[BioSQL-l] gene ontology questions (bug)

[Marc Colosimo]

I have several questions about the GO structure.

First, the old ER diagram only has ontology_term. But the version I have, 
has  ontology and ontology_term. I want to add my own terms, but with so 
many contraints, I have no clue where to start. Here is a sample 
autogenerated list of what I want to add:

Term ID Term Name       Frequency
3       reproduction    248
8       thioredoxin     39

(This was made by dChip, with Affymetrix cvs files, for those interested).

Second, I tried to load in stuff (function.ontology) from geneontology.org 
using the script load_ontology.pl.

here is the error I get:
perl load_ontology.pl --dbname bioseqdb --dbuser mcolosim --driver Pg 
~/Affymetrix/function.ontology
Parsing input ...
Loading ontology Gene Ontology:
        ... terms
DBD::Pg::st execute failed: ERROR:  Relation "term" does not exist at 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 903, <GEN0> line 9095.
Could not store GO:0000005 (ribosomal chaperone activity):

------------- EXCEPTION  -------------
MSG: error while executing statement in 
Bio::DB::BioSQL::TermAdaptor::find_by_unique_key: ERROR:  Relation "term" 
does not exist
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:909
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:820
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:249
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) load_ontology.pl:489
STACK toplevel load_ontology.pl:471

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

Finally, I was wondering if anyone has written a script to parse the gene 
association file type found at 
<http://www.geneontology.org/doc/GO.annotation.html#file> 
and  for the files at <http://www.geneontology.org/#ontologies>?

Thanks,

marc