Re: OWL2 comments -> UC#3

2009/3/3 Michel Dumontier <michel.dumontier@gmail.com>:
>
>
> On Mon, Mar 2, 2009 at 3:24 PM, Christine Golbreich <cgolbrei@gmail.com>
> wrote:
>>
>> 2009/3/2 Michel Dumontier <michel.dumontier@gmail.com>:
>> > Hi Christine,
>> >   I understand that this is meant to be illustrative - its just not
>> > particularly convincing as a use case, and it brings doubt to our
>> > ability to
>> > accurately model chemical knowledge. All atoms in a molecule are
>> > (directly
>> > or indirectly) connected to each other,irregardless of whether they are
>> > ring
>> > atoms. Even if you wanted to say "SelfConnectedAtom" as an Atom that
>> > isConnectedTo Self... what is the value in having such a class? There is
>> > none, in my opinion.
>>
>> First, you may have a property directConnectedTo (similar to
>> directPart) and an axiom SubClassOf( RingAtom HasSelf(
>> directConnectedTo)) that asserts local reflexivity for ring atoms.
>
> Yes, if you know that its a ring atom, you an certain do that, but again
> you're missing the point. being connected to itself is not particularly
> interesting
>>
>> Do you mean that Cyclic Local reflexive isConnectedTo “Self”  in Table
>> 1 of your paper has no value either ?
>> [1]
>> http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-258/paper28.pdf
>
> As described in the text of the cited paper, we initially thought so, but
> without the rest of the solution (partial ordered paths over transitive
> properties during reasoning), we don't get the intended result. so that's
> why we then tried rules, which works of course, but you have to specify the
> number of atoms in the ring you want to discover.

OK, since that table should be considered as obsolete, I may use other
chemical examples, which may be less contentious from a chemical point
of view. However,

1) As the UCs selected in the document concern real applications, it
would be great if you might give a reference of the application where
such class definitions are used, and even better a line showing the
usefulness of local refmlexivity  in reasoning (if you used it to
reason)

2)
> eg A kinase that phosphorylates itself
> Auto-Phosphorylating Kinase :=
>  subclass ( Kinase hasSelf (phosphorylates) )

Not sure which syntax you use, but this axiom does not seem correct.
To express what you mean, the pattern in FS should it not be instead
something like:

EquivalentClasses(Auto-p-A ObjectIntersectionOf(A hasSelf(p)))
e.g.
EquivalentClasses(Auto-Phosphorylating-Kinase  ObjectIntersectionOf(A
hasSelf(p)))
Auto-Phosphorylating-Kinase are kinase that phosphorylates themselves

I may also simply replace present RingAtom example by:
subclass ( Auto-Phosphorylating-Kinase hasSelf (phosphorylates) )
to express that Auto-Phosphorylating-Kinase phosphorylates themselves.

best

Christine

>>
>> > From the biochemical domain, proteins that sometimes modify themselves -
>> > some add phosphate groups in specific locations, and these proteins are
>> > therefore known as self-phosphorylating proteins. or certain RNA
>> > molecules
>> > will cleave themselves, and are known as "self-cleaving RNA" ... lots of
>> > other meaningful examples.
>>
>> Then if local reflexivity is useful, can you provide at least one real
>> UC  with an example in OWL2 which has value, to replace the ring
>> example of UC#3 ?
>
> sure,
> UC #XX - Capturing biochemical self-interaction as local reflexivity
> overview: In Biochemistry, some biomolecules will chemical modify themselves
> in such a way that it has biologically important consequences. i) Protein
> kinases are enzymes capable of adding phosphate groups to certain amino
> acids found within target proteins. Some kinases, known as
> Auto-Phosphorylating Kinases, will add phosphate groups to certain target
> amino acids that are part of itself [1]. ii) Ribozymes are catalytically
> active RNA molecules in which 7 natural types are known to cleave their own
> RNA sequences. Such cleavage may result in significant changes to viral
> replication, gene expression,  and possibly the generation of different
> protein transcripts. Such catalytically active, self-cleaving RNA make up a
> subclass of ribozymes called Self-Cleaving Ribozymes [2].
>
> Features: Local Reflexivity
> Example for: Local Reflexivity
> eg A kinase that phosphorylates itself
> Auto-Phosphorylating Kinase :=
>  subclass ( Kinase hasSelf (phosphorylates) )
> eg A ribozyme that cleaves itself
> Self-Cleaving Ribozyme :=
>  subclass ( Ribiozyme hasSelf (cleaves) )
> references :
> [1] http://www.springerlink.com/content/j36v22655088324r/
> [2] http://www.pnas.org/content/97/11/5784.full
>
>
>
>>
>> >  Now, that's not to say that the (bio)chemical work that i've presented
>> > doesn't have use cases for OWL2, its just that local reflexive has just
>> > not
>> > yet been one of them. however, we have raised good examples of QCRs
>> > (specifying the number and types of functional groups), reflexive
>> > (hasimproperpart), asymmetric (hasproperpart), role chains (hasPart o
>> > hasParticipant -> hasParticipant),  disjoint union (all atom are one of
>> > the
>> > atom types)...
>> > one or more of these are much more interesting to present as use cases
>> > from
>> > the chemical domain. i encourage you to consider these.
>>
>> For the other features we already have plenty of UCs and examples
>> available, but I may keep UC#3 as yet another example of e.g. QCR
>
> great!
>
>>
>> Christine
>
>
>
> -=Michel=-
> --
> Michel Dumontier
> Assistant Professor of Bioinformatics
> http://dumontierlab.com
>



-- 
Christine

Received on Tuesday, 3 March 2009 10:05:41 UTC