[DAS2] modification to /type request & response

Suzanna Lewis suzi at fruitfly.org
Mon Apr 11 21:27:27 UTC 2005

On Apr 11, 2005, at 1:33 PM, Allen Day wrote:

>>> I'd like to remove the constraint that all types inherit from a type.
>>>  It
>>> makes sense to keep a constraint like this in place for genome
>>> sequence
>>> features, but not any other record type.
> [...]
>>> Regarding protein feature types, I think the SO team plans to put 
>>> them
>>> in
>>> SO/SOFA since they summarize it as, "a set of terms used to describe
>>> features on a nucleotide or protein sequence." But there is no 
>>> support
>>> for
>>> proteins in SO/SOFA yet. Suzi?
>> Yes, that is pretty much where it stands. There is the intention of
>> doing this, but we have not yet gotten to that point. Including the
>> basic structural descriptions of a protein (alpha helices, beta
>> sheets...)
>> seems an obvious new addition and easy enough to do.
>> I strongly agree with Steve here that we absolutely must stay
>> away from ad hoc types. They are the sirens on the rocks:
>> alluring, but lethal.
> Regarding ad hoc types, I agree as well.  What I meant to say is that 
> we
> ought to allow non-sequence feature types be served up by DAS/2, and to
> allow extensions to those types.  Basically I'm proposing to have DAS/2
> handle non-sequence feature ontologies in the same way that it handles 
> the
> sequence feature ontology.

Hi Allen,

I don't understand, but maybe I'm muddling GFF3 with DAS/2.
In GFF3 clearly everything is sequence-based in one way or
Perhaps you could provide some scenarios/examples where
this would apply in DAS/2?


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