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Re: Advancing translational research with the Semantic Web

From: Bijan Parsia <bparsia@cs.man.ac.uk>
Date: Wed, 16 May 2007 11:43:13 +0100
Message-Id: <F8D438B7-9F81-444A-A230-55C31D5ED40A@cs.man.ac.uk>
Cc: Eric Jain <Eric.Jain@isb-sib.ch>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>

On May 16, 2007, at 11:15 AM, Phillip Lord wrote:

>
>>>>>> "EJ" == Eric Jain <Eric.Jain@isb-sib.ch> writes:
>
>   EJ> Just catching up on reading papers :-)
>
>   EJ> <http://www.biomedcentral.com/1471-2105/8/S3/S2>
>
>   EJ> "It is also useful to know who believes something and
>   EJ> why. However, there is no standard way of expressing such
>   EJ> information about a statement [...]"
>
>   EJ> Reification?
>
> That's who, not why.

No, you can do both with reification.

> The Gene Ontologies evidence codes are and
> references are much closer.
>
> Also, I am not sure of the semantics of reification.

RDF reification has very little to no built in semantics. What it  
provides is a standardized syntax.

> Does it mean "I
> made this statement", "I believe this statement" or "I am the person
> responsible for the evidence on which this statement is based".

It doesn't provide any of these propositional attitudes, but you  
could layer these on top of reification, i.e., use reification of a  
triple as the object of an "I believe..." statement. You could make a  
little "belief object" which had properties for who, when, why, to  
what degree, etc and "content" which would be the reified triple.

You can, of course, role your own reification mechanism, and that's  
what one typically does, e.g., to get n-ary predicates (or for things  
where one might have used an n-ary pred). Some stores (to my  
surprise, e.g., Jena) will take reified triples and condense them  
into a nicer internal form for querying (obviously this wouldn't help  
with a role-your-own).

In either case you have to supply the semantics of the operators  
separately, either through axioms or a special tool support.

OWL 1.1 provides a mechanism for putting annotations directly on  
axioms (which in the RDF mapping is encoded using RDF reification),  
with no specified semantics. One could use these as a hook, or just  
extend the XML or functional syntax directly.

You could also use literals.

However, all this *supports* your point. There *IS* no standardized  
way to represent this sort of information. There is a more or less  
standard (and widely loathed) hook/technique upon which you could  
build a standard mechanism for representing this sort of information.

> All
> three are independent I think.

Indeed.

Cheers,
Bijan.
Received on Wednesday, 16 May 2007 10:42:59 UTC

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