[Bioperl-l] load_ontology/GO error

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Mon Apr 19 05:54:52 EDT 2004

Hello again,

I tried to use my shiny new bioperl_db installation to load GO but it 
failed with the error message below.  I'm afraid it doesn't mean very 
much to me and my searches haven't turned up anything that demystified 
it, so I'd be grateful for any explanation or suggestions on how to fix 
the problem.

Thanks, Dave

biosql$ perl load_ontology.pl --dbname biosql_1 --dbuser bioperl 
--driver mysql --namespace "Gene Ontology" --format goflat --fmtargs 
"-defs_file,GO.defs" function.ontology process.ontology component.ontology
Parsing input ...
Loading ontology Gene Ontology:
	... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were 
("BBD_pathwayID:C1cyc","","","") FKs (1)
Column 'name' cannot be null
Could not store BBD_pathwayID:C1cyc ():

------------- EXCEPTION  -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be 
found by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
STACK Bio::DB::Persistent::PersistentObject::store 
STACK (eval) load_ontology.pl:508
STACK toplevel load_ontology.pl:490


Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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