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

[Florian Mittag]

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