[DAS2] modification to /type request & response

Allen Day allenday at ucla.edu
Sun Apr 10 04:27:50 UTC 2005


I'm proposing a change to the way type requests are handled.

Background: According to the spec, a genomic feature may be typed by a
term from the Sequence Ontology Feature Annotation (sofa), or may be typed
by a term from another ontology so long as the term inherits from a sofa

I have two problems with this.

First, there may be other records we want to type -- as a concrete
example, let's say we want to type a protein feature as part of
protein-DAS, and the type is "alpha helix", which is not in sofa and may
be difficult to have inherit from an existing sofa type.  I have other
real-world examples from the array-DAS document I'm working on, if anyone
cares to see them -- related to biological sample annotation.

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.

Second, making a /type request is, according to the spec, supposed to
return all types known to the server.  If we allow non-sofa-inheriting
types into the datasource, the result can be a *very* large document.  As
a concrete example, serving up just sofa produces a das2xml 64KB document
containing 243 types.  By linear extrapolation, mixing in the Gene
Ontology, which contains 18651 types, will produce a document in excess of
4.8MB.  My DAS server actually contains ~15 ontologies that I could
conceivably want to annotate with.

I'd like to be able to restrict a /type response to a subset of types
known by the server, perhaps using the following:

* /das/genome/type

  returns all types known to the server

* /das/genome/type?namespace=sofa.ontology

  returns all types known to the server under the "sofa.ontology" 

* /das/genome/type?namespaces

  returns all type namespaces known to the server


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