[DAS] DAS1.6: coordinate systems

Jonathan Warren jw12 at sanger.ac.uk
Thu Aug 12 11:54:24 UTC 2010

On 12 Aug 2010, at 12:16, Thomas Down wrote:

> On Thu, Aug 12, 2010 at 10:30 AM, Andy Jenkinson
> <andy.jenkinson at ebi.ac.uk>wrote:
>> Hi Thomas,
>> Uh-oh, URIs... :)
>> For coordinate systems, I think the definitions of the component  
>> pieces are
>> fairly well described. It is a pity that the species name is not  
>> given its
>> own parameter though. The sources documentation then says: "The uri
>> (required) attribute is a globally unique identifier for the  
>> coordinate
>> system. It should be a fully resolvable URL providing more  
>> information about
>> the coordinate system." This could be misleading as although the  
>> URIs _are_
>> resolvable, the content is not particularly machine friendly.
>> I am not willing to change the syntax of the coordinate system URIs  
>> out in
>> the wild, but if you need the content returned to be machine  
>> readable we
>> could replace the HTML content with an XML+XSLT combination. That  
>> is, "
>> http://www.dasregistry.org/dasregistry/coordsys/CS_DS6" would look  
>> more
>> like one of the entries in "
>> http://www.dasregistry.org/das/coordinatesystem" to a machine, and  
>> the
>> same as it currently does to a human. From a practical perspective  
>> though,
>> if a client parses the XML elements from the registry's
>> /das/coordinatesystem output, it can identify all the coordinate  
>> systems by
>> both URI and text description. Changing the output wouldn't  
>> materially
>> change what a client needs to do given either a URI or a comma  
>> separated
>> string. It is always going to need to run a HTTP get and do some  
>> parsing of
>> coordinatesystem XML. But it is certainly true that having the URI  
>> resolve
>> to the XML is a more elegant and simple to explain system, and in  
>> any case
>> the spec makes no mention of the fact that a client can even obtain  
>> the XML
>> for all the coordinate systems together.
> CS URIs pointing to XML definitely seems more symmetrical.
> Mentioning /das/coordinatesystem in the spec would help, too -- that's
> currently rather opaque.
> 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?
>        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?
If it were me I'd just add it to the known coordinate systems in the  
registry. You can ask us to do it or run a script that will add it if  
it doesn't exist already (can send you script if you want).
Having a not widely available genome in the registry wouldn't be  
harmful in any way? especially if it was coming out in the future. The  
only issue would be advertising an institute as working on this if  
they put themselves down as the authority I guess? which maybe in  
>        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?
If issue with authority advertising as above then mirror all sources  
plus private ones and change config/hardcode change of servers/clients  
to point at internal registry (which can just be a sources document  
hosted locally).


> Thomas.
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314

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