[DAS2] modification to /type request & response
lstein at cshl.edu
Tue Apr 12 16:38:41 UTC 2005
The /types?ontology=XXXXXX is a good idea. I'll make that change. Maybe
there should be a "brief" form of the /types request which returns the
> > >>> 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".
> DAS2 mailing list
> DAS2 at portal.open-bio.org
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
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