[Bioperl-l] Bio::Ontology::OBOEngine for parsing obo files?

[Nathan Liles]

Actually, yes I did find that and it works very well. Now I'm wondering, is
it possible to search for similar terms using a string instead of a
Bio::Ontology term object? For examle, I'd like to search for the synonym:
"transcription start site" and have it return all similar terms. But, it
throws an error if I pass in a simple query like that.

-Nathan

On Tue, Dec 15, 2009 at 4:05 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> That shouldn't happen I suppose, but you're not supposed really to use the
> engine directly. Rather it will be used as a backing parser by the
> Bio::OntologyIO parser you choose. Have you tried that route and found it
> not to work?
>
>        -hilmar
>
>
> On Dec 15, 2009, at 4:37 PM, Nathan Liles wrote:
>
>  Is the Bio::Ontology::OBOEngine module working or being currently
>> maintained? I tried following the documentation in the module:
>>
>> * use Bio::Ontology::OBOEngine;
>>
>> my $parser = Bio::Ontology::OBOEngine->new
>>              ( -file => "gene_ontology.obo" );
>>
>> my $engine = $parser->parse();
>>
>> *But, it throws an error when I run the file saying 'Can't locate object
>> method "parse" '. Does anyone have any experience getting this module
>> working; or, is there any alternative bioperl module to extract terms and
>> relationships out of sequence ontology files?
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>>
>>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
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