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

Chris Mungall cjm at berkeleybop.org
Wed Apr 29 16:58:15 EDT 2009


The .ontology files have been deprecated by GO. Use the .obo files  
instead.

It appears the bioperl parser for the .ontology files isn't able to  
deal with the new relations in GO. I suggest that the  
bioperl .ontology parser is deprecated too

On Apr 22, 2009, at 6:38 AM, Hilmar Lapp wrote:

> 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
>>
>>
>> _______________________________________________
>> 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 :
> ===========================================================
>
>
>
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