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

[Hilmar Lapp]

(FYI, changed to BioPerl list as this is a BioPerl issue with the old  
GO format. -hilmar)

On Jun 22, 2009, at 10:12 AM, Achille Zappa wrote:

> 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
>
>
> Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della  
> nostra RICERCA.
> Come fare:
> Nella prossima dichiarazione dei redditi metti la firma
> nell'apposito riquadro del 5 per mille,
> scrivendo anche il codice fiscale dell'Istituto Nazionale per la  
> Ricerca sul Cancro di Genova :
>  c.f. 80 100 850 108
> Istituto Nazionale per la Ricerca sul Cancro
> L.go R. Benzi, 10 -16132 Genova
> http://www.istge.it
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================