[BioSQL-l] Error when loading Gene Ontology to biosql
Carlos A. Canchaya
ccanchaya at gmail.com
Thu Jul 23 07:27:25 UTC 2009
Hi Hilmar,
thanks for the help. I've tried now this
load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass
xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo
downloaded from here
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo
and I have this error message.
--------------------- 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 /usr/local/share/perl/5.10.0/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(0x9330318)', '-db',
'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', undef, '-
throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at /tmp/BioPerl-
db-1.6.0/scripts/biosql/load_ontology.pl line 617
Any hints to know where the problem would be?
Thanks in advance,
Carlos
Carlos Canchaya
ccanchaya at gmail.com
On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote:
> 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 :
>>>>>> ===========================================================
>>>
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>>
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>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
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