[DAS2] modification to /type request & response

Lincoln Stein lstein at cshl.edu
Tue Apr 12 16:36:26 UTC 2005


The Types request returns the ontology you are using in the "ontology" 
attribute of the <TYPE> tag.  I think it is fair to insist that if you add 
a new type to the system you must prepare an ontology that describes it if 
there isn't one ready-made to inherit from.

The /type request is only supposed to return those types which are used.  I 
never expected someone to load the entire sofa database into the thing -- 
just that subportion of sofa which is actively used to annotate the 
database objects.


On Sunday 10 April 2005 12:27 am, Allen Day wrote:
> Hi,
> 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 term.
> 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"
>   namespace
> * /das/genome/type?namespaces
>   returns all type namespaces known to the server
> -Allen
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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
all emails regarding scheduling and other time-critical topics.
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