[Bioperl-l] GenBank entries creation dates
miguel.pignatelli at uv.es
Mon Apr 7 12:24:50 EDT 2008
I've noticed that the ASN.1 version of those records has a
But this is somehow strange, because the creation date obtained by you
and that obtained via ASN.1 format is 2003/11/21, but if you look at the
revision history of the record:
reports a creation date of "Oct 19 1996 12:28 AM"
I don't know how to get this, because the EMBL version of this gene:
doesn't has DT fields at all.
Chris Fields wrote:
> Strangely enough, if you use NCBI's esummary you can get both dates.
> Via Bio::DB::EUtilities in bioperl-live, if you dump out DocSum data
> (using a debugging method I added in a while back):
> use Bio::DB::EUtilities;
> # for multiple IDs use an array ref; also only use GI's (not accessions)
> my $factory = Bio::DB::EUtilities->new(
> -eutil => 'esummary',
> -db => 'protein',
> -id => 1621261);
> One gets the following tag/value pairs:
> UID: 1621261
> Caption :CAB02640
> Title :PROBABLE PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
> [Mycobacterium tuberculosis
> Extra :gi|1621261|emb|CAB02640.1|
> Gi :1621261
> CreateDate :2003/11/21
> UpdateDate :2006/11/14
> Flags :
> TaxId :83332
> Length :193
> Status :live
> ReplacedBy :
> Comment :
> I'll add in a method to grab the data element by tag (in this case, grab
> the creation date by asking for the 'CreateDate' key). Might come in
> handy for scripts.
> On Apr 7, 2008, at 7:48 AM, Heikki Lehvaslaiho wrote:
>> You probably know this but:
>> - Your entry example below is a GenPept entry, not a GenBank entry
>> - The NCBI sequence format "genbank" has only the last modified date.
>> I do not know about other formats (ASN.1, ...)
>> - NCBI Entrez is a great tool but it obscures the source database.
>> - If you really are working on real GenBank entries, you can use the
>> number to see find corresponding EMBL (and Swiss-Prot) flat file
>> formats that
>> have both creation and last modified dates.
>> Post to the list if you have trouble getting the dates from
>> formats using bioperl.
>> On Monday 07 April 2008 12:12:58 Miguel Pignatelli wrote:
>>> 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
>>> 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,
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> ______ _/ _/_____________________________________________________
>> _/ _/
>> _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
>> _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
>> _/ _/ _/ SANBI, South African National Bioinformatics Institute
>> _/ _/ _/ University of Western Cape, South Africa
>> _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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