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

Serguei Krivov Serguei.Krivov at uvm.edu
Wed Oct 26 13:32:01 PDT 2005 

It seems that the natural way to specify authority is to assign attribute to
classes   and there is a temptation to go this way  right away, just because
it is most obvious solution. But this would lead us away from OWL-DL and the
things would become unreasonable and hence useless.  But in normal design
situation there are at least several alternatives and here assigning
attribute to classes is not the only way to do this job. I am sure there are
2, 3 or 4 alternative ways to do the same thing remaining in the domain of
OWL-DL. I give the solution that came to my mind : for class Species we
define attribute speciesAauthority, for classes Animal, Plants and Fungi we
define attribute kingdomAuthority , for Arthropoda, Chordata, etc we define
attributes phylumAuthority etc. Now there are two ways to do that. If we
define that on the level of Species, then each species will have compulsory
5 (or 6) attributes for speciesAauthority, kingdomAuthority. If we define
kingdomAuthority on the level of classes of kingdom rank then
kingdomAuthority is not mandatary for instance of class species. After we
have done it one or another way it is easy to say:

 

          

          here xxx is not the same as  yyy.( I do not know if xxx is class,
genus or something else).   

 

While doing so we are implicitly creating different possible instances of
the same species depending on authorities on kingdoms, phylum, classes , etc
and thus we have a number of formally different classifications, which is
probably what taxonomists want.

 

          If we think a bit more about this subject we may find a couple of
more ways to assign separate authorities to  kingdoms, phylum, classes , etc
remaining in OWL-DL .

 

ciao,

serguei

 

Sorry, more clarification - say you have a Canis named by Linnaeus in 1758
(I'm making this up) and a family Canidae named by Joesephus in 10 AD
(stretching here).... and Canis is a subclass of Canidae... how does this
work?

 

Dave

----- Original Message ----- 

From: dave thau <mailto:thau at learningsite.com>  

To: Serguei <mailto:Serguei.Krivov at uvm.edu>  Krivov ; 'bertram'
<mailto:ludaesch at ucdavis.edu>  ; 'Nico <mailto:franz at nceas.ucsb.edu>  Franz'


Cc: seek-kr-sms at ecoinformatics.org 

Sent: Wednesday, October 26, 2005 11:33 AM

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

 

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 <mailto:Serguei.Krivov at uvm.edu>  Krivov 

To: 'dave thau' <mailto:thau at learningsite.com>  ; 'bertram'
<mailto:ludaesch at ucdavis.edu>  ; 'Nico <mailto:franz at nceas.ucsb.edu>  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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