- From: Christine Golbreich <cgolbrei@gmail.com>
- Date: Mon, 2 Mar 2009 21:24:17 +0100
- To: Michel Dumontier <michel.dumontier@gmail.com>
- Cc: W3C OWL Working Group <public-owl-wg@w3.org>
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. 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 > 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 ? > 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 Christine > -=Michel=- > On Mon, Mar 2, 2009 at 10:36 AM, Christine Golbreich <cgolbrei@gmail.com> > wrote: >> >> Hi Michel, >> >> Since I did not get any feedback from the group providing another real >> UC with an example of local reflexivity, I propose to keep UC#3. >> >> Although the terminology in paper [1] might not be really explicit or >> universal, I suggest to stick on it to fix the example. >> Thus, I have replaced RingMolecule by RingAtom see the diff >> >> http://www.w3.org/2007/OWL/wiki/index.php?title=New_Features_and_Rationale&diff=18595&oldid=18593. >> There are 2 advantages: >> 1) This matches the semantics of a RingAtom accordiing to the SWRL >> rule proposed to identify a RingAtom in this paper. >> 2) This illustrates the local reflexivity feature by a simple example >> from a real referenced UC >> >> (BTW. the purpose here is not to recognize a ring atom, or to discuss >> global restrictions, but only to give an illustrative example ) >> >> If you don't like this example, since a Cyclic Structure is asserted >> to be Local reflexive in Table 1, if you prefer, we may then replace >> RingMolecule by RingStructure ... like in that table. >> >> Please, let me know how you feel about it. >> >> Option 2. move UC#3 from the 2.2.1 F4: Self Restriction for >> illustrating other features in another section BUT provide another UC >> for Local refelexivity >> >> Option 3. remove UC#3 from the document >> >> Christine >> >> 2009/1/23 Michel Dumontier <michel.dumontier@gmail.com>: >> > Hi all, >> > >> > In reference to [1], comment [2] describes the details as erroneous. >> > While >> > the comment is valid, what is more troubling is that the conclusion >> > drawn is >> > incorrect. The cited references [3][4] specifically discusses how the >> > proposed set of OWL (1.1) features was insufficient to capture the ring >> > structure between connected atoms, and must be dealt with either with >> > SWRL >> > rules, and possibly with description graphs. So, while reflective >> > properties >> > maybe useful in other domains (for instance, to assert that the >> > mereological >> > relation has_part is reflective), it is not particularly useful, at this >> > time, in the domain of chemical structure. >> > -=Michel=- >> > >> > [1] http://www.w3.org/TR/owl2-new-features/#Use_Case_.233_-_Classification_of_chemical_compounds_.5BHCLS.5D >> > >> > [2] http://lists.w3.org/Archives/Public/public-owl-comments/2009Jan/0021.html >> > >> > [3] http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-258/paper28.pd >> > [4] http://www.webont.org/owled/2008dc/papers/owled2008dc_paper_20.pdf >> >> >> >> * Local reflexivity (can now define a chemical ring, although I defer >> >> to >> >> chemist opinions on this such as Egon (already commented), Colin?, >> >> Michel?) >> > >> > >> > >> > is erroneous. In our paper, we described how OWL2 was not sufficient to >> > fully describe molecular structure because it was not possible to >> > specify a >> > partial ordered path >> > >> >> >> >> * Qualified Cardinality (histone example: a H3K4m3 has been methylated >> >> exactly 3 times) >> >> * The new reflexive, irreflexive, and asymmetric property axioms >> >> * Features that increase compatibility of OWL 2 with OBO and SNOMED! >> >> >> >> Thank you for your excellent work! >> >> >> >> HCLS IG has a few applications where rules are used in combination with >> >> OWL/RDF. In general, being able to build OWL out of RIF is an appealing >> >> form >> >> of interoperability. So, I have some concerns about the fact that in >> >> RIF the >> >> xsd numeric types have disjoint value spaces (as in XSD1.1, unlike >> >> current >> >> OWL 2 drafts). I am also concerned to learn that there are different >> >> data >> >> types in RIF versus OWL. For example, maybe OWL-RL could be implemented >> >> on >> >> top of RIF, but this could become impractical if there are data type >> >> issues. >> >> I hope that the data type issues between OWL and RIF can eventually be >> >> resolved. >> >> >> >> BTW, it would be useful to have a short overview of the document set >> >> that >> >> briefly explains the content/purpose of each document. >> >> >> >> Best, >> >> Scott >> >> >> >> Typo in http://www.w3.org/TR/owl2-new-features/ : >> >> E.g.; a frontal lobe is part of a brain memisphere or a car is part of >> >> a >> >> car memisphere -> hemisphere >> >> >> >> P.S. Handy for HCLS folks!: >> >> Property chain inclusion (from RequirementsDraft): >> >> SubPropertyOf( PropertyChain( locatedIn partOf ) locatedIn ) (UC#7) >> >> >> >> If x is locatedIn y, and y is partOf z, then x is locatedIn z; for >> >> example >> >> a disease located in a part is located in the whole. >> >> >> >> -- >> >> M. Scott Marshall >> >> http://staff.science.uva.nl/~marshall >> >> http://adaptivedisclosure.org >> >> >> >> >> > >> > >> > >> > -- >> > Michel Dumontier >> > Assistant Professor of Bioinformatics >> > http://dumontierlab.com >> > >> >> >> >> -- >> Christine > > > > -- > Michel Dumontier > Assistant Professor of Bioinformatics > http://dumontierlab.com > -- Christine
Received on Monday, 2 March 2009 20:24:52 UTC