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

Hilmar Lapp hlapp at gmx.net
Wed Apr 22 09:38:53 EDT 2009


Hi Carlos,

I am moving your inquiry to the BioPerl list, as the tool is a part of  
Bioperl-db and uses BioPerl for parsing the ontologies.

In your case, the goflat parser in BioPerl seems to balk at the second  
one of the input files. It may be that the input file is (was?)  
corrupted, that does happen every once in a while. More likely though  
is that the goflat parser hasn't kept up with some format changes.  
Have you tried using the obo format version instead?

	-hilmar

On Apr 20, 2009, at 11:44 AM, Carlos A. Canchaya wrote:

> Hi guys
>
> I'm working with biosql and I try to figure out how to load  
> ontologies into biosql.
>
> I've tried
>
> load_ontology.pl   --driver mysql --dbuser carlos --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,
>
>
> ------------------- WARNING ---------------------
> MSG: DBLink exists in the dblink of _default
> ---------------------------------------------------
>
> ------------- EXCEPTION -------------
> MSG: format error (file 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 Bio::OntologyIO::dagflat::_parse_flat_file /usr/local/share/ 
> perl/5.10.0/Bio/OntologyIO/dagflat.pm:627
> STACK Bio::OntologyIO::dagflat::parse /usr/local/share/perl/5.10.0/ 
> Bio/OntologyIO/dagflat.pm:284
> STACK Bio::OntologyIO::dagflat::next_ontology /usr/local/share/perl/ 
> 5.10.0/Bio/OntologyIO/dagflat.pm:317
> STACK toplevel /usr/local/share/biosql/bioperl-db/scripts/biosql/ 
> load_ontology.pl:604
> -------------------------------------
>
> Any suggestion?
>
> Cheers,
>
> Carlos
>
>
> _______________________________________________
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> 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 :
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