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Re: Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept => Class Species Cougar

From: Pat Hayes <phayes@ihmc.us>
Date: Fri, 4 Dec 2009 12:02:08 -0600
Cc: Peter DeVries <pete.devries@gmail.com>, public-lod@w3.org, dmozzherin@gmail.com
Message-Id: <AEF54337-CDD9-412A-82D8-3FF8517DC40A@ihmc.us>
To: Bob Morris <morris.bob@gmail.com>

On Dec 4, 2009, at 11:14 AM, Bob Morris wrote:

>> In any civilized ontology language, a class is an instance. Use OWL  
>> 2 from
>> now on.
>> Pat
>
> Ah, a nice idea, but I doubt it will accomplish what Pete is trying to
> do (Or my limited understanding of OWL 2 is wrong---which is a good
> hypothesis). http://www.w3.org/TR/2009/REC-owl2-syntax-20091027/#Metamodeling
> says that when a  resource is mentioned as both an individual and a
> class, the two mentions are interpreted independently.

Well, true, so its not perfect. But it is better than OWL 1 in this  
regard.

>  My
> understanding of that is that it will not be possible to put any
> semantics on one of them that implies semantics on the other.

If you cash out what 'putting semantics on' amounts to, the only issue  
that arises has to do with identity. Owl 2 style punning allows A  
sameAs B when considered as individuals but not A sameClassAs B as  
classes. So you have to go to the trouble of asserting the appropriate  
identity, or even asserting it twice. Other than this, I believe  
everything works out as it should.

>
> I'd be happy to have it explained why that understanding is wrong,
> especially by a simple example that the Manchester OWL2 validator
> agrees is OWL2 DL (or even better, OWL2 RL)

I confess I have not messed with the Manchester validators.

Pat

>
> Bob Morris
>
>
>
> On Fri, Dec 4, 2009 at 11:12 AM, Pat Hayes <phayes@ihmc.us> wrote:
>>
>> On Dec 1, 2009, at 9:14 PM, Peter DeVries wrote:
>>
>> Hi Bob,
>> I came about this after it was suggested to me that a species might  
>> be best
>> represented as a class.
>> It also occurred to me that an ontology that works to describe  
>> mosquito
>> species would probably be very different than an ontology used to  
>> describe
>> members of the cat family.
>> What I thought was that there are times when you want to treat a  
>> species as
>> an instance and other time you want to treat it as a class.
>>
>> In any civilized ontology language, a class is an instance. Use OWL  
>> 2 from
>> now on.
>> Pat
>>
>> Thinking out loud here.
>> The lightweight representations shown in this
>> example http://rdf.taxonconcept.org/ses/v6n7p.rdf
>> are used when you just need something simple that gives you the basic
>> information and maps concepts.
>> However, it really does not document what you mean by the URI. By  
>> that I
>> mean, it does not provide any information that will allow you to
>> determine what species concept you should apply for a given specimen.
>> For that you will need something more complex, that can be loaded  
>> as needed.
>> Something more like this representation.
>> http://rdf.taxonconcept.org/owlses/v6n7p/2009-12-01.owl (Initially an
>> individual file made with Protege)
>>
>> How would these be used?
>> Lets say that an individual Cougar was observed within the  
>> boundaries of the
>> state of Wisconsin.
>> That individual is an instance, however, from that you should be  
>> able to
>> reason that the species
>> http://rdf.taxonconcept.org/ses/v6n7p
>>
>> was observed within the State of Wisconsin.
>> This should allow you to then run queries on species observed in a
>> particular geographic location as shown in these examples.
>> http://about.geospecies.org/sparql.xhtml
>>
>> You should also be able to make other assertions at the species  
>> concept
>> level based on data from collections of individuals.
>> For example, the mosquito Culex territans femalesfeedPrimarily on  
>> Anurans
>> (frogs and toads)
>> How do I determine if the cat I have captured is Puma concolor vs  
>> Puma
>> yagouaroundi? (or another less obvious example)
>> See
>> http://rdf.taxonconcept.org/ses/v6n7p and  http://rdf.taxonconcept.org/ses/Hq5OE
>> and from there get the related owl documents. The owl documents  
>> should
>> provide some information that will allow you to determine
>> which concept is the best match for the captured specimen.
>> At least that is what I would like to do. :-)
>> - Pete
>> On Tue, Dec 1, 2009 at 8:30 PM, Bob Morris <morris.bob@gmail.com>  
>> wrote:
>>>
>>> On Tue, Dec 1, 2009 at 8:40 PM, Peter DeVries <pete.devries@gmail.com 
>>> >
>>> wrote:
>>>> Hi LOD'ers,
>>>> [...]
>>>> I was thinking that the species itself should be a class so that
>>>> individuals
>>>> of that species would be instances of that class.
>>>> Probably another skos:Concept class.
>>>> So an individual species concept class like that for the Cougar  
>>>> would be
>>>> an
>>>> instance of a skos:Concept (SpeciesConcept) class and also be a
>>>> skos:Concept
>>>> class (Cougar) of it's own.
>>>> Individual animals would be instances of the skos:Concept class
>>>> (Cougar).
>>>> [...]
>>>
>>> Umm, if every species concept is a class, about how many classes, in
>>> your estimate,  would there be in a comprehensive ontology?
>>>
>>> --Bob
>>>
>>>
>>>
>>> --
>>> Robert A. Morris
>>> Professor of Computer Science (nominally retired)
>>> UMASS-Boston
>>> 100 Morrissey Blvd
>>> Boston, MA 02125-3390
>>> Associate, Harvard University Herbaria
>>> email: ram@cs.umb.edu
>>> web: http://bdei.cs.umb.edu/
>>> web: http://etaxonomy.org/FilteredPush
>>> http://www.cs.umb.edu/~ram
>>> phone (+1)617 287 6466
>>
>>
>>
>> --
>> ----------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> GeoSpecies Knowledge Base
>> About the GeoSpecies Knowledge Base
>> ------------------------------------------------------------
>>
>> ------------------------------------------------------------
>> IHMC                                     (850)434 8903 or (650)494  
>> 3973
>> 40 South Alcaniz St.           (850)202 4416   office
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>> phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes
>>
>>
>>
>>
>
>
>
> -- 
> Robert A. Morris
> Professor of Computer Science (nominally retired)
> UMASS-Boston
> 100 Morrissey Blvd
> Boston, MA 02125-3390
> Associate, Harvard University Herbaria
> email: ram@cs.umb.edu
> web: http://bdei.cs.umb.edu/
> web: http://etaxonomy.org/FilteredPush
> http://www.cs.umb.edu/~ram
> phone (+1)617 287 6466
>

------------------------------------------------------------
IHMC                                     (850)434 8903 or (650)494 3973
40 South Alcaniz St.           (850)202 4416   office
Pensacola                            (850)202 4440   fax
FL 32502                              (850)291 0667   mobile
phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes
Received on Friday, 4 December 2009 18:02:51 UTC

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