[seek-kr-sms] algorithms and the owlfication of taxon
Bertram Ludaescher
ludaesch at ucdavis.edu
Mon Oct 31 06:08:28 PST 2005
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>
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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"
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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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