[Bioperl-l] experimental IO module for exporting OWL from GFF

Chris Fields cjfields at illinois.edu
Thu Jun 25 21:35:06 EDT 2009


I agree.  Just to note, FeatureIO (even though it's in core) will be  
operated on at some future point to be simplified (and likely will  
move away from Bio::SF::Annotated).

chris

On Jun 25, 2009, at 8:08 PM, Mark A. Jensen wrote:

> This sounds very Dev to me. Also cool.
> MAJ
> ----- Original Message ----- From: "Chris Mungall" <cjm at berkeleybop.org 
> >
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, June 25, 2009 8:32 PM
> Subject: [Bioperl-l] experimental IO module for exporting OWL from GFF
>
>
>>
>> I've written a module Bio::FeatureIO::seqont_owl, which generates   
>> Sequence Ontology compliant RDF/OWL. This will allow for example   
>> loading of GFF into triplestores and inference using OWL reasoners.
>>
>> - It's experimental, fairly incomplete, and subject to change
>> - Relies on an experimental extension of SO
>> - Probably of interest to a minority of bp users
>> - It's not yet fully documented (but there will be a paper)
>> - It doesn't introduce any additional dependencies (all done via   
>> XML::Writer, which is already a dependency)
>> - Doesn't otherwise impinge on existing code
>>
>> I'd like to get this under source control. Is the appropriate  
>> place  for this:
>>
>> - HEAD
>> - a branch
>> - bioperl-dev
>> - a separate repository
>>
>> ?
>>
>> Cheers
>> Chris
>>
>>
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