[seek-kr-sms] algorithms and the owlfication of taxon
Serguei Krivov
skrivov at uvm.edu
Mon Oct 31 08:50:47 PST 2005
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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> 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
>
> _______________________________________________
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