[Bioperl-l] Error in loading into biosql database

[Siddhartha Basu]

Hi,

I am using the script 'load_seqdatabase.pl' to upload the swissprot 
entries in the biosql database. But i am getting the following error

======================================================================


DBD::mysql::st execute failed: Table 'biosql.ontology_term' doesn't 
exist at 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 791, <GEN0> line 111.

------------- EXCEPTION  -------------
MSG: Could not store #1946:
------------- EXCEPTION  -------------
MSG: error while executing statement in 
Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key: Table 
'biosql.ontology_term' doesn't exist
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:797
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:218
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::SeqAdaptor::store_children 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:225
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) /home/basu/bin/load_seqdatabase.pl:424
STACK toplevel /home/basu/bin/load_seqdatabase.pl:423

--------------------------------------


STACK toplevel /home/basu/bin/load_seqdatabase.pl:433

===========================================================================

As far as i understand that the error points to the table ontologly_term 
which does not exist in latest biosql schema and it has been changed to 
the table term in its latest version.  So the question is why the script 
is trying to find a table which does not exist the sql schema.

Any ideas/suggestions how to get around this problem.



-Siddhartha