- From: Ian Horrocks <ian.horrocks@comlab.ox.ac.uk>
- Date: Thu, 5 Mar 2009 22:26:36 +0000
- To: Christine Golbreich <cgolbrei@gmail.com>
- Cc: Michel Dumontier <michel.dumontier@gmail.com>, W3C OWL Working Group <public-owl-wg@w3.org>
It may not be super useful/used in actual applications, but I don't see what is wrong with our old friend the Narcissist for illustrating/ motivating local reflexivity. Clearly every instance of this class loves his/her-self, but it is clearly not true to say that loves is reflexive in general. Ian On 3 Mar 2009, at 15:11, Christine Golbreich wrote: > 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 Thursday, 5 March 2009 23:28:03 UTC