Re: blog: semantic dissonance in uniprot

On Mar 26, 2009, at 12:28 AM, Peter Ansell wrote:

> 2009/3/26 Pat Hayes <phayes@ihmc.us>:
>> Well, if you can tell us how to do some weaving, we maybe can make  
>> progress.
>> The properties of sameAs are fairly easy to list. It is transitive,
>> reflexive, symmetric and substitutive: if A sameAs B and something  
>> is true
>> of A, then its also true of B.  So, which of these _aren't_ correct  
>> for the
>> application you have in mind? Can you say why not (an example will  
>> do)?
>> "Less rigorous" doesn't cut it.
>
> It is easy in theory to state a property from logic theory in a truly
> rigourous once-correct-always-correct way for every potential context,
> but in reality each context will find a different value to each
> combination of the properties you refer to

If this really is true, then just give up trying to express this in  
OWL or any other ontology language, especially one for use on the Web.  
The whole point of such formalizations is that they mean the same in  
their context of use as they did in their context of creation/ 
publication. That is what they are _for_, the reason why people want  
ontologies in the first place. If you have something that means  
different things at different times to different people, you should  
not be in the ontology-writing game in the first place. (This has  
nothing to do with 'rigour', by the way.)

> , in the range between,
> utterly pedantic to the point of being completely uninterpretable to a
> non logic theory expert and still both correct and incorrect depending
> on the scenario, up to a laise faire "not cutting it" method where
> "shock horror" database records are referred to as *both* instances
> and classes of molecules at the same time!

Logics can be surprisingly flexible. ISO Common Logic has no problems  
with something being both a class and an instance at the same time,  
for example. In (non-Web, but rigorous) work we did for IARPA, our  
formalisms could have a single thing being simultaneously an  
individual, a property, a class and a proposition. I suggest, rather  
than trying to second-guess what you see as the intellectual failings  
of logical "rigor", just tell us what you want to say. If you can't  
even say it yourself in free English, how can you expect us to give  
you a formalism which can say it?

> Some of the applications of
> biological data would shock someone used to complete rigour but they
> turn out to be sufficient evidence for people making statements about
> things in the sciences. Some people find the flexibility to be
> liberating.

I do myself. But one can combine flexibility with "rigor".

>
> The whole idea of the Global Graph fails to take into account the fact
> that statements which are included may have been designed for limited
> scenarios,

Then they should not be published on the Web. You are simply playing  
the wrong game here.

> where for instance the exact rigourous nature of something
> is either not known, was previously thought to be rigourously correct,
> or was previously thought to be practical in a limited scenario.
> Trying to make things work in the Global Graph doesn't require weaving
> in my opinion, it requires some clean chopping, where within domains
> things are accepted, but outside of that, rigour is logically limited
> if only because it is impossible to prove that outside of the
> Global-Graph-knowledge-universe that a particular statement has a
> useful meaning if the person doing the human verification isn't an all
> over expert and all knowledgeable about the truth. If there was only
> one statement in the Global Graph that was actually incorrect it might
> be practical to apply rules and determine where it breaks before
> attempting to fix the break and try again.
>
> It might sound drastic but it would eliminate all of this continuous
> banter if people stopped trying to make things work in the global
> context and in the process confuse everyone else who only really
> wanted to use the knowledge in their local field of work. The whole
> idea of logic theory applied to practical knowledge only seems to be
> suited to limited areas where there is absolute and full understanding
> of every property and interaction in the system being described

You could not be more wrong. It is absolutely of the essence of logics  
that they give incomplete descriptions of things and do not require  
full understandings of everything. .

> , or
> else you might say something which is later found to be *false!*
>
> Admittedly we probably need to find an alternative to sameAs

Fine. Tell us what you want this alternative to be like, what  
inferences it should support. Tell us _something_ about it. If you  
can't even make a start on answering questions like this, then you  
simply have nothing to say. At which point, it would be best for  
everyone if you took Wittgenstein's advice, and stopped saying things.

> because
> it is clear that within its theory, it has a complete universal set of
> properties which will actually interfere with people trying
> frantically to do some of the more pedantic global graph operations
> where knowledge is assumed not to be dirty (turns out that is false),
> and it is complete (also turns out that is false). If sameAs really is
> just useful for relating synonyms within equivalent ontological
> environments it wouldn't surprise me. It really has some quite drastic
> implications even if you choose to map between any two arbitrary
> knowledge bases with different ontological trees being used to define
> the class and properties surrounding the target URI's.
>
> If we could even define an alternative intraGraphSameAs to be workable
> only within a limited idea of graphs in RDF databases and/or
> "namespaces" then it would still be usable in its global sense but
> still be recognisable as more than "seeAlso" for people working in a
> limited knowledge sphere.

In _what ways_ would it be "more than seeAlso"? What inferences would  
it support that seeAlso is not adequate for? Just a few examples would  
be a start.

Pat

> An alternative interGraphSameAs to sameAs
> that has implications for mapping between graphs/databases/namespaces
> would have to be drawn out in a different way because it deals with
> different contexts. Ideally reasoners could actually determine an
> error statistic based on the reliance of a reasoning operation on a
> combination of intraGraphSameAs and interGraphSameAs, although they
> could already do that with sameAs if graphs are loaded with statements
> based on databases instead of a single huge Global Graph.
>
> Cheers,
>
> Peter
>
>

------------------------------------------------------------
IHMC                                     (850)434 8903 or (650)494 3973
40 South Alcaniz St.           (850)202 4416   office
Pensacola                            (850)202 4440   fax
FL 32502                              (850)291 0667   mobile
phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes

Received on Thursday, 26 March 2009 06:46:20 UTC