[DAS2] segments and types

Andrew Dalke dalke at dalkescientific.com
Fri Oct 27 19:56:27 UTC 2006

A couple of observations about what I've seen in existing
DAS1 servers.  Nothing here concerns format changes.

There are four different ways to handle segments:
   1) Don't provide segment information
        "Our clients know the segment because of the id
         so they don't need a segments document"
   2) use "size" (pre-DAS 1.0 spec)
   3) use "start"/"stop" (DAS 1.0 spec)
       - with variations, like "0", "0" meaning the length is undefined
           (and even "1", "0", with a size="2", for one server!)
   4) use a "version" field

The last is mostly used for protein sequences, that I've seen.
Its an aspect of #1 ("9pti" means "bovine pancreatic trypsin
inhibitor structure from PDB") as an abstract identifier, with
the version used to make it concrete ("with the update because
the first release had a typo")  I think it can be encapsulated
in the uri scheme we now use because each version gets it own
identifier, and since the client knows all versions there's no

The folks at EBI/Sanger (what's the correct collective term;
Hinxton? Genome Campus?) know which servers provide which
systems so many servers don't provide coordinates.

In some cases, like rabbit, the server will generate about
120,000 segments, one for each scaffold.  It takes quite some time
(a minute or more) to generate the output.  In theory this is
static and can be precomputed by the server.

For my own knowledge, when do people want the complete list
of segments?  When do they want the length?  You, yes, you
there, in front of the computer.  When do you you want to
use it?

Let me stress -- this is not a request to change anything.  I
would like to know for my own sake, for writing the documentation,
and for how much emphasis to put on this for the validation.

As another observation, the Sanger/EBI servers also don't
do much with the types document. Some don't even handle the
request.  Eugene said that no one had asked him to add it.
It's there now (thanks Eugene).

I think this is because most of their servers only had a single
type and the solution was "display everything."  They are
running into difficulties with this for a few new servers and
will be need type support, and type filter support soonish.

					dalke at dalkescientific.com

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