.
>
> -Karen
>
>
> On Tue, 30 Jan 2007, Pankaj Jaiswal wrote:
>
>> Got it. We will use the GB one.
>> 
>> BTW GenBank ID is different than the GenBank Accession. GenBank ID is the 
>> ID exclusive for the GenBank database entry. One GB accession can have 
>> mappings to several GenBank IDs.
>> 
>> Pankaj
>> 
>> Karen Christie wrote:
>>> 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.
>>> 
>>> -Karen
>>> 
>>> 
>>> 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
>>> generic_url: http://www.ebi.ac.uk/embl/
>>> generic_url: http://www.ddbj.nig.ac.jp/
>>> generic_url: http://www.ncbi.nlm.nih.gov/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
>>>> 
>>> 
>> 
>> -- 
>> 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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