[DAS] DAS1.6: coordinate systems

Jonathan Warren jw12 at sanger.ac.uk
Thu Aug 12 14:45:38 UTC 2010

On 12 Aug 2010, at 15:35, Andy Jenkinson wrote:

> On 12 Aug 2010, at 12:16, Thomas Down wrote:
>> A few other questions (don't really have "preferred" answers to any  
>> of these, just trying to test the boundaries):
>>        1. What do you expect a server to do if it sees a CS URI  
>> that it hasn't seen before?
> I assume you mean an alignment server receiving such a URI as a  
> parameter? If so I think there is only one realistic thing it can do  
> right now, which is return nothing (i.e. no alignments). It is not  
> an authority on which coordinate systems are real and which aren't,  
> it just knows about the ones it is using. In essence it simply has  
> no data for the requested subject because it doesn't recognise the  
> subject. We could invent error situations for things like this, but  
> that would make DAS more complex for little gain IMO..
>>        2. If my organization has sequenced a new genome and is  
>> running some internal DAS stuff on that while we finish annotating,  
>> etc., what URI do we use for the coordinate system?
>>        3. If my organization is running an internal mirror of the  
>> central DAS registry, would I mirror the CS URIs ("http://das.bigpharma.com/dasregistry/coordsys/CS_DS40/ 
>> ").  Still point to dasregistry.org?  Something else?
> As Jon says, I think it's easier just to create the coordinate  
> system in the registry. At the moment you need admin privileges to  
> do that via the interface, but I implemented a programmatic version  
> of this wherein the registry accepts POSTed coordinate system XML  
> (sans URI) and replies with the same (with URI included). It is  
> restricted to allow you to create new authority/versions, but not  
> new "segment types": so you can create "GRCh_38,Chromosome,Homo  
> sapiens" but not "GRCh_37,wibble,Homo sapiens". We were a bit wary  
> of opening up the ability to do the latter in fear of ending up with  
> different spellings of the same thing, or other similar issues.
> I suppose the same thing could be made available to registered users  
> in the interface (possibly at the same time reworking it to use the  
> web services underneath).
This functionality is currently available in the interface for admin  

>> Thomas.
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
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Telephone: 01223 492314

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