[Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal

Ewan Birney birney at ebi.ac.uk
Thu Aug 11 17:09:07 EDT 2005

Hilmar Lapp wrote:
> On Aug 10, 2005, at 2:03 PM, Chris Mungall wrote:
>> Regarding 'magic' in SeqIO - not sure this is required. You can already
>> plug in your own factories here, we just need to extend this with feature
>> factories. The default method will continue to produce relatively light
>> SF::Generics?
> Right, this is exactly what I was thinking. A feature factory that 
> creates ontology-compliant features will also probably need to have 
> something like an OntologyTermResolver, in order to check a given 
> feature type (primary_tag) against an ontology that sits somewhere 
> (local file, local database, remote database, or even remote file).

Ok - I'll hold off the magic for the moment, but I think it would
be nice to have just-enough of SO in-built into Bioperl so one
could do something like:

   $seqio = Bio::SeqIO->new( -file => "-", -format => 'EMBL', -feature_converter => 'SO');

and the "right thing" happens.

Does anyone want to propose an alt name to


But for that is it ok for me to implement and commit?

>     -hilmar

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