[BioSQL-l] Problem when trying to persist GO in BioSQL

[Andreas Dräger]

Dear all,

Unfortunately, I am still having trouble while loading the Gene Ontology 
into my BioSQL database. I installed BioSQL, downloaded the file 
gene_ontology_edit.obo from the Gene Ontology homepage 
(http://www.geneontology.org/GO.downloads.ontology.shtml), installed the 
BioPerl package bioperl-db-1.5.2_100 as described in the INSTALL file 
and tried the following:

./scripts/biosql/load_ontology.pl \
--host localhost --dbname biosql \
--dbuser myUser \
--dbpass 'myPassword' \
--driver mysql \
--namespace "Gene Ontology" \
--format obo \
gene_ontology_edit.obo

I received the following error message:

Bio::OntologyIO: obo cannot be found
Exception
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::OntologyIO::obo. Can't locate 
Bio/OntologyIO/obo.pm in @INC (@INC contains: 
/usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi 
/usr/lib/perl5/site_perl/5.8.7/i386-linux-thread-multi 
/usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi 
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi 
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 
/usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 
/usr/lib/perl5/site_perl 
/usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi 
/usr/lib/perl5/vendor_perl/5.8.7/i386-linux-thread-multi 
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi 
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi 
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 
/usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 
/usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.8/i386-linux-thread-multi 
/usr/lib/perl5/5.8.8 .) at 
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 394.

STACK Bio::Root::Root::_load_module 
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:396
STACK (eval) /usr/lib/perl5/site_perl/5.8.8/Bio/OntologyIO.pm:255
STACK Bio::OntologyIO::_load_format_module 
/usr/lib/perl5/site_perl/5.8.8/Bio/OntologyIO.pm:254
STACK Bio::OntologyIO::new 
/usr/lib/perl5/site_perl/5.8.8/Bio/OntologyIO.pm:165
STACK toplevel ./scripts/biosql/load_ontology.pl:525

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

For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "term_factory" on an undefined value at 
./scripts/biosql/load_ontology.pl line 531.
[root at u-172-c052 bioperl-db-1.5.2_100]# vim scripts/biosql/load_ontology.pl


I am grateful for any hint what I can do to solve this problem and to 
store the GO in my database.

Cheers,
Andreas