[BioSQL-l] gene ontology questions revisited

[Daniel Lang]

Hi,
In june there was a discussion about redundant GO-Terms in GO-flat files and 
the related problems when integrating into the database(see Re: gene ontology 
questions (bug)Tue Jun 3 15:01:54 EDT 2003).
I think I´m confronted with the same problem...
I wanted to load my biosql instantation with the actual go-flat files using 
the load_ontology.pl likes this:

perl ../load_ontology.pl --dbuser biosql --dbpass 'xxx' --dbname bioseqdb 
--driver Pg --namespace "Gene Ontology" --format goflat --fmtargs 
"-defs_file,GO.defs" --testonly function.ontology process.ontology 
component.ontology
Parsing input ...
Loading ontology Gene Ontology:
        ... terms
Could not store GO:0001529 (elastin):

------------- EXCEPTION  -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found by 
unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) ../load_ontology.pl:489
STACK toplevel ../load_ontology.pl:471

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

By running safe mode, it is obvious that there are multiple 
erroneous/redundant entries...

I also tried former releases back to 2003-05-01, and encountered the same 
difficulties.

Is this the same problem or am I having other problems?
If not, has anyone contacted the GO people about this issue yet?

Thanks in advance,
Daniel
 
-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

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