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Re: Advancing translational research with the Semantic Web

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 17 May 2007 23:07:05 -0400
Message-Id: <5D48C2ED-9154-4F60-9567-6035922AF96B@gmail.com>
Cc: public-semweb-lifesci@w3.org
To: Eric Jain <Eric.Jain@isb-sib.ch>

On May 17, 2007, at 6:34 PM, Eric Jain wrote:

> There does indeed seem to be an existing has_participant predicate,  
> but is there also a "protein expression process" class? This would  
> seem rather contrived, from a biologists (if not an ontologists)  
> point of view (all we want to say, after all, is that the protein  
> can be found in some tissue)!

If you want to say that the protein is found in some tissue, that's  
what should be said. However, in your email you wrote that the  
protein is expressed in the tissue. They are not the same, and I  
think that in our semweb representations we should take care to not  
confuse them, though in language they are easily interchanged and we  
still (often) understand what each other is talking about.

If it is know to be found in the tissue I would make the subclass be  
the subclass of the protein each instance of which  is located in  
some instance of the tissue. No processes involved at all.

> Using widely used concepts and predicates is no doubt a good thing.  
> But if you can instead make do with core RDF features, that's even  
> better -- not everyone uses OBO, no matter how "foundational" it  
> may be :-)

I don't think we can make due with core RDF features, if we want to  
have agents that make reasonably inferences based on what they are  
told. RDF is just too weak to do much of anything in this direction.  
OTOH, if the RDF is always going to be interpreted by a human -  
essentially you are using RDF as an opaque (from a machine agent  
point of view) syntax, then there is no problem. I guess I am hoping  
my machines to help me more than that.

> Note that the reification "design pattern" allows you to add  
> attribution information on statements that you did not at first  
> think would ever need such information, without breaking the data  
> model.

As long as those statements are single triples. It gets more involved  
when statements are more than a single triple, as they often will be.

-Alan


Received on Friday, 18 May 2007 03:07:06 UTC

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