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

[Hilmar Lapp]

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