[seek-kr-sms] algorithms and the owlfication of taxon
Shawn Bowers
sbowers at ucdavis.edu
Thu Nov 3 07:11:12 PST 2005
It looks like the paper you reference describes a "semantics" for RDF(S).
Here is a modal theory for RDF by P. Hayes:
http://www.w3.org/TR/rdf-mt/
Here is an older approach, again by P. Hayes, that I find a bit more
straightforward:
http://www.w3.org/TR/2003/NOTE-lbase-20031010/
In this note, e.g., you have axioms such as:
rdf:type(?x ?y) implies ?y(?x)
rdfs:Class(?y) implies (?y(?x) iff rdf:type(?x ?y))
That is, if x is an instance of y then y(x). And, if y is an rdfs class
then x is an instance of y if type(x, y). (Here you see second order
creap.)
Here is another:
rdfs:subClassOf(?x ?y) implies
(rdfs:Class(?x) and rdfs:Class(?y) and (forall (?u)(?x(?u) implies
?y(?u)))
There are a bunch more.
-shawn
On Thu, 3 Nov 2005, Bertram Ludaescher wrote:
>
> Shawn:
>
> Can you remind us what RDF(S) translates to in first-order logic, once
> you remove all the pointy brackets, URIs, and other noise?
>
> In OWL-DL I clearly see this (at least the DL suggests it ;-), that
> is, we are looking at a particular description logic..
>
> What are we looking at --in terms of first-order logic-- when we look
> at RDF(S)? I haven't looked at RDF(S) in a while, but recall it was
> messy (logicians tend to avoid that stuff ;-)
>
> But here is some stuff from the Stanford folks:
>
> http://www.ksl.stanford.edu/people/dlm/daml-semantics/abstract-axiomatic-semantics.html
>
> >>> On Wed, 02 Nov 2005 17:48:56 -0800
> >>> Shawn Bowers <sbowers at ucdavis.edu> wrote:
> SB>
> SB> I think the assumption here is that we need to use OWL-DL. Whereas at face
> SB> value, RDF(S) seems to have the needed elements.
> SB>
> SB> -shawn
> SB>
> SB> Serguei Krivov wrote:
> >> The question is how to assign whole classes as values of properties and
> >> stay in
> >> OWL-DL. Suppose someone whant to say "Book b1 is about lions" and "Book b2 is
> >> about African lions" which is natural in rdfs as :
> >> (b1, subject, Lion)
> >> (b2, subject AfricanLion)
> >> (see Approach 1 in the paper)
> >>
> >> The main message of this paper is as follows: If you want to support in OWL-DL
> >> such data structures along with the derivations "hey pals, book b2 is also
> >> about Lions" then use existential property value restriction
> >> b1 has type restriction(someValuesFrom Lion)
> >> b2 has type restriction(someValuesFrom AfricanLion)
> >>
> >> DL reasoner then could derive that
> >> b2 has type restriction(someValuesFrom Lion)
> >>
> >> see approach 4. This is pretty much it; approaches 2 and 3 looks too
> >> artificial
> >> and perhaps they are mentioned just to fill in the space.
> >>
> >> serguei
> >>
> >>
> >> Quoting Bertram Ludaescher <ludaesch at ucdavis.edu>:
> >>
> >>> Mark:
> >>>
> >>> Good finding.
> >>>
> >>> Any volunteers for reviewing this document carefully and relating it
> >>> to our ongoing TAXON / KR-SMS discussion?
> >>>
> >>> Bertram
> >>>
> >>>
> >>>
> >>>>>> On Wed, 26 Oct 2005 12:07:13 -0700
> >>>>>> Mark Schildhauer <schild at nceas.ucsb.edu> wrote:
> MS>
> MS> Hi All,
> MS> I think Dave put his finger on it that this is the primary obstacle with
> MS> using OWL-DL to model biological taxonomies, viz. that we want to
> MS> flexibly use classes as instances-- so we can get the advantages of
> MS> inheritance from the class structure, but also reference classes as
> MS> property-values. There is some discussion of this issue on the w3 site--
> MS>
> MS> http://www.w3.org/TR/swbp-classes-as-values/
> MS>
> MS> I'm still reviewing this document myself, but it seems very relevant to
> MS> our quandary...
> MS>
> MS> cheers,
> MS> Mark
> MS> /
> MS>
> MS> /dave thau wrote:
> MS>
> >>>>> Ok, does this deal with upper level classes having different
> >>>>> authorities? Or does this run into a problem where you're treating a
> >>>>> class like an instance?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>> ----- Original Message -----
> >>>>> *From:* Serguei Krivov <mailto:Serguei.Krivov at uvm.edu>
> >>>>> *To:* 'dave thau' <mailto:thau at learningsite.com> ; 'bertram'
> >>>>> <mailto:ludaesch at ucdavis.edu> ; 'Nico Franz'
> >>>>> <mailto:franz at nceas.ucsb.edu>
> >>>>> *Cc:* seek-kr-sms at ecoinformatics.org
> >>>>> <mailto:seek-kr-sms at ecoinformatics.org>
> >>>>> *Sent:* Wednesday, October 26, 2005 9:29 AM
> >>>>> *Subject:* RE: algorithms and the owlfication of taxon
> >>>>>
> >>>>>
> >>>>>
> >>>>> There are many ways to represent biological taxonomies in OWL. The
> >>>>> main problem here is how to avoid a second order style logic i.e.
> >>>>> assigning properties to classes rather then specifying properties
> >>>>> of objects by defining classes. There is temptation to use owl as
> >>>>> meta- language of taxonomy rather then as the language of taxonomy
> >>>>> (which it is intended to be), or say it metaphorically writing OWL
> >>>>> interpreter for OWL.
> >>>>>
> >>>>>
> >>>>>
> >>>>> I believe this could be easily avoided. Here is how I would
> >>>>> represent the part of taxonomies from Dave's design document:
> >>>>>
> >>>>> Each instance of class species would have attributes hasKingdom,
> >>>>> hasPhylum, etc. One could also add hasAuthority, hasReference etc.
> >>>>> And so we describe species exactly as humans do. Now the question
> >>>>> is how to say that all Anthropoda are Animals and all Chordata are
> >>>>> Animals. It is easy in OWL if we use subsumption axioms on
> >>>>> anonymous classes:
> >>>>>
> >>>>> this states that anonymous class hasKingdom:Animals (property
> >>>>> value restriction) is subclass of anonymous class
> >>>>> hasPhylum:Anthropoda. Now when subsumption relation is established
> >>>>> one could use owl reasoner to check consistency
> >>>>>
> >>>>>
> >>>>>
> >>>>> ciao,
> >>>>>
> >>>>> serguei
> >>>>>
> >>>>>
> >>>>>
> >>>>> --------------------------------------------------------------------------------------
> >>>>>
> >>>>> Serguei Krivov, Assist. Research Professor,
> >>>>>
> >>>>> Computer Science Dept. & Gund Inst. for Ecological Economics,
> >>>>>
> >>>>> University of Vermont; 590 Main St. Burlington VT 05405
> >>>>>
> >>>>> phone: (802)-656-2978
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> -----Original Message-----
> >>>>> From: dave thau [mailto:thau at learningsite.com]
> >>>>> Sent: Wednesday, October 26, 2005 11:22 AM
> >>>>> To: Serguei.Krivov at uvm.edu; bertram
> >>>>> Subject: algorithms and the owlfication of taxon
> >>>>>
> >>>>>
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>>
> >>>>>
> >>>>> Attached are two documents you may find interesting. The first
> >>>>> was the
> >>>>>
> >>>>> first assignment in my algorithms class. The puzzle I described
> >>>>> yesterday
> >>>>>
> >>>>> is part II.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Second, when I first started working on SEEK, I tried to pitch OWL
> >>>>> as the
> >>>>>
> >>>>> most appropriate representation for the Taxon stuff, but didn't
> >>>>> get too
> >>>>>
> >>>>> far. I did a little work doing a couple of representations, and a
> >>>>>
> >>>>> graduate student of Susan Gauch went further in documenting
> >>>>> options. This
> >>>>>
> >>>>> dates from about 3 years ago, and we were all just learning OWL
> >>>>> DL, so it
> >>>>>
> >>>>> may be poorly informed. But it'll give you a notion of the
> >>>>> thinking at
> >>>>>
> >>>>> the time.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>> ------------------------------------------------------------------------
> >>>>>
> >>>>> _______________________________________________
> >>>>> Seek-kr-sms mailing list
> >>>>> Seek-kr-sms at ecoinformatics.org
> >>>>> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
> >>>>>
> >>>>>
> MS>
> MS>
> MS> --
> MS> Mark Schildhauer, Ph.D. 735 State St., Suite 300
> MS> Director of Computing, NCEAS Santa Barbara CA 93101
> MS> Phone: 805-892-2509 FAX: 805-892-2510
> MS> Email: schild at nceas.ucsb.edu
> MS>
> MS>
> MS> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
> MS> <html>
> MS> <head>
> MS> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
> MS> <title></title>
> MS> </head>
> MS> <body bgcolor="#ffffff" text="#000000">
> MS> Hi All,<br>
> MS> <br>
> MS> I think Dave put his finger on it that this is the primary obstacle
> MS> with using OWL-DL to model biological taxonomies, viz. that we want to
> MS> flexibly use classes as instances-- so we can get the advantages of
> MS> inheritance from the class structure, but also reference classes as
> MS> property-values. There is some discussion of this issue on the w3
> MS> site--<br>
> MS> <br>
> MS> <a class="moz-txt-link-freetext"
> >>> href="http://www.w3.org/TR/swbp-classes-as-values/">http://www.w3.org/TR/swbp-classes-as-values/</a><br>
> MS> <br>
> MS> I'm still reviewing this document myself, but it seems very relevant to
> MS> our quandary...<br>
> MS> <br>
> MS> cheers,<br>
> MS> Mark<br>
> MS> <i><br>
> MS> <br>
> MS> </i>dave thau wrote:
> MS> <blockquote cite="mid004301c5da5b$c9a65f10$0100007f at localhost"
> MS> type="cite">
> MS> <meta http-equiv="Content-Type" content="text/html; ">
> MS> <meta content="MSHTML 6.00.2800.1491" name="GENERATOR">
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> >>> 77.95pt 1.0in 77.95pt; }
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> MS> <div><font face="Arial" size="2">Ok, does this deal with upper level
> MS> classes having different authorities? Or does this run into
> >>> a problem
> MS> where you're treating a class like an instance?</font></div>
> MS> <div> </div>
> MS> <div><font face="Arial" size="2">Dave</font></div>
> MS> <blockquote
> MS> style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px;
> >>> padding-left: 5px; margin-left: 5px; margin-right: 0px;"
> MS> dir="ltr">
> MS> <div
> MS> style="font-family: arial; font-style: normal; font-variant:
> >>> normal; font-weight: normal; font-size: 10pt; line-height: normal;
> >>> font-size-adjust: none; font-stretch: normal;">-----
> MS> Original Message ----- </div>
> MS> <div
> MS> style="background: rgb(228, 228, 228) none repeat scroll 0%;
> >>> -moz-background-clip: initial; -moz-background-origin: initial;
> >>> -moz-background-inline-policy: initial; font-family: arial;
> >>> font-style: normal; font-variant: normal; font-weight: normal;
> >>> font-size: 10pt; line-height: normal; font-size-adjust: none;
> >>> font-stretch: normal;"><b>From:</b>
> MS> <a title="Serguei.Krivov at uvm.edu"
> MS> href="mailto:Serguei.Krivov at uvm.edu">Serguei Krivov</a> </div>
> MS> <div
> MS> style="font-family: arial; font-style: normal; font-variant:
> >>> normal; font-weight: normal; font-size: 10pt; line-height: normal;
> >>> font-size-adjust: none; font-stretch: normal;"><b>To:</b>
> MS> <a title="thau at learningsite.com"
> >>> href="mailto:thau at learningsite.com">'dave
> MS> thau'</a> ; <a title="ludaesch at ucdavis.edu"
> MS> href="mailto:ludaesch at ucdavis.edu">'bertram'</a> ; <a
> MS> title="franz at nceas.ucsb.edu" href="mailto:franz at nceas.ucsb.edu">'Nico
> MS> Franz'</a> </div>
> MS> <div
> MS> style="font-family: arial; font-style: normal; font-variant:
> >>> normal; font-weight: normal; font-size: 10pt; line-height: normal;
> >>> font-size-adjust: none; font-stretch: normal;"><b>Cc:</b>
> MS> <a title="seek-kr-sms at ecoinformatics.org"
> MS>
> >>> href="mailto:seek-kr-sms at ecoinformatics.org">seek-kr-sms at ecoinformatics.org</a>
> MS> </div>
> MS> <div
> MS> style="font-family: arial; font-style: normal; font-variant:
> >>> normal; font-weight: normal; font-size: 10pt; line-height: normal;
> >>> font-size-adjust: none; font-stretch: normal;"><b>Sent:</b>
> MS> Wednesday, October 26, 2005 9:29 AM</div>
> MS> <div
> MS> style="font-family: arial; font-style: normal; font-variant:
> >>> normal; font-weight: normal; font-size: 10pt; line-height: normal;
> >>> font-size-adjust: none; font-stretch: normal;"><b>Subject:</b>
> MS> RE: algorithms and the owlfication of taxon</div>
> MS> <div><br>
> MS> </div>
> MS> <div class="Section1">
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">There are many ways to represent biological
> MS> taxonomies in OWL. The main problem here is how to avoid a second order
> MS> style logic i.e. assigning properties to classes rather then specifying
> MS> properties of objects by defining classes. There is temptation to use
> MS> owl as meta- language of taxonomy rather then as the language of
> MS> taxonomy (which it is intended to be), or say it metaphorically writing
> MS> OWL interpreter for OWL.</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">I believe this could be easily avoided. Here
> MS> is how I would represent the part of taxonomies from Dave’s design
> MS> document:</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"><img
> MS> src="cid:part1.09000004.04090504 at nceas.ucsb.edu" height="396"
> MS> width="423"></span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Each instance of class species would have
> MS> attributes hasKingdom, hasPhylum, etc. One could also add hasAuthority,
> MS> hasReference etc. And so we describe species exactly as humans do. Now
> MS> the question is how to say that all Anthropoda are Animals and all
> MS> Chordata are Animals. It is easy in OWL if we use subsumption axioms on
> MS> anonymous classes:</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"><img
> MS> src="cid:part2.07080303.09040809 at nceas.ucsb.edu" height="222"
> MS> width="262"></span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">this states that anonymous class
> MS> hasKingdom:Animals (property value restriction) is subclass of
> MS> anonymous class hasPhylum:Anthropoda. Now when subsumption
> >>> relation is
> MS> established one could use owl reasoner to check consistency
> >>> </span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">ciao,</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">serguei</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size:
> >>> 10pt;">--------------------------------------------------------------------------------------</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Serguei Krivov</span></font>, Assist.
> MS> Research Professor,</p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Computer Science Dept. & Gund Inst. for
> MS> Ecological Economics, </span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">University</span></font> of Vermont; 590 Main
> MS> St. Burlington VT 05405</p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">phone: (802)-656-2978</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">-----Original Message-----<br>
> MS> From: dave thau [<a class="moz-txt-link-freetext"
> >>> href="mailto:thau at learningsite.com">mailto:thau at learningsite.com</a>]
> >>> <br>
> MS> Sent: </span></font>Wednesday, October 26, 2005 11:22 AM<br>
> MS> To: <a class="moz-txt-link-abbreviated"
> >>> href="mailto:Serguei.Krivov at uvm.edu">Serguei.Krivov at uvm.edu</a>;
> >>> bertram<br>
> MS> Subject: algorithms and the owlfication of taxon</p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Hello,</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Attached are two documents you may find
> MS> interesting. The first was the</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">first assignment in my algorithms
> >>> class. The
> MS> puzzle I described yesterday</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">is part II.</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Second, when I first started working on SEEK,
> MS> I tried to pitch OWL as the</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">most appropriate representation for the Taxon
> MS> stuff, but didn't get too</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">far. I did a little work doing a
> >>> couple of
> MS> representations, and a</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">graduate student of Susan Gauch went further
> MS> in documenting options. This</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">dates from about 3 years ago, and we were all
> MS> just learning OWL DL, so it</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">may be poorly informed. But it'll
> >>> give you a
> MS> notion of the thinking at</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">the time.</span></font></p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;"></span></font> </p>
> MS> <p class="MsoPlainText"><font face="Courier New" size="2"><span
> MS> style="font-size: 10pt;">Dave</span></font></p>
> MS> </div>
> MS> </blockquote>
> MS> <pre wrap="">
> MS> <hr size="4" width="90%">
> MS> _______________________________________________
> MS> Seek-kr-sms mailing list
> MS> <a class="moz-txt-link-abbreviated"
> >>> href="mailto:Seek-kr-sms at ecoinformatics.org">Seek-kr-sms at ecoinformatics.org</a>
> MS> <a class="moz-txt-link-freetext"
> >>> href="http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms">http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms</a>
> MS> </pre>
> MS> </blockquote>
> MS> <br>
> MS> <br>
> MS> <pre class="moz-signature" cols="72">--
> MS> Mark Schildhauer, Ph.D. 735 State St., Suite 300
> MS> Director of Computing, NCEAS Santa Barbara CA 93101
> MS> Phone: 805-892-2509 FAX: 805-892-2510
> MS> Email: <a class="moz-txt-link-abbreviated"
> >>> href="mailto:schild at nceas.ucsb.edu">schild at nceas.ucsb.edu</a>
> MS>
> MS> </pre>
> MS> </body>
> MS> </html>
> MS> _______________________________________________
> MS> Seek-kr-sms mailing list
> MS> Seek-kr-sms at ecoinformatics.org
> MS> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
> >>>
> >>> _______________________________________________
> >>> Seek-kr-sms mailing list
> >>> Seek-kr-sms at ecoinformatics.org
> >>> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
> >>>
> >>
> >>
> >>
> >> _______________________________________________
> >> Seek-kr-sms mailing list
> >> Seek-kr-sms at ecoinformatics.org
> >> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
> >>
> >>
> SB>
> SB> _______________________________________________
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