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

Hilmar Lapp hlapp at gnf.org
Thu Aug 11 15:52:32 EDT 2005

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).

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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