W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2007

Re: Advancing translational research with the Semantic Web

From: Chris Mungall <cjm@fruitfly.org>
Date: Mon, 21 May 2007 12:17:16 -0700
Message-Id: <DF072F57-8D84-475A-BD7D-44843C5F17F2@fruitfly.org>
Cc: Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci@w3.org
To: Pat Hayes <phayes@ihmc.us>


On May 21, 2007, at 11:24 AM, Pat Hayes wrote:

>
>>  >>>>> "CM" == Chris Mungall <cjm@fruitfly.org> writes:
>>
>>
>>   >> Out of curiosity, can you describe how different or similar this
>>   >> is to the result that you can achieve in the N-ary relation
>>   >> design pattern for OWL?
>>   >>
>>   >> Obviously, building things into the DL is nice, but it's not
>>   >> currently representable in OWL, so would require tooling  
>> support,
>>   >> while the OWL N-ary relation pattern doesn't.
>>
>>   CM> I'm afraid I'm unclear how to state the OWL n-ary relation
>>   CM> pattern (http://www.w3.org/TR/swbp-n-aryRelations) where I
>>   CM> really need it. In all the examples given, the "lifted"[*] n- 
>> ary
>>   CM> relation was never truly a relation in the first place and
>>   CM> always better modeled as a class. It's kind of cheating.
>>
>> Well, it is kind of cheating, yes, although if it works...
>
> No, really, its not cheating. This reduction of n-ary relations to  
> binary+unary relations is quite general and quite sound, and has  
> been known and thoroughly understood for over a century. It can  
> always be done, and it often makes perfectly good intuitive sense.  
> The 'thing' that the arguments all relate to is something like the  
> event, or fact, or situation, or state of affairs that holds, etc..  
> (choose your favorite terminology)

Sorry, I shouldn't have used a pejorative term like cheating, I was  
just pointing out that if I am presented with a template for a  
solution for problem X and that solution is to transform to  
representation Y, this doesn't help if my problem was actually X2 and  
I would have used Y for X in the first place.

Or let me be more concrete: using an ontology like BFO (perhaps DOLCE  
too) as a guiding framework, one would use owl classes and not owl  
object properties for diagnoses, observations, purchases and flight  
segments (the examples given in the n-ary note). Applying the same  
pattern to relations that should be modeled as relation leads to more  
design decisions and more complex representations.

>>
>>   CM> What if my n-ary relation is transitive or if the 3rd argument
>>   CM> is a temporal interval over which the relation holds?
>>
>> The former is hard because it's not clear what do you with n-ary
>> relationships. I think that this is true for any
>> representation. Fundamentally, if you say "a is part of b" and I say
>> "b is part of c", then is "a part of c" and according to whom?
>
> Right, it simply isn't clear what 'transitive' means for relations  
> other than binary. Try writing it out as an axiom in logic to see  
> all the different possibilities.

This would have to be done on a case by case basis. I believe someone  
is working on this for the time-indexed temporal relations in the OBO  
relation ontology

>>
>> It is possible to use build on top of the n-ary relationship, for
>> example a symmetric property. Perhaps you could do the same for
>> transitivity if you could work out exactly what the semantic should
>> be.
>>
>>
>>   CM> I think the former is doable with property role chains.  
>> Updating
>>   CM> the n-ary relations note with this - and all the other omitted
>>   CM> details, such as how to re-represent domain/range, functional
>>   CM> properties, n- ary relations in restrictions etc - would take a
>>   CM> lot of work and would make it utterly terrifying to the naive
>>   CM> user.
>
> Well, naive users probably shouldn't be trying to represent  
> functional relations with more than one argument. This kind of  
> thing just IS complicated.
>
> My advice to new users is to forget completely about N-ary  
> relations. Tell yourself that there are no relations in nature  
> above binary. If you think you need one, re-think what you are  
> trying to say so that it all fits into the binary case. Chances are  
> this will be fairly easy to do, and as a side-effect, you will  
> probably then be much more clear on what exactly it is that you  
> want to say about transitivity, functionality, domains and so forth.

I'm afraid that one of the core ontologies we are using disagrees  
with this:
http://genomebiology.com/2005/6/5/R46

>> Yep, but I think that this reflects the underlying complexities of
>> life.
>
> Exactly. Although I would prefer to say, the complexities of  
> awkward modes of describing life.
>
>>
>>   CM> Nevertheless the results are clunky and will need special tool
>>   CM> support [**] to avoid going insane. In general I am wary of
>>   CM> design pattern type things - they are usually a sign that the
>>   CM> language lacks the constructs required to express things
>>   CM> unambiguously and concisely. It sounds like DLR could provide
>>   CM> this, which would be great.
>>
>> Well, this I would agree with. Folding design patterns in, would be
>> nice.
>
> Agreed. We made this a central feature of our COE graphic OWL  
> editor, in that a user can design a 'template' (a chunk of OWL with  
> gaps in it) and give it a name, then just drag-and-drop one into a  
> new OWL concept map and fill in the missing parameters. Its a  
> simple device and not perfect, but it does seem to be useful.
>
> Pat Hayes
> -- 
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Received on Monday, 21 May 2007 19:17:43 UTC

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