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

[Florian Mittag]

Ok, that's a relieve. Thanks for the quick answer!

- Florian

On Thursday, 6. August 2009 15:46, Hilmar Lapp wrote:
> 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

-- 
Dipl. Inf. Florian Mittag
Universität Tuebingen
WSI-RA, Sand 1
72076 Tuebingen, Germany
Phone: +49 7071 / 29 78985  Fax: +49 7071 / 29 5091