[BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair

[Daniel Lang]

Hi,
I am trying to populate a biosql database (postgres) with "home-made" 
RichSeqs objects. On first sight, I looks like everything is OK, but 
when I retrieve the sequences and write them e.g. in genbank format, 
there are some sequences, where the qualifiers are doubled or even tripled:
...
FEATURES             Location/Qualifiers
      source          1..551
                      /tissue_type="mixture of chloronemata, caulonemata and
                      malformed buds"
                      /tissue_type="mixture of chloronemata, caulonemata and
                      malformed buds"
                      /tissue_type="mixture of chloronemata, caulonemata and
                      malformed buds"
                      /clone_lib="normalized full length cDNA library,
                      chloronemata, caulonemata and malformed buds"
                      /clone_lib="normalized full length cDNA library,
                      chloronemata, caulonemata and malformed buds"
                      /clone_lib="normalized full length cDNA library,
                      chloronemata, caulonemata and malformed buds"
                      /sub_species="patens"
                      /sub_species="patens"
                      /sub_species="patens"
                      /clone="pphb37e20"
                      /clone="pphb37e20"
                      /clone="pphb37e20"
                      /organism="Physcomitrella patens subsp. patens"
                      /organism="Physcomitrella patens subsp. patens"
                      /organism="Physcomitrella patens subsp. patens"
                      /mol_type="mRNA"
                      /mol_type="mRNA"
                      /mol_type="mRNA"
                      /db_xref="taxon:145481"
                      /db_xref="taxon:145481"
                      /db_xref="taxon:145481"
      ATAIL           1..28
                      /ACTION="annot"
                      /ACTION="annot"
                      /ACTION="annot"
                      /ORIENT="REVERSE"
                      /ORIENT="REVERSE"
                      /ORIENT="REVERSE"
...

Of course, the underlying data is non-redundant...
Correspondingly, these qualifier_values are stored redundantly in the 
seqfeature_qualifier_value table with a different rank:

seqfeature_id | term_id | rank | 
                value
---------------+---------+------+--------------------------------------------------------------------------------------------------------------------
              1 |       5 |    1 | pphb37e20
              1 |       5 |    2 | pphb37e20
              1 |       5 |    3 | pphb37e20
              1 |       6 |    1 | normalized full length cDNA library, 
chloronemata, caulonemata and malformed buds
              1 |       6 |    2 | normalized full length cDNA library, 
chloronemata, caulonemata and malformed buds
              1 |       6 |    3 | normalized full length cDNA library, 
chloronemata, caulonemata and malformed buds


But when I write the constructed object in genbank or embl format in the 
first place, the qualifiers are correct?!
Bio::Annotation::Reference s are also affected...

Additionally not all data I intend to insert is integrated...

Here a code snipplet:
  if($seq->isa("Bio::AnnotatableI")) {
		flatten_annotations($seq->annotation);
	    }
	    $adp= $db->get_object_adaptor($seq);
	
	    my $pseq = $db->create_persistent($seq)  unless 
$seq->isa("Bio::DB::PersistentObjectI");
	    $pseq->namespace($namespace);
	    $pseq->store();
	    $adp->commit();

Any ideas what is happening?

Additionally I´d like to know if there is an adapter or a way to store 
Bio::SeqFeature::SimilarityPair s in the schema yet?

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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