Re: blog: semantic dissonance in uniprot

On Mar 26, 2009, at 3:52 PM, Oliver Ruebenacker wrote:

>     Hello Pat, All,
>
> On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes <phayes@ihmc.us> wrote:
>>>  Just because it refers to a set of things does not mean I need to
>>> model it by an owl:Class.
>>
>> No, but if it really is a set, that would be a very good idea.
>
>  Actually, I doubt a protein is a set. It seems to me, in Systems
> Biology, a protein is an operator working on statistical ensembles,
> from which we can derive expectation values and variances.

Um. OK, you obviously know more about this than I do, but I very much  
doubt if any ontology notation is capable of expressing what you here  
describe.

>
>> Well, it was a problem with OWL DL that an class couldnt be an  
>> instance of
>> another class. I gather this has been fixed (about time) in OWL 2,   
>> There is
>> obsolutely no logical or fundamental reason why classes should not be
>> allowed to be in other classes, for examples like this one.
>
>  An OWL Full reasoner takes much longer to compute than an OWL DL
> reasoner. What good are classes if you don't intend to instantiate?

I was referring to OWL 2, not OWL Full. It is the new version of OWL,  
in last call as we write. The DL version of it runs at DL efficiencies  
and allows classes of classes, kinda (using punning, it works for most  
applications). And BTW, instantiating classes is fast and easy in just  
about any formalism. The speed cost comes from the fact that more  
expressive languages allow stranger edge cases which have to be  
checked by complete reasoners. But all these complexity results are  
worst-case, and normal-case behavior is often very different.

>
>>> Similarly, a typical approach would be to have a class Protein and  
>>> an
>>> instance EGFR ("a protein") that refers to a large number of  
>>> molecules
>>> scattered all over the globe.
>
>> Um.. this seems confused to me, mixing up ideas from mereology with  
>> classes.
>> A 'large number of molecules scattered all over the globe' sounds  
>> like a
>> mereological sum. Which is fine, and pretty well axiomatized  
>> already with
>> off-the-shelf ontologies. BUt there is no point in also having a  
>> class of
>> these things, since this just confuses sums with classes. What are  
>> the
>> elements of the class? The sum or the individual molecules? If the  
>> latter,
>> we don't need the sum; if the former, we don't need the class.
>
>  Ensemble operators are not sets. The whole is more than the sum of  
> its parts.

Well, OK, but then the whole class/property paradigm seems to not  
apply. Classes in any DL language _are_ sets.

>
>> I agree it makes sense. But to be exact, whats been found in fruit  
>> fly
>> embyos are molecules of the (same) protein, not the same molecules  
>> of the
>> protein. If this is important for reasoning (and I bet it will be),  
>> then
>> your ontology needs to distinguish protein molecules from proteins.  
>> And if
>> it doesn't, then I'd predict it is going to get its knickers in a  
>> twist.
>
>  You may be talking of single molecules, but I am not, so your
> confusion does not apply to me.

Im glad to hear it. You did however refer to protein being found in  
fruit fly embryos. My point applies whether this protein in the fly is  
thought of as molecules or as a compound. The point is that there is  
something analogous to a type/token or type/instance distinction here,  
that your ontology needs to be sensitive to, if it is to avoid  
becoming completely confused. It needs to distinguish the protein-as- 
biochemical-type from the protein-as-property-of-pieces-of-matter. The  
latter can be found in places: the former cannot.

Pat

>
>     Take care
>     Oliver
>
> -- 
> Oliver Ruebenacker, Computational Cell Biologist
> BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
> Center for Cell Analysis and Modeling
> http://www.oliver.curiousworld.org
>
>

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Received on Saturday, 28 March 2009 14:57:02 UTC