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

Nico Franz franz at nceas.ucsb.edu
Wed Oct 26 13:55:24 PDT 2005


Hi all:

Not sure this will be of help, but what we're representing in the 
taxonomic concept schema roughly looks like this:

TaxonConcept (with GUID) [Quercus L. sec. FNA 1997]
Name [Quercus L.]
Source [FNA 1997]
Relationships to subsumed taxonconcepts ("children") [is a parent of 
Quercus robur L. sec. FNA 1997; is a parent of Quercus longifolia Nix. 
sec. FNA 1997; ...]
Associated specimens (often a least one type specimen, sometimes series 
of specimens) [Kew no. 1234567]
Character diagnosis ["trees, with lobulate leaves, fruits are acorns..."]

There will be multiple classifications of e.g. "Quercus" according to 
different sources. Names will be reused frequently but with different 
definitions (i.e. as different concepts with different information 
content specified in the above structure). Also keep in mind that not 
all information (subsumed elements, diagnoses) will be there all the 
time, but almost always both contribute to the definition ("meaning") of 
a TaxonConcept as understood by taxonomists and other biologists. 
Because of the nestedness it's clear that elements that function as 
"instances" at a higher level immediately become "classes" (with 
properties) at the next lower level.

Best,

Nico



Serguei Krivov wrote:

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