[BioSQL-l] Error when loading Gene Ontology to biosql
Chris Fields
cjfields at illinois.edu
Fri Jul 24 00:39:25 UTC 2009
The warning is interesting, as it derives from our rollback of feature/
annotation stuff in bioperl. It indicates the specified DBLink is
duplicated in the Bio::Ontology::Term.
The exception makes sense in light of that (and seems to confirm the
link was already present).
chris
On Jul 23, 2009, at 7:49 AM, Hilmar Lapp wrote:
> Hi Carlos - that's an odd error that we haven't seen yet. My first
> impulse would be to suspect that your database wasn't empty when you
> ran this, and that the error you got is due to a term in the input
> file clashing with one you already have in the database.
>
> You can check this by looking into your database:
>
> SQL> SELECT * FROM term WHERE identifier = 'GO:0001404' or name =
> 'invasive growth';
>
> Does this return anything?
>
> Note that load_ontology.pl is perfectly equipped to update an
> existing ontology - check the POD and look for the --lookup command
> line option (and the several options following it in the POD with
> which you can modify the exact update behavior). By default though
> the script will assume that it is loading a new ontology.
>
> -hilmar
>
> On Jul 23, 2009, at 3:27 AM, Carlos A. Canchaya wrote:
>
>> 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 _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
>>>>
>>>>
>>>> _______________________________________________
>>>> BioSQL-l mailing list
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>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>>
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>
>>
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>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
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