[seek-kr-sms] algorithms and the owlfication of taxon
dave thau
thau at learningsite.com
Mon Oct 31 07:21:59 PST 2005
Looks really good.
I'll take a crack at it.
Dave
----- Original Message -----
From: "Bertram Ludaescher" <ludaesch at ucdavis.edu>
To: "Mark Schildhauer" <schild at nceas.ucsb.edu>
Cc: "dave thau" <thau at learningsite.com>; "Nico Franz"
<franz at nceas.ucsb.edu>; <seek-kr-sms at ecoinformatics.org>
Sent: Monday, October 31, 2005 6:08 AM
Subject: Re: [seek-kr-sms] algorithms and the owlfication of taxon
>
> 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/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; ">
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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-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
>
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