[seek-kr-sms] algorithms and the owlfication of taxon
Bertram Ludaescher
ludaesch at ucdavis.edu
Thu Nov 3 08:07:52 PST 2005
Shawn:
Thanks for the quick reply --- P. Hayes' looks like a good reference!
Bertram
>>> On Thu, 3 Nov 2005 07:11:12 -0800 (PST)
>>> Shawn Bowers <sbowers at ucdavis.edu> wrote:
SB>
SB> It looks like the paper you reference describes a "semantics" for RDF(S).
SB> Here is a modal theory for RDF by P. Hayes:
SB>
SB> http://www.w3.org/TR/rdf-mt/
SB>
SB> Here is an older approach, again by P. Hayes, that I find a bit more
SB> straightforward:
SB>
SB> http://www.w3.org/TR/2003/NOTE-lbase-20031010/
SB>
SB> In this note, e.g., you have axioms such as:
SB>
SB> rdf:type(?x ?y) implies ?y(?x)
SB> rdfs:Class(?y) implies (?y(?x) iff rdf:type(?x ?y))
SB>
SB> That is, if x is an instance of y then y(x). And, if y is an rdfs class
SB> then x is an instance of y if type(x, y). (Here you see second order
SB> creap.)
SB>
SB> Here is another:
SB>
SB> rdfs:subClassOf(?x ?y) implies
SB> (rdfs:Class(?x) and rdfs:Class(?y) and (forall (?u)(?x(?u) implies
SB> ?y(?u)))
SB>
SB> There are a bunch more.
SB>
SB> -shawn
SB>
SB>
SB>
SB>
SB> On Thu, 3 Nov 2005, Bertram Ludaescher wrote:
SB>
>>
>> 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">
MS> <style>@page Section1 {size: 8.5in 11.0in; margin: 1.0in
>> >>> 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> _______________________________________________
SB> Seek-kr-sms mailing list
SB> Seek-kr-sms at ecoinformatics.org
SB> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
>>
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