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

[Serguei Krivov]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20051026/3745cd95/attachment-0001.htm
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 13528 bytes
Desc: not available
Url : http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20051026/3745cd95/attachment-0002.jpg
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 7445 bytes
Desc: not available
Url : http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20051026/3745cd95/attachment-0003.jpg