[seek-kr-sms] algorithms and the owlfication of taxon

[Shawn Bowers]

Why not just use RDF(S)?  Or is there some more fundamental reason one would
need to use OWL for this?

-shawn

Mark Schildhauer wrote:
> Hi All,
> 
> I think Dave put his finger on it that this is the primary obstacle with 
> using OWL-DL to model biological taxonomies, viz. that we want to 
> flexibly use classes as instances-- so we can get the advantages of 
> inheritance from the class structure, but also reference classes as 
> property-values.  There is some discussion of this issue on the w3 site--
> 
> http://www.w3.org/TR/swbp-classes-as-values/
> 
> I'm still reviewing this document myself, but it seems very relevant to 
> our quandary...
> 
> cheers,
> Mark
> /
> 
> /dave thau wrote:
>> 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
>>
>> ------------------------------------------------------------------------
>>
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>>   
> 
> 
> -- 
> Mark Schildhauer, Ph.D.                        735 State St., Suite 300
> Director of Computing, NCEAS               Santa Barbara CA 93101
> Phone: 805-892-2509      FAX: 805-892-2510
> Email: schild at nceas.ucsb.edu
> 
> 
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