Re: OWL2 comments -> UC#3

On Tue, Mar 3, 2009 at 5:05 AM, Christine Golbreich <cgolbrei@gmail.com>wrote:

> 2009/3/3 Michel Dumontier <michel.dumontier@gmail.com>:
> - Show quoted text -
> >
> >
> > 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,
>

Which table are you referring to? The one in the paper?? LOL.. you can't
conclude that from this discussion.


>
> 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)
>

I gave you a use case, as you requested. Just because it hasn't been used
(yet) doesn't invalidate its prospective utility.



>
> 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
>

sure, this could then be used to discover members of such a class. there's
your example you asked about above.


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

fine

-=Michel=-


>
> best
>
> Christine
> - Show quoted text -
>
> >>
> >> > 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
>



-- 
Michel Dumontier
Assistant Professor of Bioinformatics
http://dumontierlab.com