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

Wed Jul 22 11:08:20 UTC 2009

Hi Florian,
Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't use gene_ontology.1_2.obo, but as you can see instead I used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo). However, I don't understand why I can't use gene_ontology.obo which I think, does not differ a lot with gene_ontology.1_2.obo at the beginning of the two files. Thanks a lot again, Florian and Hilmar.
song

----- Original Message -----
From: Florian Mittag <florian.mittag at uni-tuebingen.de>
Date: Wednesday, July 22, 2009 10:44
Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql
To: Song Haili <haili at mpiz-koeln.mpg.de>
Cc: biosql-l at lists.open-bio.org

> 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 :
> > > ===========================================================