[seek-kr-sms] algorithms and the owlfication of taxon
Shawn Bowers
sbowers at ucdavis.edu
Wed Nov 2 17:48:56 PST 2005
I think the assumption here is that we need to use OWL-DL. Whereas at face
value, RDF(S) seems to have the needed elements.
-shawn
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
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>> 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" 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
>>
>
>
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