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

Wed Jul 22 18:15:29 UTC 2009

Please leave off the --fmtargs GO.defs argument - this is not a file  
in the .obo format.

	-hilmar

On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote:

> Hi guys,
>
> I've tried to execute load_ontologies following your suggestions as
>
> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass  
> xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo  
> gene_ontology.1_2.obo
>
> However I have many warnings first
>
> --------------------- WARNING ---------------------
> MSG: DBLink exists in the dblink of _default
> ---------------------------------------------------
>
> and then
>
> --------------------- WARNING ---------------------
> MSG: DBLink exists in the dblink of _default
> ---------------------------------------------------
> Could not store term GO:0001404, name 'invasive growth':
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to  
> be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- 
> live//Bio/Root/Root.pm:357
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ 
> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ 
> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ 
> perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284
> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ 
> load_ontology.pl:812
> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617
> -----------------------------------------------------------
>
> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824
>        main::persist_term('-term',  
> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db',  
> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', undef,  
> '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at /tmp/ 
> BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617
>
>
> Any ideas why?
>
> Thanks in advance,
>
> Carlos
>
>
> Carlos  Canchaya
> ccanchaya at gmail.com
>
>
>
> On Jul 22, 2009, at 1:08 PM, Song Haili wrote:
>
>> 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 :
>>>>> ===========================================================
>>
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================