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

[Song Haili]

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