[DAS2] modification to /type request & response

Allen Day allenday at ucla.edu
Mon Apr 11 20:33:40 UTC 2005

>> 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.


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