[Bioperl-l] GenBank entries creation dates

Miguel Pignatelli 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 
"creation-date" tag.
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:

http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val=CAB02640

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:

http://www.ebi.ac.uk/cgi-bin/dbfetch?db=emblcds&id=CAB02640&style=raw

doesn't has DT fields at all.

M;


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);
> 
> $factory->print_DocSums;
> 
> ---------------------------------------
> 
> One gets the following tag/value pairs:
> 
> UID: 1621261
> Caption             :CAB02640
> Title               :PROBABLE PYRIMIDINE OPERON REGULATORY PROTEIN PYRR 
> [Mycobacterium tuberculosis
>              H37Rv]
> Extra               :gi|1621261|emb|CAB02640.1|[1621261]
> 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.
> 
> chris
> 
> On Apr 7, 2008, at 7:48 AM, Heikki Lehvaslaiho wrote:
> 
>> Miguel,
>>
>> 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 
>> accession
>> 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 
>> EMBL/Swiss-Prot
>> formats using bioperl.
>>
>> Yours,
>>
>>     -Heikki
>>
>> 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
>>> 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
>>
>>
>>
>> -- 
>> ______ _/      _/_____________________________________________________
>>      _/      _/
>>     _/  _/  _/  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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> 
> 
> 


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