[Bioperl-l] Load_ontology.pl warnings and exceptions

Law, Annie Annie.Law at nrc-cnrc.gc.ca
Wed Jul 21 14:50:13 EDT 2004 

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

--------------------------------------

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