[Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO

Allen Day allenday at ucla.edu
Mon Oct 11 13:51:26 EDT 2004

Look at Bio::FeatureIO::gff in bioperl-live.  It currently supports
lookup/validation of ontology terms via Bio::Ontology::OntologyStore, but
doesn't do and cardinality or type/relation enforcement which you seem to
be alluding to below.

I'd be very pleased if you want to work on this too.  Or anyone else on
these lists, for that matter :-).


On Mon, 11 Oct 2004, Steffen Grossmann wrote:

> Dear all,
> I fancy very much the approach taken by SO(FA) 
> (http://song.sourceforge.net/) to standardize the vocabulary used for 
> sequence annotation. Also, the GFF3 format is a nice way to represent 
> SO-compatible annotations and it would be a great thing to have this all 
> working seamlessly with bioperl.
> A first step towards such a seamless integration into bioperl would be a 
> parser which is able to read/write hierarchically nested feature 
> collections from/to GFF3 files. Such a parser should make use of the 
> GFF3 specific 'ID' and 'Parent' tags.
> Of course, I know about the 'Bio::Tools::GFF' and 
> 'Bio::SeqFeature::Tools' modules, where some related stuff can be found. 
> The problem is that the 'Bio::Tools::GFF' module doesn't respect the 
> 'Parent' and 'ID' tag structure and grouping in the 'Unflattener' 
> approach is also done conceptually different.
> Does anybody know about whether there is someone working on such a 
> project? Or, if there is no such project, is someone interested in 
> joining to start it?
> Thanks in advance for any response!
> Steffen

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