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

Thu Aug 6 13:46:06 UTC 2009

The warnings are fine. They simply indicates that a dbxref is being  
added to the term that it already had.

Part of the reason for that happening may be that Bioperl-db doesn't  
support different kinds of dbxrefs for terms yet, if I recall  
correctly, so once retrieved from the database they all end up in the  
_default category.

	-hilmar

On Aug 6, 2009, at 5:43 AM, Florian Mittag wrote:

> Hi!
>
> On Friday, 24. July 2009 02:39, Chris Fields wrote:
>> 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).
>
> I'm getting the same warnings with my custom DB2 driver and with  
> MySQL, but
> the script completes successfully. I get them when loading the Gene  
> Ontology
> and the Sequence Ontology.
>
> -------------------- WARNING ---------------------
> MSG: GOC:mah exists in the dblink of _default
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: PMID:12297042 exists in the dblink of _default
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: GOC:mah exists in the dblink of _default
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: GOC:rph exists in the dblink of _default
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: PMID:12930826 exists in the dblink of _default
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: PMID:15012271 exists in the dblink of _default
> ---------------------------------------------------
>
> [...]
> Done with sequence.
> Done, cleaning up.
>
>
> What to do?
>
> - Florian
>
>>
>> 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.ob
>>>> o
>>>>
>>>> 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

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