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

Chris Fields cjfields at illinois.edu
Mon May 4 13:51:23 EDT 2009


We can note it as deprecated for the next minor release (1.7).

chris

On Apr 29, 2009, at 3:58 PM, Chris Mungall wrote:

> 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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>
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