[BioSQL-l] Problem when trying to persist GO in BioSQL

[Andreas Dräger]

Dear all,

Thank you for your advice! Now it works, but not completely. It seems 
that there is either a problem with the ontology file I downloaded from 
GO (gene_ontology_edit.obo) or an error in the script:

./scripts/biosql/load_ontology.pl --host localhost --dbname bioseqdb 
--dbuser myUser --dbpass 'myPasswd' --driver mysql --namespace "Gene 
Ontology" --format obo gene_ontology_edit.obo



And it works:



Loading ontology gene_ontology:
         ... terms
         ... relationships
         Done with gene_ontology.
Loading ontology biological_process:
         ... terms



But then I receive the following messages:



-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were 
("GO:0007125","invasive growth","OBSOLETE (was not defined before being 
made obsolete).","X","") FKs (46)
Duplicate entry 'invasive growth-46-X' for key 3
---------------------------------------------------
Could not store term GO:0007125, name 'invasive growth':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to be 
found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: main::persist_term ./scripts/biosql/load_ontology.pl:802
STACK: ./scripts/biosql/load_ontology.pl:607
-----------------------------------------------------------

  at ./scripts/biosql/load_ontology.pl line 814
         main::persist_term('-term', 
'Bio::Ontology::OBOterm=HASH(0xa1b502c)', '-db', 
'Bio::DB::BioSQL::DBAdaptor=HASH(0x8ba793c)', '-termfactory', 'undef', 
'-throw', 'CODE(0x87406d8)', '-mergeobs', ...) called at 
./scripts/biosql/load_ontology.pl line 607