[DAS2] URIs for sequence identifiers

Ed Erwin ed_erwin at affymetrix.com
Mon Mar 13 23:56:56 UTC 2006

Andrew Dalke wrote:

>>There are several servers that understand more than one coordinate
>>system and can return the same type of data in different coordinates.  
>>(depending on which type of accession code/range was used for the
>>request ) E.g. there are a couple of zebrafish servers that speak
>>both  in Chromosome and Scaffold coordinates. (reason perhaps
>>being that zebrafish is an organism that seems to be very difficult
>>to assemble ?)
> The current DAS system does not support this because of how
> it does segment identifiers.
> Problem #1: We need two entry points, one to view the segments
> in Scaffold space, the other to view them in Chromosome space.
> Solution #1 (don't like it though).
> Add a "source=" attribute to the CAPABILITY and allow multiple
> segments capabilities

> Problem #2: feature searches return features from either namespace

A different solution:

Scaffold and Chromosome coordinate systems are served by separate DAS/2 
servers.  Each server returns data from one and only one namespace.

Those separate servers can, behind-the-scenes, use the same database.

DAS/2 clients, like IGB, would choose to connect to either the 
Scaffold-based server or the Chromosome-based server, but not usually to 
both at once.

Does this handle all the issues?


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