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use of Uniprot accession Vs GenBank Accession in With column

Emily Dimmer edimmer at ebi.ac.uk
Wed Jan 31 03:07:02 PST 2007


Hi,

Just a quick note, GenBank Accessions are exactly the same as EMBL 
accessions. All EMBL accessions are cross-referenced in UniProt. 
Therefore if you *did* want to find a UniProtKB accession, you should be 
able just to enter the  GenBank accession into the UniProt website (or 
search via SRS etc...) and it will bring up the quivalent UniProt entry 
(I do realize that for some groups there is an issue of a UniProtKB 
accession not yet existing for an equivalent GenBank accession).

Cheers,
Emily

Midori Harris wrote:

> 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
>>>
>>


-- 
 ************************************
    Emily Dimmer
    GOA and IntAct Database Curator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
 ************************************




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