Re: OWL2 comments -> UC#3

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.


>
> > 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