[Bioperl-l] Load_ontology.pl warnings and exceptions

Hilmar Lapp hlapp at gmx.net
Fri Jul 30 12:27:18 EDT 2004 

It doesn't seem you need to be concerned. The warnings are most likely  
all triggered by entries that have been obsoleted or merged. It does  
appear though that your unique index on the term table does not include  
the Is_Obsolete column. Unless you made some strict decisions to keep  
obsolete terms out and you enforce them in each load or update by the  
respective choice of arguments, I'd recommend you change the unique key  
to be over the tuple of (name, is_obsolete, ontology_id).

	-hilmar

On Wednesday, July 21, 2004, at 07:50  PM, Law, Annie wrote:

> Hi,
>
> Previously, I used load_ontology.pl and got about 5 exceptions or  
> warnings.
> Recently, while using the same bioperl and bioperl-db
> Setups. I tried to use the same version of load_ontology.pl again with  
> the
> latest information from GO ontology.  Now it seems that I get about 90
> warnings exceptions about 50 listed after ..terms and others listed  
> after
> ...relationships during the run.  I'm pretty sure that only the input  
> to the
> scripts has changed.  Is this a normal outcome?
>
> Are these warnings only a reflection of the source file and an  
> annotation of
> work in progress or is there something that I
> Am missing?  I wanted to eliminate the interference of previously  
> existing
> data so I went and created a new database, loaded the
> Bioperl schema and used the load_ncbi_taxonomy.pl script then I used  
> the
> load_ontology.pl script.
>
> Here is the output of the run.  It seems to me that they are all  
> complaints
> of duplicate entries.
> All of the bioperl is 1.4 and was installed around this past March.
>
> I would appreciate some insight.
> Thanks,
> Annie.
>
> Script started on Wed 21 Jul 2004 01:27:45 PM EDT
>> perl /root/bioperl-db/scripts/biosql/load_ontology.pl --dbuser=
> =user1 --dbpass=pass1 --dbname mydatabase --safe --computetc  
> --noobsolete
> --names
> space "Gene Ontology" --format goflat --fmtargs
> "-defsfile,/root/bioperl-db/data/GO.defs" /ro
> oot/bioperl-db/data/function.ontology  
> /root/bioperl-db/data/process.ontology
> /root/bioperl-db
> b/data/component.ontology
> Parsing input ...
> Loading ontology Gene Ontology:
> 	... terms
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0001529","elastin","","") FKs (1)
> Duplicate entry 'elastin-1' for key 2
> ---------------------------------------------------
> Could not store GO:0001529 (elastin):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005581","collagen","","") FKs (1)
> Duplicate entry 'collagen-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005581 (collagen):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005676","condensin complex","","") FKs (1)
> Duplicate entry 'condensin complex-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005676 (condensin complex):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005699","kinetochore","","") FKs (1)
> Duplicate entry 'kinetochore-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005699 (kinetochore):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005716","synaptonemal complex","","") FKs (1)
> Duplicate entry 'synaptonemal complex-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005716 (synaptonemal complex):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005717","chromatin","","") FKs (1)
> Duplicate entry 'chromatin-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005717 (chromatin):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005718","nucleosome","","") FKs (1)
> Duplicate entry 'nucleosome-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005718 (nucleosome):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0005733","small nucleolar RNA","","") FKs (1)
> Duplicate entry 'small nucleolar RNA-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005733 (small nucleolar RNA):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were
> ("GO:0006326","bent DNA binding","","") FKs (1)
> Duplicate entry 'bent DNA binding-1' for key 2
> ---------------------------------------------------
> Could not store GO:0006326 (bent DNA binding):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found
> by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

More information about the Bioperl-l mailing list