[seek-kr-sms] OWL - taxonomy

[Serguei Krivov]

Hi Nico,

I am glad that we have this email conversation which also helps me to
understand the real complexity of the world taxonomists live in. It is
certainly not as simple as I thought it is; and perhaps that real taxonomies
may not be easily captured by an OWL ontology with *simple* structure. But,
I am sure that with  some tricks we could express the major part of it in
OWL. 

 

I'll try to answer  your questions, that I found in text. 

 

 

It is possible (in 

OWL) to regard the species at the tips of the tree as both individuals 

and classes, but only so long as we guarantee "strict correspondence" 

between these two views.

=> Does this mean we have to restrict and name upfront the actual 

physical specimens that a species viewed as a class may contain? 

 

 No, absolutely not.

In 

taxonomy each species name is assigned to a single holotype specimen, 

but of course the intensional definition of that species (i.e. its 

diagnosis) may refer to many specimens, including specimens not yet born...

=> Could you clarify is slightly non-technical what a "strict 

correspondence" of species as individual vs. class means? I don't fully 

understand yet.

 

It merely means that whenever we introduce a name for a species we write two
owl names- one for a class that denote this species , another is for an
individual that denotes this species, then we should write perhaps one axiom
that establishes a correspondence between them, saying for example that for
all class ClSpeciesNameX property hasSpecies has value indSpeciesNameX:

 

ClSpeciesNameX <-> hasSpecies:indSpeciesNameX 

 

The class ClSpeciesNameX is a subclass of the top class Specimen (if we
choose specimen to be our bottom individuals. The individual indSpeciesNameX
works as a descriptor and could have been a string.

 

IMHO, before making such double representation we should try to circumvent
it (in the name of Simplicity!) and see if there is way to go with more
simple approach when only specimens are individuals. Can't we just treat it
as a   logical error that has to be corrected, when some authors take say
phylim or genus classes as individuals. My hypothesis is that such
correction would not change anything in the positive content of those
taxonomies.

 

 

=> Your first suggested solution is basically to switch to an ostensive 

definition for C. pilosa since this species does not fully comply with 

the intensional definition of its superclass Cyclanthura. Taxonomists do 

that too to a degree. 

 

I think here we have a mixture of ostensive and intensive definition. And
now suppose that species are still classes, then the definition will be
still intensive:

 

Cyclanthura equivalent to

 Union ( Intersection( Morph12 Morph25 Morph27) Cyclanthura-pilosa )

 

(no curly brackets around Cyclanthura-pilosa)

 

But at the same time there IS a way to think of C. 

pilosa as having Morph 27. Certainly the critical evolutionary 

preocursors for having Morph27 should still exist in C. pilosa's genetic 

make-up. It is just that another subsequent "mutation" has led to the 

suppression of Morph27 in the phenotype of C. pilosa (the actual visible 

morphology of the beetles in this species).

=> I am wondering whether this point is too academic to push further or 

whether it is a very central issue. Taxonomists often have a very 

complex notion of what a "character" (Morph) is, and as I said there is 

a transformational way to reconcile the fact that C. pilosa doesn't seem 

to have Morph27 yet is still correctly intensionally defined as a member 

of Cyclanthura which does have Morph27.

=> Might be a hard problem to solve...(modal logic?; non-monotonic?; 

please elaborate if you think it's promising). From a perspective of 

taxonomy we wouldn't want to give up on character-based definitions just 

because some members of subclasses "have moved on" in the course of 

evolution and further refined or lost their ancestors features (at least 

phenotypicallly; snakes do have lots of suppressed genes for making legs).

 

*On some level of details* it is very easy to say such things in OWL. Create
a shadowy class (individual)

Cyclanthura-pilosa'. Require that

 

Cyclanthura-pilosa' subclass of (or member of)  Intersection( Morph12
Morph25 Morph27)

 

Connect original class (individual) Cyclanthura-pilosa with the shadowy
class via some property such as geneticMutation. Pretty easy to do when
things are individuals:

 

 Cyclanthura-pilosa'- geneticMutation--> Cyclanthura-pilosa

 

When they are classes it is more complex:

 

Cyclanthura-pilosa' subclass of (Exist geneticMutation. Cyclanthura-pilosa)

 

Cyclanthura-pilosa as before is not subclass (does not belong to)

Intersection( Morph12 Morph25 Morph27)

 

This is  of course just one simple way of describing it, I cant be sure   if
this will convey all necessary information.. If we work on it we may find
something more expressive/intelligent.  My aim in our discussion is much
more modest then to offer a solution that takes carte about all the main
problems.  The aim is just to start thinking about it. The only complete
thesis that I can suggested now as a conjecture is that if use some design
trick then we could do a lot even in OWL-DL.

 

ciao,

serguei 

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