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

[Hilmar Lapp]

This is odd - it would mean that you don't have the obo.pm parser, or  
that it can't be loaded. Maybe there is some kind of version mix  
going on here?

Could you check that you have the file Bio/OntologyIO/obo.pm in the  
directory where you've installed BioPerl?

If yes, can you do

	$ perl -MBio::OntologyIO::obo

and let me know what happens?

	-hilmar

On May 7, 2008, at 8:58 AM, Andreas Dräger wrote:
> 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

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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