- From: Christine Golbreich <cgolbrei@gmail.com>
- Date: Tue, 3 Mar 2009 16:11:29 +0100
- To: Michel Dumontier <michel.dumontier@gmail.com>
- Cc: W3C OWL Working Group <public-owl-wg@w3.org>
2009/3/3 Michel Dumontier <michel.dumontier@gmail.com>: > > > 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 OK, then not getting another real application UC from the group, I may use this to "illustrate" local ref, but we should be aware of its limitation i.e. 1) it has not yet been used in a real application 2) the same problems as those met with your RingAtom (global restrictions) hold. Christine > -=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 > -- Christine
Received on Tuesday, 3 March 2009 15:12:08 UTC