[BioSQL-l] Error when loading Gene Ontology to biosql
Carlos A. Canchaya
ccanchaya at gmail.com
Wed Jul 22 15:05:49 UTC 2009
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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