[Bioperl-l] GenBank entries creation dates

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Wed Apr 9 09:25:16 EDT 2008


Hi, Miguel,

I do not know whether the data file is publically available. However,
you can perform 'real time' query via id1_fetch:

####step 1: generate GI file #####
id1_fetch -query 'YOUR-GENBANK-QUERY-STRING' -lt none -db Nucleotide
-out qfile

####step 2: retrieve revisions for GIs stored in qfile #####

id1_fetch -lt revisions -qf qfile  -fmt fasta -db Nucleotide

Good luck!

Wenwu Cui

> -----Original Message-----
> From: Miguel Pignatelli [mailto:miguel.pignatelli at uv.es]
> Sent: Wednesday, April 09, 2008 7:33 AM
> To: Cui, Wenwu (NIH/NLM/NCBI) [C]
> 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.i
> d
> > 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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