[BioSQL-l] Problem when trying to persist GO in BioSQL

[Hilmar Lapp]

Hi Andreas - it seems that the GO download you have has two terms  
with name 'invasive growth', which are both obsoleted, but have  
different GO IDs.

That's a somewhat nasty situation and happens occasionally (ask the  
GO people if you want to know more on why exactly that's necessary).  
If you're loading the ontology fresh into your database you can avoid  
all that by simply leaving all obsolete terms outside using the -- 
noobsolete switch. There are other options for handling obsolete  
terms (see the script's POD) that should allow you to stay out of  
that trouble for updates too.

	-hilmar

On May 8, 2008, at 2:52 AM, Andreas Dräger wrote:
> Dear all,
>
> Thank you for your advice! Now it works, but not completely. It  
> seems that there is either a problem with the ontology file I  
> downloaded from GO (gene_ontology_edit.obo) or an error in the script:
>
> ./scripts/biosql/load_ontology.pl --host localhost --dbname  
> bioseqdb --dbuser myUser --dbpass 'myPasswd' --driver mysql -- 
> namespace "Gene Ontology" --format obo gene_ontology_edit.obo
>
>
>
> And it works:
>
>
>
> Loading ontology gene_ontology:
>         ... terms
>         ... relationships
>         Done with gene_ontology.
> Loading ontology biological_process:
>         ... terms
>
>
>
> But then I receive the following messages:
>
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were ("GO:0007125","invasive growth","OBSOLETE (was not defined  
> before being made obsolete).","X","") FKs (46)
> Duplicate entry 'invasive growth-46-X' for key 3
> ---------------------------------------------------
> Could not store term GO:0007125, 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/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: main::persist_term ./scripts/biosql/load_ontology.pl:802
> STACK: ./scripts/biosql/load_ontology.pl:607
> -----------------------------------------------------------
>
>  at ./scripts/biosql/load_ontology.pl line 814
>         main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH 
> (0xa1b502c)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8ba793c)',  
> '-termfactory', 'undef', '-throw', 'CODE(0x87406d8)', '- 
> mergeobs', ...) called at ./scripts/biosql/load_ontology.pl line 607

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