[DAS2] <CATEGORY> elements

Andrew Dalke dalke at dalkescientific.com
Mon Feb 6 16:03:07 UTC 2006

One discussion point from today is the <CATEGORY> elements.

The current draft of the spec says they look like this

       <CATEGORY type="segments" query_id="volvox/1/segments">
           <FORMAT name="fasta" mimetype="text/x-fasta" />
           <FORMAT name="raw" mimetype="text/plain" />
       <CATEGORY type="types" query_id="volvox/1/types">
           <FORMAT name="das2xml" mimetype="text/x-das-featuretype+xml" 
       <CATEGORY type="features" query_id="volvox/1/features">
           <FORMAT name="das2xml" mimetype="text/x-das-type+xml" />
       <CATEGORY type="locks" query_id="volvox/1/locks" />

Andreas Prlic pointed out that since the document says
the "volvox" version "1" url is already known ("volvox/1")
and the type="segments" then the query_id can be built
from appending "segments" to the "volvox/1" (plus the "/")
to get "volvox/1/segments".

I originally responded from a ReST purity argument, in that
URLs should not be constructed from non-URL data.  This
lets Thomas, for example, use GUIDs for the objects rather
than the hierarchical structure I and others recommend.

During discussion a better answer came up, which I think
we talked about earlier but which is worth emphasizing
is that the "query_id"s don't need to be on the same server.

For example, the "regions" URL may and likely will point
to a common reference server, and a database may offer
only one set of "types" for all of the "features".

That is, something like this

   DAS server example.com
      genome A
         version x
           segments at "ensembl.org/das2/genome_A/build_1/segments"
           features at "example.com/A/version_x/features"
           types at "example.com/A/types"

         version y
           segments at "ensembl.org/das2/genome_A/build_1/segments"
           features at "example.com/A/version_y/features"
           types at "example.com/A/types"

         version z
           segments at "ensembl.org/das2/genome_A/build_2/segments"
           features at "example.com/A/version_z/features"
           types at "example.com/A/types"

   DAS server biodas.org
      genome A
         version 1
           segments at "ensembl.org/das2/genome_A/build_2/segments"
           features at "example.com/A/1/features"
           types at "example.com/A/types"  (note: on other server!)

					dalke at dalkescientific.com

More information about the DAS2 mailing list