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

[Song Haili]

Hello All,
The previous error was solved by the help of Florian. Florian, Thank you very much.
But I got another error using the way Florian suggested. I thought it was because parameter --fmtargs was not specified. So I tried to include it with the value "-defs_file, GO.defs", but it didn't work. I think maybe GO.defs is not the right file. Is it?  But how or where to get the right file if it is. Or any other ideas about how to solve this error? Thank you very much in advance.
command:
perl load_ontology.pl --driver Pg --host pg-server --dbname sifter  --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" --noobsolete
error:
------------- EXCEPTION -------------
MSG: OBO File Format Error -
Cannot find tag format-version and/ default-namespace . These are required header.

STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518
STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209
STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342
STACK toplevel load_ontology.pl:604
-------------------------------------

----- Original Message -----
From: Florian Mittag <florian.mittag at uni-tuebingen.de>
Date: Tuesday, July 21, 2009 14:41
Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql
To: biosql-l at lists.open-bio.org

> 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
> > -------------------------------------
> 
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