[DAS2] modification to /type request & response

Chervitz, Steve Steve_Chervitz at affymetrix.com
Mon Apr 11 19:35:03 UTC 2005

Allen Day writes:
> 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.

One aim of DAS/2 is to disallow the "anything goes" policy for feature
typing, and to constrain them to be part of some ontology or related to a
term in an existing ontology so that DAS/2 clients have a chance of making
sense of them.

The DAS/2 grant contemplates how to extend an existing ontology, but doesn't
discuss plans for incorporating types that don't fit into any established
ontology. Here's the relevant snippet from the grant:

"Using a standard sequence ontology does not preclude extending the
ontology.  One of the advantages of using RDF and OWL to specify ontologies
is that there is a formal mechanism for anyone to extend an existing
ontology, which gives rise to distributed ontologies.  This ability to
extend ontologies is built on the same URI linking concepts previously
discussed regarding feature ids.  Thus for example someone with detailed
knowledge of some the biology of repetitive sequences, for instance, may be
annotating repeat data and want a much finer classification of repeat types
than is specified in the reference ontology. They can define an extension of
the existing ontology via RDF that refers to the existing ontology and
specifies the extension (such as LINE-variantX isa type of LINE), then serve
up DAS sequence features that refer to this extended ontology rather than
the reference ontology.  But because the referenced ontology formally
extends the standard ontology, a DAS client could still be aware that
LINE-variantX is a type of repeat, if for example it wants to display all
repeats using the same color.  Many software tools are now available to make
such ontology extensions easy."

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?

It does seem like there should be an avenue for people to say, "Here's a new
type that doesn't belong to any established ontology (or if it does, I'm not
sure where it goes)." Could such an avenue be opened without having it be

Interesting google result: Searching for "protein sequence feature ontology"
gives about 35,000 hits, the second of which is the DAS/2 spec introduction!


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