[Bioperl-l] Could not load GO terms to BioSQL

[Holland, Richard]

On attempting to load the current GO definitions I get this:

bifo6.agresearch.co.nz>
/usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl --host
bifo6 --dbname seqstore --dbuser zzzz --dbpass zzzz  --driver Oracle
--namespace "Gene Ontology" --lookup --remove --format goflat --fmtargs
"-defs_file,/raidset/tmp/goterms/GO.defs.txt"
/raidset/tmp/goterms/function.ontology.txt
Parsing input ...
Loading ontology Gene Ontology:
        ... terms
DBD::Oracle::st execute failed: ORA-01401: inserted value too large for
column (DBD ERROR: OCIStmtExecute) [for Statement "INSERT INTO dbxref
(dbname, accession, version) VALUES (?, ?, ?)" with ParamValues: :p3=0,
:p1='MetaCyc', :p2='TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN'] at
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line
1001, <GEN0> line 10575.

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values
were ("MetaCyc","TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN","0") FKs ()
ORA-01401: inserted value too large for column (DBD ERROR:
OCIStmtExecute)
---------------------------------------------------
Could not store GO:0000010 (trans-hexaprenyltranstransferase activity):

------------- EXCEPTION  -------------
MSG: create: object (Bio::Annotation::DBLink) failed to insert or to be
found by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda
ptor.pm:207
STACK Bio::DB::BioSQL::TermAdaptor::store_children
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/TermAdaptor.pm:291
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda
ptor.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda
ptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/Persistent/PersistentObje
ct.pm:270
STACK (eval)
/usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl:506
STACK toplevel
/usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl:488

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

bifo6.agresearch.co.nz>

Simple fix is to adjust the size of the accession column in dbxref. I
have doubled it to 64 characters. Could someone verify this is sensible
and see if the schema could be updated to match? I don't have access to
CVS to do it myself.

PS. Whilst you're at it could you also modify the rank column of
bioentry_reference to allow numbers up to 3 digits long, not 2, as per
my previous email.

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279



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