[BioSQL-l] gene ontology questions revisited

[Daniel Lang]

On Friday 19 September 2003 05:22, you wrote:
> Let me know if the response I just sent for Raphael's posting doesn't
> answer or doesn't apply to your problem.
Problem solved, thanks!
But another one occurred while loading the data:
-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values were 
("MetaCyc","2-PYRONE-4\,6-DICARBOXYLATE-LACTONASE-RXN","0") FKs ()
ERROR:  value too long for type character varying(40)
---------------------------------------------------
Could not store term relationship (2-pyrone-4,6-dicarboxylate lactonase 
activity,IS_A,carboxylic ester hydrolase 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/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::TermAdaptor::store_children 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/TermAdaptor.pm:290
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:215
STACK Bio::DB::Persistent::PersistentObject::create 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:243
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170
STACK Bio::DB::Persistent::PersistentObject::create 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:243
STACK (eval) ../load_ontology.pl:516
STACK toplevel ../load_ontology.pl:515

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

DBD::Pg::st execute failed: ERROR:  value too long for type character 
varying(40) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BaseDriver.pm 
line 1001, <GEN3> line 2377.

Seems that some entries for term.name are longer as the expected 40 chars 
because of a backslash used to escape a comma in the molecule name:(

As I´m not familiar with the GOflat format, I also had a look at the files 
(and those from may) and it seems, that the escaping is always done in this 
field.

A quick´n dirty solution would be to eliminate the backslashes in the files, 
but can I update the database so easily with load_ontology.pl ?

Daniel 

-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

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