[MOBY-l] Objects used for discovery

[Phillip Lord]

>>>>> "Ken" == Ken Steube <steube at sdsc.edu> writes:

  Ken> Hi all...there were two or three discussions during the meeting
  Ken> that I have thought about, and I'm beginning to think we're
  Ken> going down a bad road.  Let's try to flesh them out here.

  Ken> First topic:

  Ken> We had a brief discussion about input objects and their use for
  Ken> discovery.

  Ken> The issue was: given a sequence I want to be able to discover
  Ken> all I can do with that sequence including BLASTing it, feature
  Ken> analysis, and anything else anyone ever thinks of.  But then in
  Ken> order to simplify the handling of inputs and outputs I
  Ken> suggested having a BLAST input object which extends a sequence
  Ken> object to include the usual BLAST parameters.  Feed it into any
  Ken> BLAST service and you'll have everything needed to run BLAST
  Ken> (including your sequence).

  Ken> But now this issue arose: If you try to discover with a BLAST
  Ken> object will you get the same thing you'd get if you tried to
  Ken> discover with just a sequence object?  Since you've specialized
  Ken> your sequence object to include BLAST parameters you might miss
  Ken> some of the other services that might be discovered.  But in my
  Ken> opinion by going from a sequence to BLAST input you should have
  Ken> broadened the types of services you can discover.  You still
  Ken> have the sequence and can discover feature searches and
  Ken> anything else, but now you have other bits as well and can
  Ken> whatever else is allowed with those bits such as BLASTing.

This appears to be a subclass relationship. So BLAST sequence is a
subclass of Sequence, in which case you can do with a BLAST sequence
anything that you can with a sequence. Although it might well affect
the way that you rank the services. So a service which operates on a
BLAST sequence is probably to be preferred over a Sequence. 

Of course its possible that some services operate on a property of
BLASTSequence that a Sequence itself does not have, in which case you
will, as you say, want to broaden your range of services. This is the
sort of thing that we hope to achieve using OWL based descriptions of
the services. 

Cheers

Phil