I like the examples on this page http://code.google.com/p/ala-bie/wiki/OntologyCompetency
However they illustrate several problems with using taxon names.
These queries only work if the species, families, and genera are unique strings.
What about identical taxa that are marked up using different names?
What do you do about taxa that are organized into different clades by different groups?
I think this is a better example.
What plants are expected in Door County Wisconsin that are classified by the USDA Plants Database as "Forb/Herb"
select distinct ?s, ?o as ?image, ?class, ?order, ?family, ?sciname where {
?s rdf:type txn:SpeciesConcept.
?s rdf:type usda_plant:Growth_Habit_Forb_Herb.
?s txn:isExpectedIn door_county_wi:.
?s txn:class ?class.
?s txn:order ?order.
?s txn:family ?family.
?s txn:hasScientificName ?sciname.
optional {?s txn:thumbnail ?o.}.
}
ORDER BY ASC(?sciname)
limit 650
- Pete
On Thu, Jul 14, 2011 at 10:10 AM, Bob Morris
<morris.bob@gmail.com> wrote:
There is a series of jokes, and an entire TV quiz show, essentially
starting from the meme "What is the question to which the answer is
<X>". Now, I am not a biologist (surprise!), so it is likely that
domain ignorance leaves me unable to understand whether all the
postings in the thread about new DwC term resolution are arguing from
the same set of questions their authors hope to have answered by a
resolution of the term "Individual". (It's even a little unclear to
me whether everybody has the same notion of "resolution of a term",
but that's a whole different discussion, which would contain a lot of
uses of "rdf:type" and the contentious "rdfs:domain").
I speculate that lengthy term definition debates would be shorter if
they started with agreement on competency questions for the term.
Competency questions are sort of usage scenarios cast as questions.
See http://marinemetadata.org/references/competencyquestionsoverview .
Bob Morris
On Thu, Jul 14, 2011 at 2:41 AM, Richard Pyle <deepreef@bishopmuseum.org> wrote:
> My turn to disagree (strongly, in this case). It's not an instance of a
> taxon, it's an instance of an Organism. A taxon is merely a non-factual
> (i.e., opinion-based) attribute of an organism, secondarily associated via
> an Identification instance.
>
> I could probably be comfortable with "OrganismInstance"; but in that case,
> why not just "Organism" as Paul suggested? Isn't "Instance" sort of implied
> by all the classes?
>
> I am certainly open to debate about where the "upper boundary" of an
> instance of this class, and I agree that "population" could be interpreted
> more as a low level of "taxon", rather than a high level of "organism". But
> I certainly don't think that instances of this class should be limited to a
> singular organism. Would a coral head then constitute thousands of
> instances of this class? Surely such colonies could be collapsed into a
> single instance of this class. And the same would likely also be useful for
> colonies of insects (ants, termites, bees, etc.), as well as small groups
> (pack of wolves, pod of whales, etc.); not to mention a specimen "lot" in a
> Museum collection.
>
> I agree it should have only *one* taxon, but that there should be no upper
> limit on the rank of this taxon. If more than one taxon is identified, then
> there needs to be a separate instance of this class for each identified
> taxon. But this only applies when multiple taxa are acknowledged -- it does
> NOT restrict multiple taxa being linked to the same instance via multiple
> identifications when there is a difference of opinion about what the correct
> taxon identity should be. In other words, an instance of this class may be
> identified as "A" *or* "B", but could not legitimately be identified as "A"
> *and* "B" simultaneously (except, perhaps in the case of hybrids, but that's
> another situation altogether).
>
> More later.
>
> Aloha,
> Rich
>
>> -----Original Message-----
>> From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-
>> bounces@lists.tdwg.org] On Behalf Of Gregor Hagedorn
>> Sent: Tuesday, July 12, 2011 10:09 AM
>> To: Steven J. Baskauf
>> Cc: tdwg-content@lists.tdwg.org
>> Subject: Re: [tdwg-content] New terms need resolution: "Individual"
>>
>> > represent a single taxon. I think that Individual is probably not a
>> > good name due to confusion with the technical use of that term
>> elsewhere.
>>
>> TaxonInstance seems to me to be perhaps most precise.
>> Personally I have a problem merging individual with population, since
>> population -> metapopulation -> subspecies form a continuum in my
>> understanding. But I am quite willing to be pragmatical :-)
>>
>> Gregor
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content@lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
>
> _______________________________________________
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>
--
Robert A. Morris
Emeritus Professor of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390
IT Staff
Filtered Push Project
Department of Organismal and Evolutionary Biology
Harvard University
email: morris.bob@gmail.com
web: http://efg.cs.umb.edu/
web: http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ram
phone (+1) 857 222 7992 (mobile)
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
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Email:
pdevries@wisc.eduTaxonConcept &
GeoSpecies Knowledge Bases
A Semantic Web,
Linked Open Data Project
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