[BioSQL-l] Can I load ontologies into BioSQL?

[Achille Zappa]

Hi guys

I'm working with biosql and I try to figure out how to load ontologies
into biosql.

I've tried to load the flat files gene ontologies :

load_ontology.pl   --driver mysql --dbuser xxx --dbpass xxx --host
localhost --dbname biosql --namespace "Gene Ontology" --format goflat
--fmtargs "-defs_file,GO.defs"  function.ontology process.ontology
component.ontology

as in the script info but I have an error,

a lot of  ------------ WARNING ---------------------
MSG: DBLink exists in the dblink of _default
---------------------------------------------------
and at the end
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: format error (file /home/user/Download/process.ontology) offending line:
     -negative regulation of angiogenesis ; GO:0016525 ; synonym:down
regulation of angiogenesis ; synonym:down\-regulation of angiogenesis
; synonym:downregulation of angiogenesis ; synonym:inhibition of
angiogenesis % negative regulation of developmental process ;
GO:0051093 % regulation of angiogenesis ; GO:0045765

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::OntologyIO::dagflat::_parse_flat_file
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:627
STACK: Bio::OntologyIO::dagflat::parse
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:284
STACK: Bio::OntologyIO::dagflat::next_ontology
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:317
STACK: load_ontology.pl:604
-----------------------------------------------------------

could you help me?
is it possible to use the OBO format with the loader?
those GO flat files are deprecated by the Gene Ontology site
is there a list of format to use with the biosql perl scripts?

thank you
regards
Achille





-- 
Achille Zappa
-Bioinformatics
 National Cancer Research Institute (IST)
 Largo Benzi 10
 16132 Genova - ITALY
 Tel. 010 5737288
-IEIIT - Sezione di Genova
 National Research Council (CNR)
 via De Marini, 6
 16149 Genova - ITALY


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