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

[Hilmar Lapp]

Hi Achille,

according to Chris Mungall from the GO Consortium, the .ontology files  
have been deprecated by GO. You should use the .obo files instead, and  
BioPerl has a parser for that (and load_ontology.pl supports all  
formats that BioPerl supports).

There has been a near identical issue report earlier (April 20 - I  
don't have the thread from the archives at hand). According to Chris,  
the BioPerl parser for the .ontology files appears to fail to deal  
with the new relations in GO, and so with the obsoletion of  
the .ontology format we have scheduled the respective parser for  
deprecation.

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