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

[Mark Schildhauer]

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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