[DAS] Re: DAS web service proposal

Lincoln Stein lstein at cshl.org
Sat May 24 13:08:49 EDT 2003

Hi Brian,

I appreciate this and admire the thought that went into it.  

I wonder whether we shouldn't explicitly separate the concept of a "feature on 
a genome" from "a biological object?"  I keep bumping into this issue over 
and over again, where people get stuck on the confusion between these three 

	a) a generic class of feature, such as "SINE repeat element"
	b) a specific feature, such as "this H. sapiens ALU element consensus"
	c) the position of the feature on the genome, such as "the ALU element
		match that is right here"

By separating these concepts out, a DAS feature would then distinguish:

	- an LSID that indicates the feature's Sequence Ontology type (a)
	- an LSID that provides access to the rich biological description of 
	this object (b)
	- an LSID that refers to a particular instance of this object on a genome (c)

I imagine that "the biological context" that you refer to in the proposal is 
type (b).  There should be a query interface for these objects and a way to 
retrieve them that is distinct from the process of querying a feature by its 
location and type that is provided by baseline DAS.


On Friday 23 May 2003 08:31 pm, Brian Gilman wrote:
> Hey Lincoln,
>     Here's the proposal that I wrote with a colleague of mine on
> sourceforge. We haven't implemented this idea as he has been on vacation.
> I'd like to know your thoughts!
>     One last note, there is code in the word doc that shows excalty how to
> turn a das server into a SOAP server and how SOAP adds value to das.
>                                 -B

Lincoln Stein
lstein at cshl.org
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
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