[Bioperl-l] load_seqdatabase.pl

[Roy Chaudhuri]

Hi Krzysztof,

The reasons for this are discussed in this post on the BioSQL list:
http://lists.open-bio.org/pipermail/biosql-l/2005-March/000751.html

In short - BioPerl does not perform any magic to insert the db_xref 
feature tags where you might expect (ie. the seqfeature_dbxref table). 
It should be possible to write a SeqProcessor to do so, although it's 
pretty easy to access them where they are with a query like:
SELECT * FROM seqfeature_qualifier_value s JOIN term t USING(term_id) 
WHERE t.name='db_xref'

Roy.

On 16/02/2010 17:03, 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