[DAS2] modification to /type request & response

Allen Day allenday at ucla.edu
Mon Apr 11 21:49:57 UTC 2005

On Mon, 11 Apr 2005, Suzanna Lewis wrote:

> 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
> another.
> Perhaps you could provide some scenarios/examples where
> this would apply in DAS/2?

I can't think of anything in genome-DAS that should not have its primary
type be a sequence feature type, or some derivative of an existing
sequence feature type.

An example of where I need to do this is outside the genome service -- in
the array-DAS service.  I need to be able to attach types to biological
source materials that participate in experiments.  For example, I might
want to annotate a skeletal muscle sample from a morbidly obese human from
the mouse anatomical ontology as "skeletal muscle".  I'd also attach the
type "morbidly obese", which is an extension to the mammalian phenotype
ontology type "obese".


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