[Bioperl-l] GenBank entries creation dates

John N Calley CALLEY_JOHN_N at LILLY.COM
Wed Apr 9 09:45:23 EDT 2008


You might want to keep in mind that the creation date is not always 
reliable. I am aware of one example where the recorded creation date 
precedes the sequencing date by several months (as determined by the trace 
file date). NCBI was not able to explain exactly what happened but (as I 
recall) hypothesized that some dates had been scrambled in a database 
rebuild. If there was interest I could probably pull up more details.

John Calley



Miguel Pignatelli <miguel.pignatelli at uv.es> 
Sent by: bioperl-l-bounces at lists.open-bio.org
04/09/2008 07:32 AM
Please respond to
miguel.pignatelli at uv.es


To
"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov>
cc
bioperl-l at bioperl.org
Subject
Re: [Bioperl-l] GenBank entries creation dates






Wow, impressive, thanks Wenwu for the information, I have never used 
this tool before. The problem is that I need to know all the revision 
history (or at least the creation date) for *all* the GIs present in nr 
(well, or at least a significant portion of it) and this tool queries 
via web.

The existence of this tool confirms me that this information is 
available somewhere, is it possible to download the data that contains 
this information?

Thanks again,

M;


Cui, Wenwu (NIH/NLM/NCBI) [C] wrote:
> Hi, Miguel:
> 
> id1_fetch can do it. Detailed instruction can be found at: 
> 
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.section.ch_demo.id
> 1_fetch.html
> 
> Here is an example:
> 
>> id1_fetch -lt revisions -flat '12:74311105' -fmt fasta
> GI        Loaded      DB    Retrieval No.
> --        ------      --    -------------
> 74311105  12/07/2007  NCBI  19766263
> 74311105  01/23/2007  NCBI  16325656
> 74311105  03/30/2006  NCBI  13131204
> 74311105  03/03/2006  NCBI  12915541
> 74311105  03/02/2006  NCBI  12885275
> 74311105  12/03/2005  NCBI  12259793
> 74311105  09/09/2005  NCBI  11257262
> 74311105  09/09/2005  NCBI  11242667
> 
> Wenwu Cui PhD
> NCBI/NLM/NIH
> 
>> -----Original Message-----
>> From: Miguel Pignatelli [mailto:miguel.pignatelli at uv.es]
>> Sent: Monday, April 07, 2008 6:13 AM
>> Cc: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] GenBank entries creation dates
>>
>> Hi all,
>>
>> Is there any way to obtain the date of creation of individual GenBank
>> entries? I don't mean the "last revision" date that can be found in
> the
>> first line of a GenBank file.
>>
>> I can access this creation date by looking at the "revision history"
> of
>> any GenBank entry (for example, see
>> http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val=74311105),
>> but I need a systematic (and local=fast) way to access this
>> information.
>>
>> Any help would be very appreciated,
>> Thank you very much in advance,
>>
>> M;
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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