[BioSQL-l] Error when loading Gene Ontology to biosql

[Florian Mittag]

Hi!

AFAIK the goflat format is deprecated. Use the .obo files and format instead, 
that should work.

perl load_ontology.pl --driver Pg --host pg-server --dbname sifter
	--dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo
        gene_ontology.1_2.obo --noobsolete


On Tuesday 21 July 2009 12:11, Song Haili wrote:
> Dear all,
> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN
> a few days before. Until now, I can load taxonomy and sequence data into
> database successfully. However, I got the following error message when
> trying to load Gene Ontology data into biosql database. Any help will be
> appreciated. Jane
>
> command used:
> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser
> sifter --dbpass password －－namespace "Gene Ontology" --format goflat
> component.ontology process.ontology function.ontology --fmtargs
> "-defs_file, GO.defs" --noobsolete
>
> error:
> ------------- EXCEPTION -------------
> MSG: Could not open －－namespace: No such file or directory
> STACK Bio::Root::IO::_initialize_io
> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK
> Bio::OntologyIO::dagflat::parse
> /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277
> STACK Bio::OntologyIO::dagflat::next_ontology
> /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330
> STACK toplevel load_ontology.pl:604
> -------------------------------------