[seek-kr-sms] algorithms and the owlfication of taxon
Joseph Goguen
goguen at cs.ucsd.edu
Thu Nov 3 13:59:25 PST 2005
Dear Serguei and others,
Ive written papers giving detailed arguments about the differences between
machine semantics and human semantics and the dangers of confusing them.
You can find the latest at
http://www.cse.ucsd.edu/~goguen/pps/onto5.pdf
It draws on recent work in sociology, cognitive science, philosophy and
mathematics to make its case, and was intended mainly as a rebuttal to the
hard (and i think naive) "realism" of Barry Smith.
Cheers,
joseph
Serguei Krivov wrote:
>Bertram, thanks for correcting me. I apologize for messing up with
>copy-paste of my really favorite reference.
>
>Not that I agree with all the things in "Is SW hype?" E.g. statements about
>semantics on page 37: "People have semantics but machines do not" seems
>naïve to me. But the critics of RDF(S) and all the collection of jokes about
>its design are really cool.
>
>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: Bertram Ludaescher [mailto:ludaesch at ucdavis.edu]
>Sent: Thursday, November 03, 2005 11:28 AM
>To: Serguei Krivov
>Cc: 'Shawn Bowers'; seek-kr-sms at ecoinformatics.org; 'Serguei Krivov'
>Subject: Re: [seek-kr-sms] algorithms and the owlfication of taxon
>
>
>Ah! Finallly everyone is getting out their fun references -- good!
>
>:-)
>
>BTW, the paper below does NOT have the promised title. But here it is:
>
>http://www.hpl.hp.com/personal/marbut/isTheSemanticWebHype.pdf
>
>Fun reading indeed..
>
>Bertram
>
>
>
>>>>On Thu, 3 Nov 2005 10:59:20 -0500
>>>>"Serguei Krivov" <Serguei.Krivov at uvm.edu> wrote:
>>>>
>>>>
>SK>
>SK> Shawn,
>SK> My objections to "second order metaprogramming" in OWL where merely
>SK> aesthetical, the question was about simplicity. Otherwise there is no
>any
>SK> serious problem with second order logics.
>SK>
>SK> The main problem with RDF(S) is its inconsistency. If one could derive
>SK> good==bad or true==false, then what could we do with it? And here is the
>SK> most popular attack on SW and RDF(S) (Title "Is semantic web hype?"
>)which
>SK> you would surely enjoy to read:
>SK> http://rewerse.net/publications/download/REWERSE-RP-2005-90.pdf
>SK>
>SK> serguei
>SK>
>SK>
>SK> -----Original Message-----
>SK> From: seek-kr-sms-bounces at ecoinformatics.org
>SK> [mailto:seek-kr-sms-bounces at ecoinformatics.org] On Behalf Of Shawn
>Bowers
>SK> Sent: Thursday, November 03, 2005 10:41 AM
>SK> To: Serguei Krivov
>SK> Cc: 'Serguei Krivov'; seek-kr-sms at ecoinformatics.org
>SK> Subject: Re: [seek-kr-sms] algorithms and the owlfication of taxon
>SK>
>SK>
>SK> I think RDF(S) solves real problems that OWL doesn't, and vice versa.
>SK> Logicians shouldn't be so wimpy and should suck it up and admit secord
>SK> order statements exist.
>SK>
>SK> -shawn
>SK>
>SK> On Thu, 3 Nov 2005, Serguei Krivov wrote:
>SK>
>
>
>>>Relation between FOL and RDF(S) has been discussed in: Horrocks,
>>>Patel-Schneider, Three Theses of Representation in the Semantic Web
>>>
>>>
>>>
>SK>
>http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/p50-orrocks.pdf
>
>
>>>Perhaps it is a good reference to corroborate the statement "logicians
>>>
>>>
>SK> try
>
>
>>>to avoid RDF(S)".
>>>
>>>serguei
>>>
>>>
>>>
>>>-----Original Message-----
>>>From: seek-kr-sms-bounces at ecoinformatics.org
>>>[mailto:seek-kr-sms-bounces at ecoinformatics.org] On Behalf Of Shawn Bowers
>>>Sent: Thursday, November 03, 2005 10:11 AM
>>>To: Bertram Ludaescher
>>>Cc: seek-kr-sms at ecoinformatics.org; Serguei Krivov
>>>Subject: Re: [seek-kr-sms] algorithms and the owlfication of taxon
>>>
>>>
>>>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:
>>>>
>>>>
>>>>
>>>>
>SK>
>http://www.ksl.stanford.edu/people/dlm/daml-semantics/abstract-axiomatic-sem
>
>
>>>antics.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
>>>>
>>>>
>SK> 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
>>>>>>
>>>>>>
>SK> and
>
>
>>>>>>stay in
>>>>>>OWL-DL. Suppose someone whant to say "Book b1 is about lions" and
>>>>>>
>>>>>>
>SK> "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
>>>>>>
>>>>>>
>SK> in
>
>
>>>OWL-DL
>>>
>>>
>>>>>>such data structures along with the derivations "hey pals, book b2
>>>>>>
>>>>>>
>SK> 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
>>>>>>>>>
>>>>>>>>>
>SK> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>SK>
>----------------------------------------------------------------------------
>
>
>>>----------
>>>
>>>
>>>>>>>>>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
>>>>
>>>>
>SK> 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"
>>>>
>>>>
>SK>
>href="http://www.w3.org/TR/swbp-classes-as-values/">http://www.w3.org/TR/swb
>
>
>>>p-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; }
>>>>>>>
>>>>>>>
>>>>MS> P.MsoNormal {
>>>>MS> FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New
>>>>
>>>>
>Roman"
>
>
>>>>MS> }
>>>>MS> LI.MsoNormal {
>>>>MS> FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New
>>>>
>>>>
>Roman"
>
>
>>>>MS> }
>>>>MS> DIV.MsoNormal {
>>>>MS> FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New
>>>>
>>>>
>Roman"
>
>
>>>>MS> }
>>>>MS> A:link {
>>>>MS> COLOR: blue; TEXT-DECORATION: underline
>>>>MS> }
>>>>MS> SPAN.MsoHyperlink {
>>>>MS> COLOR: blue; TEXT-DECORATION: underline
>>>>MS> }
>>>>MS> A:visited {
>>>>MS> COLOR: purple; TEXT-DECORATION: underline
>>>>MS> }
>>>>MS> SPAN.MsoHyperlinkFollowed {
>>>>MS> COLOR: purple; TEXT-DECORATION: underline
>>>>MS> }
>>>>MS> P.MsoPlainText {
>>>>MS> FONT-SIZE: 10pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Courier New"
>>>>MS> }
>>>>MS> LI.MsoPlainText {
>>>>MS> FONT-SIZE: 10pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Courier New"
>>>>MS> }
>>>>MS> DIV.MsoPlainText {
>>>>MS> FONT-SIZE: 10pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Courier New"
>>>>MS> }
>>>>MS> DIV.Section1 {
>>>>MS> page: Section1
>>>>MS> }
>>>>MS> </style>
>>>>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"
>>>>
>>>>
>SK> 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>
>>>>
>>>>
>SK>
>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
>>>>
>>>>
>SK> 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.
>>>>
>>>>
>SK> 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.
>>>>
>>>>
>SK> 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:
>>>>
>>>>
>SK>
>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
>>>>
>>>>
>SK> 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"
>>>>
>>>>
>SK> 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
>>>>
>>>>
>SK> 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
>>>>
>>>>
>SK> 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
>>>>
>>>>
>SK> 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
>>>>
>>>>
>SK> 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"
>>>>
>>>>
>SK>
>href="mailto:Seek-kr-sms at ecoinformatics.org">Seek-kr-sms at ecoinformatics.org<
>
>
>>>/a>
>>>
>>>
>>>>MS> <a class="moz-txt-link-freetext"
>>>>
>>>>
>SK>
>href="http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-
>
>
>SK>
>sms">http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-s
>
>
>>>ms</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
>>>
>>>
>>>_______________________________________________
>>>Seek-kr-sms mailing list
>>>Seek-kr-sms at ecoinformatics.org
>>>http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
>>>
>>>
>>>
>>>
>SK> _______________________________________________
>SK> Seek-kr-sms mailing list
>SK> Seek-kr-sms at ecoinformatics.org
>SK>
>http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-kr-sms
>SK>
>SK> _______________________________________________
>SK> Seek-kr-sms mailing list
>SK> Seek-kr-sms at ecoinformatics.org
>SK>
>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
>
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