[BioSQL-l] Problem loading GO.

[Leighton Pritchard]

Hi,

I've been trying to upload the GO into a clean BioSQL (MySQL, 1.4.1)
schema using the BioPerl bp_load_ontology.pl script, with the OBOv1.0,
OBOv1.2, and the most recent flatfiles from
http://www.geneontology.org/GO.downloads.ontology.shtml - none of my
attempts have been successful.  The errors below are from a Linux
installation, but the same errors are thrown on OS X, too.  I am using
the most recent versions of BioPerl and bioperl-db, installed via CPAN:

[lpritc at lplinuxdev sequence_data]$ perl -MBio::Root::Version -e 'print
$Bio::Root::Version::VERSION,"\n"'
1.005002102

and bioperl-db 1.5.2.

I have attached the traceback below (running with --safe throws a number
of equivalent errors), and I would be grateful for any help you might be
able to offer with setting me on track to fixing this.

SOFA is loaded without issues, you might be pleased to hear ;)

Thanks in advance,

L.


########

[lpritc at lplinuxdev sequence_data]$ bp_load_ontology.pl --host localhost
--dbname biosql --namespace "Gene Ontology" --dbuser lpritc --dbpass
******** --format obo ~/Downloads/gene_ontology_edit.obo
Loading ontology gene_ontology:
        ... terms
        ... relationships
        Done with gene_ontology.
Loading ontology biological_process:
        ... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values
were ("","","0","") FKs ()
Column 'dbname' cannot be null
---------------------------------------------------
Could not store term GO:0018901, name '2,4-dichlorophenoxyacetic acid
metabolic process':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::DBLink) 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::TermAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
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 /usr/bin/bp_load_ontology.pl:805
STACK: /usr/bin/bp_load_ontology.pl:610
-----------------------------------------------------------


[lpritc at lplinuxdev sequence_data]$ bp_load_ontology.pl --host localhost
--dbname biosql --namespace "Gene Ontology" --dbuser lpritc --dbpass
******** --format goflat --fmtargs ~/Downloads/GO.defs
~/Downloads/function.ontology   
Loading ontology Gene Ontology:
        ... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values
were ("MetaCyc","2\,3-DIHYDROXYINDOLE-2\,3-DIOXYGENASE-RXN","0","") FKs
()
Duplicate entry '2\,3-DIHYDROXYINDOLE-2\,3-DIOXYGENASE-RX-MetaCyc-0' for
key 2
---------------------------------------------------
Could not store term GO:0047528, name '2\,3-dihydroxyindole 2
\,3-dioxygenase activity':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::DBLink) 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::TermAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
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 /usr/bin/bp_load_ontology.pl:805
STACK: /usr/bin/bp_load_ontology.pl:610
-----------------------------------------------------------

 at /usr/bin/bp_load_ontology.pl line 817
        main::persist_term('-term',
'Bio::Ontology::GOterm=HASH(0xa6afb9c)', '-db',
'Bio::DB::BioSQL::DBAdaptor=HASH(0x9b5afd0)', '-termfactory',
'Bio::Ontology::TermFactory=HASH(0x9f40d10)', '-throw',
'CODE(0x96f6b68)', '-mergeobs', ...) called
at /usr/bin/bp_load_ontology.pl line 610


-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland DD2 5DA
e:lpritc at scri.ac.uk            w:http://bioinf.scri.ac.uk/lp
gpg/pgp: 0xFEFC205C
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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