[DAS] DAS1.6: coordinate systems

Thomas Down thomas.a.down at gmail.com
Thu Aug 12 11:16:47 UTC 2010

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?

        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?


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