[Bioperl-l] Re: [BioSQL-l] Bio::SeqFeature::Generic score & source tags in Biosql

[Hilmar Lapp]

$feature->source_tag is controlled vocabulary in biosql and therefore a 
foreign key on the seqfeature table to the term table (source_term_id). 
Source_tag isn't used by the rich sequence format like embl or Genbank; 
instead the tag in fact has a predefined default value most of the time 
(e.g., 'Genbank/EMBL/Swissprot' if the sequence is from - you guessed 
it - Genbank, Embl, or Swissprot). If you set a value then it should be 
present as a foreign key to the term table.

score I thought gets translated into a tag/value pair, and would hence 
end up as value in the seqfeature_qualifier_value table. I just 
realized that this is apparently not the case. The problem is that 
score() is actually not defined in Bio::SeqFeatureI. I'm not sure what 
the best approach here is; maybe adding the translation to to 
Bio::SeqFeature::AnnotationAdaptor would be the best way to implement 
this.

	-hilmar


On Thursday, April 8, 2004, at 05:37  AM, Daniel Lang wrote:

> Hi,
> I´m wondering why the score & source tags of the GenericFeature 
> objects I insert attached to RichSeqs into a biosql db are missing in 
> seqfeature_qualifier_value?
> Are they somewhere else?
> I´ve set them using Bio::SeqFeature::Generic::score() & source()...
> Other tags I added using add_tag_value method are present...
>
> Do those to have special meaning? - Because source is also missing and 
> score becomes /note="score..." when writing the Objects directly to 
> genbank format...
>
> Thanks in advance,
> Daniel
>
> -- 
>
> Daniel Lang
> University of Freiburg, Plant Biotechnology
> Sonnenstr. 5, D-79104 Freiburg
> phone: +49 761 203 6988
> homepage:  http://www.plant-biotech.net/
> e-mail: daniel.lang at biologie.uni-freiburg.de
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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