[Bioperl-l] experimental IO module for exporting OWL from GFF
Chris Fields
cjfields at illinois.edu
Fri Jun 26 01:35:06 UTC 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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