[Bioperl-l] GFF and LocatableSeq refactoring

[Scott Cain]

Hi Hilmar and all,

Actually, Chado stores sources as a dbxref for the feature (where the  
db.name is "GFF_source") and the source can be any string, which is  
what the GFF3 spec indicates.

I think the source was intended to be free text to allow the creator  
maximum flexibility when making the GFF; it also allows lots of  
flexibility when defining what features go into a particular track in  
GBrowse: you can have lots of gene features in your GFF, but you can  
segregate them according to what their source attributes are.

Additionally, some applications (SynBrowse comes to mind) overload the  
source value and require them to conform to a certain syntax.

So, what I'm trying to say is, source should probably just stay a  
simple string.

Scott

On Aug 18, 2009, at 11:46 AM, Hilmar Lapp wrote:

>
> On Aug 17, 2009, at 7:42 PM, Robert Buels wrote:
>
>> I can see how this might be a good idea, or it might be overkill.  
>> Anybody have thoughts on having feature _sources_ strongly typed  
>> with ontology terms?
>
>
> It's how BioSQL and Chado would store it anyway. I'm not sure  
> whether GFF3 requires it, possibly not.
>
> But when you make everything else ontology-typed, why exempt one  
> property that also stands to benefit from more predictable values?
>
> 	-hilmar
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research