[DAS] Retrieving feature information

[Oliver Lyttelton]

Dear Developers,
    Please consider this plea, it is heartfelt.

When I first heard about DAS, I was in a lecture at Imperial College on 
distributed Bioinformatics. The concept seemed perfect, the idea of allowing 
anyone with annotations to publish them in a standard format, which a single 
genome browser could interpret, creating a virtual free market on the 
internet, and thus improving the quality of annotation information for 
everyone.

Since I have been using the system, I have come across one massive problem 
with it, and that is the problem that there is no server-side conversion of 
coordinate systems during feature requests.

I understand the reason for wanting to store features at the lowest (and 
therefore most stable) level of granularity. However, I fail to see why this 
prevents real-time server-side conversion.

My basic premise is that a "dumb user" such as myself, ought to be able to 
query (programatically) a DAS annotation server in the coordinate system of 
their choice, and retrieve a list of all annotations stored on that server, 
in the same coordinate system. At the moment the amount of conversion 
required is prohibitive.

The task for the server is to translate the request location into chromosome 
coordinates, and then recurse down through the hierarchy picking up feature 
info at each level and translating it all into the client coordinate system. 
This strikes me as a server-side type job not client side, and if someone 
wrote the code once, it would save every client side program from having to 
do the same job.

To prevent queries returning too much info you could limit the number of 
features returned to a specific number...

Let me know what you think,

Best regards to everyone,

Oliver Lyttelton (MSc Project Imperial College)

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