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

Wed Jul 22 08:44:18 UTC 2009

Hi Song,

just to be clear: Did you download the file gene_ontology.1_2.obo from 
http://www.geneontology.org/GO.downloads.ontology.shtml ?

(http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo)

You need to specify the correct file then, because the command you described 
expects a file called "gene_ontology.obo", which is not the orginial name of 
the file to download.

On Wednesday 22 July 2009 09:50, Song Haili wrote:
> Hello Hilmar,
> Thank you very much for your help.
> I got the same error even I don't use the argument --fmtargs. Actually that
> was the first try before I use --fmtargs. Any idea on how to solve this
> problem? Thanks 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 --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: Hilmar Lapp <hlapp at gmx.net>
> Date: Tuesday, July 21, 2009 19:19
> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql
> To: Song Haili <haili at mpiz-koeln.mpg.de>
> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org
>
> > Song: GO.defs is not in OBO format. Where did you find that you
> > need 
> > it when you load .obo formatted files? You don't need the --
> > fmtargs 
> > argument for .obo files other than if you want to specify the
> > ontology 
> > name.
> >
> > 	-hilmar
> >
> > On Jul 21, 2009, at 11:32 AM, Song Haili wrote:
> > > 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
> > >>> -------------------------------------
> > >>
> > >> _______________________________________________
> > >> BioSQL-l mailing list
> > >> BioSQL-l at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biosql-l
> > >
> > > _______________________________________________
> > > BioSQL-l mailing list
> > > BioSQL-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biosql-l
> >
> > --
> > ===========================================================
> >
> > : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp
> >
> > at gmx dot net :
> > ===========================================================