[MOBY] [MOBY-l] Objects used for discovery

[Mark Wilkinson]

MOBY Central already works this way.

M


On Mon, 2003-03-17 at 13:05, Ken Steube wrote:
> Hi all...there were two or three discussions during the meeting that I
> have thought about, and I'm beginning to think we're going down a bad
> road.  Let's try to flesh them out here.
> 
> First topic:
> 
> We had a brief discussion about input objects and their use for
> discovery.
> 
> The issue was:  given a sequence I want to be able to discover all I
> can do with that sequence including BLASTing it, feature analysis, and
> anything else anyone ever thinks of.  But then in order to simplify
> the handling of inputs and outputs I suggested having a BLAST input
> object which extends a sequence object to include the usual BLAST
> parameters.  Feed it into any BLAST service and you'll have everything
> needed to run BLAST (including your sequence).
> 
> But now this issue arose:  If you try to discover with a BLAST object
> will you get the same thing you'd get if you tried to discover with
> just a sequence object?  Since you've specialized your sequence object
> to include BLAST parameters you might miss some of the other services
> that might be discovered.  But in my opinion by going from a sequence
> to BLAST input you should have broadened the types of services you can
> discover.  You still have the sequence and can discover feature
> searches and anything else, but now you have other bits as well and
> can whatever else is allowed with those bits such as BLASTing.
> 
> I think we can really make MOBY discovery more powerful than the
> current design.  All you have to do is to discover based on the BLAST
> input object and all the objects that share an ISA or HASA
> relationship with it. This is fairly simple do implement as long as
> our discovery is a logical OR operation for input object types.
> 
> Second topic:  later!
> 
> Ken
> 
> -------------------------------------
> Ken Steube            steube at sdsc.edu
> San Diego Supercomputer Center @ UCSD
> San Diego, California             USA
> 
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