[BioSQL-l] gene ontology questions revisited

[Hilmar Lapp]

Let me know if the response I just sent for Raphael's posting doesn't answer
or doesn't apply to your problem.

    -hilmar

BTW steht's Atlantic noch? Und's Crash?

On 9/17/03 4:03 AM, "Daniel Lang" <daniel.lang at biologie.uni-freiburg.de>
wrote:

> 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
> 

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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