[Bioperl-l] Building biosql database errors

[Sean Davis]

I am trying to build a biosql database on a mysql database.  I have mysql
and biosql schema running and can successfully load some data, but for a
proportion of the data when loading ontology or locuslink, I get the
following (many times).  Am I doing something wrong, or is this to be
expected?  I would just push on with --safe (as given below), but clearly
part of the data is not loaded correctly after looking at the result.  I
have the same problem when loading locuslink.  Any input is appreciated.

Thanks,
Sean


% perl ../../../bioperl-db/scripts/biosql/load_ontology.pl --safe --fmtargs
"-defs_file,GO.defs" --dbuser sdavis --dbpass mic2222 --namespace "Gene
Ontology" --format goflat component.ontology.2004-02-01
process.ontology.2004-02-01 function.ontology.2004-02-01

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
("GO:0042597","periplasmic space","The region between the inner
(cytoplasmic) and outer membrane (Gram-negative bacteria) or inner membrane
and cell wall (fungi).","") FKs (84)
Duplicate entry 'periplasmic space-84' for key 2
---------------------------------------------------
Could not store term relationship (periplasmic space (sensu
Fungi),IS_A,periplasmic space):

------------- EXCEPTION  -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found
by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Library/Perl/5.8.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::Persistent::PersistentObject::create
/Library/Perl/5.8.1/Bio/DB/Persistent/PersistentObject.pm:243
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Library/Perl/5.8.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170
STACK Bio::DB::Persistent::PersistentObject::create
/Library/Perl/5.8.1/Bio/DB/Persistent/PersistentObject.pm:243
STACK (eval) ../../../bioperl-db/scripts/biosql/load_ontology.pl:548
STACK toplevel ../../../bioperl-db/scripts/biosql/load_ontology.pl:547

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