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

[Ken Steube]

Can you address the situation of having a BLAST input object?  Last
weekend we said that if we decided to create and use a BLAST input object
for discovery then we wouldn't discover services with a sequence as input.

The idea we had of discovering against a sequence object plus some other
data that the user gets queried for is confusing and maybe hard to
support.

I understand that we can already tell what objects share an ISA and HASA
relationship to, say, BlastInputObject. But knowing them is not good
enough. We need to use these other objects in discovery.

Ken

-------------------------------------
Ken Steube            steube at sdsc.edu
San Diego Supercomputer Center @ UCSD
San Diego, California             USA

On 18 Mar 2003, Mark Wilkinson wrote:

> 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
> >
> > _______________________________________________
> > moby-l mailing list
> > moby-l at biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
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