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Re: OWL2 comments

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Fri, 23 Jan 2009 14:36:00 -0500
Message-ID: <c8edab680901231136r56204cd8t1b86e68fcb57e1c@mail.gmail.com>
To: public-owl-comments@w3.org
Cc: Colin Batchelor <BatchelorC@rsc.org>
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
Received on Friday, 23 January 2009 19:36:49 GMT

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