[BioSQL-l] some problems with loading GenBank

[Hilmar Lapp]

Hi Krzysztof - your question really is about the BioPerl object- 
relational mapping to BioSQL, and I see you have posted your question  
to the BioPerl list already.

Roy's answer there is correct - where stuff ends up depends solely on  
the object-relational mapping (which put feature tag/value pairs into  
feature_qualifier_value) and the structure of the sequence object in  
BioPerl. You can easily manipulate the destination of stuff by  
manipulating the BioPerl object itself to have the representation you  
want. If there are certain feature tags that have a special meaning to  
you (such as being dbxrefs), pull them out of feature tag/values and  
add them back in as Bio::Annotation::DBLink annotation on the sequence  
(or the feature). Writing a SeqProcessor will allow you to do that  
seamlessly; i.e., you do not need to change BioPerl itself, since  
load_seqdatabase.pl allows you to specify the SeqProcessors you want  
to employ.

	-hilmar

On Feb 16, 2010, at 11:59 AM, Krzysztof Sarapata wrote:

> Hi
>
>
>
> I've loaded GenBank file into bioSQL structure with  
> "load_seqdatabase.pl" script.
>
> Is it correct that each entity (qualifier) from FEATURES even  
> "db_xref"  e.g.
>
>
>
> FEATURES             Location/Qualifiers
>
>     source          1..257719
>
>                     /organism="Homo sapiens"
>
>                     /mol_type="genomic DNA"
>
>                     /db_xref="taxon:9606"
>
>                     /chromosome="1"
>
>                     .....
>
>                    /db_xref="GeneID:100287102"
>
>
>
> is put into  "Seqfeature Qualifier Value" table, if we have exactly  
> table "Dbxref"?
>
> Why value of this qualifier (db_xref) isn't put into "Dbxref" table?
>
>
>
> With regards
>
> Krzysztof Sarapata
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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