[BioSQL-l] BioSQL conflict with swissprot and NCBI taxonomy

[Raphael A. Bauer]

Hello,

i've got some trouble parsing the ncbi tyxonomy into an existing biosql 
schmema populated with swissport.

To parse the NCBI i used from /scripts/ in the biosql schema:
perl load_ncbi_taxonomy.pl --dbname columbaTax --driver Pg --host 
localhost --dbuser biosql --download --directory ~/wbi/.
Loading NCBI taxon database in /vol/fob-vol3/mi02/rbauer/wbi/.:

and to parse the swissprot i used from bioperl-db:
perl load_seqdatabase.pl --host localhost --dbuser rbauer --dbname
bioseqdb --namespace swissprot --driver Pg--format swiss 
/SwissProtDB/sprot41.dat

the error message is the following:

Loading /local/sprot_weekly.dat ...
DBD::Pg::st execute failed: ERROR:  Cannot insert a duplicate key into 
unique in                                                dex taxon_pkey 
at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Pg/SpeciesAdaptor 
                                          Driver.pm line 356, <GEN0> 
line 385883.
Could not store O18759:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Species) failed to insert or to be found by 
unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5 
   .8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::Persistent::PersistentObject::create 
/usr/lib/perl5/site_perl/5.8 
     .0/Bio/DB/Persistent/PersistentObject.pm:243
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5 
   .8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5. 
    8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8. 
      0/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) load_seqdatabase.pl:446
STACK toplevel load_seqdatabase.pl:429


...in my opinion it is due to the fact that swissprot has some kind of 
taxonomy in it's OC lines that are a part of the NCBI taxonomy. (parsed 
already in table term)

So my question is if there is a way to integrate swissprot and ncbi in 
one biosql schema.
Or if it is better to keep NCBI and swissprot seperated in own biosql 
schemas and map them together lateron to get a mapping from ncbi and 
swissprot...

Many thanks in advance,

Raphael Bauer