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

dave thau thau at learningsite.com
Wed Oct 26 11:33:36 PDT 2005


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 
  To: 'dave thau' ; 'bertram' ; 'Nico Franz' 
  Cc: 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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