I like the examples on this page <a href="http://code.google.com/p/ala-bie/wiki/OntologyCompetency">http://code.google.com/p/ala-bie/wiki/OntologyCompetency</a><div><br></div><div>However they illustrate several problems with using taxon names.</div>
<div><br></div><div>These queries only work if the species, families, and genera are unique strings.</div><div><br></div><div>What about identical taxa that are marked up using different names?</div><div><br></div><div>What do you do about taxa that are organized into different clades by different groups?</div>
<div><br></div><div>I think this is a better example.</div><div><br></div><div>What plants are expected in Door County Wisconsin that are classified by the USDA Plants Database as "Forb/Herb"</div><div><br></div>
<div><div><font class="Apple-style-span" face="'courier new', monospace">PREFIX txn: <<a href="http://lod.taxonconcept.org/ontology/txn.owl#">http://lod.taxonconcept.org/ontology/txn.owl#</a>></font></div><div>
<font class="Apple-style-span" face="'courier new', monospace">PREFIX rdf: <<a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a>></font></div><div><font class="Apple-style-span" face="'courier new', monospace">PREFIX dcterms: <<a href="http://purl.org/dc/terms/">http://purl.org/dc/terms/</a>></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">PREFIX door_county_wi: <<a href="http://sws.geonames.org/5250768/">http://sws.geonames.org/5250768/</a>></font></div><div><font class="Apple-style-span" face="'courier new', monospace">PREFIX usda_plant: <<a href="http://lod.taxonconcept.org/ontology/usda_plants.owl#">http://lod.taxonconcept.org/ontology/usda_plants.owl#</a>> </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">select distinct ?s, ?o as ?image, ?class, ?order, ?family, ?sciname where {</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> ?s rdf:type txn:SpeciesConcept.</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> ?s rdf:type usda_plant:Growth_Habit_Forb_Herb.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> ?s txn:isExpectedIn door_county_wi:.</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> ?s txn:class ?class.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> ?s txn:order ?order.</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> ?s txn:family ?family.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> ?s txn:hasScientificName ?sciname.</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> optional {?s txn:thumbnail ?o.}.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> }</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> </font></div><div><font class="Apple-style-span" face="'courier new', monospace"> ORDER BY ASC(?sciname)</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"> limit 650</font></div></div><div><br></div><div>See the screen shots etc at this <a href="http://bit.ly">bit.ly</a> link <a href="http://bit.ly/qRh7xG">http://bit.ly/qRh7xG</a></div>
<div><br></div><div>There are additional examples here: <a href="http://www.taxonconcept.org/example-sparql-queries/">http://www.taxonconcept.org/example-sparql-queries/</a></div><div><br></div><div>- Pete<br><br><div class="gmail_quote">
On Thu, Jul 14, 2011 at 10:10 AM, Bob Morris <span dir="ltr"><<a href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
There is a series of jokes, and an entire TV quiz show, essentially<br>
starting from the meme "What is the question to which the answer is<br>
<X>". Now, I am not a biologist (surprise!), so it is likely that<br>
domain ignorance leaves me unable to understand whether all the<br>
postings in the thread about new DwC term resolution are arguing from<br>
the same set of questions their authors hope to have answered by a<br>
resolution of the term "Individual". (It's even a little unclear to<br>
me whether everybody has the same notion of "resolution of a term",<br>
but that's a whole different discussion, which would contain a lot of<br>
uses of "rdf:type" and the contentious "rdfs:domain").<br>
<br>
I speculate that lengthy term definition debates would be shorter if<br>
they started with agreement on competency questions for the term.<br>
Competency questions are sort of usage scenarios cast as questions.<br>
See <a href="http://marinemetadata.org/references/competencyquestionsoverview" target="_blank">http://marinemetadata.org/references/competencyquestionsoverview</a> .<br>
<br>
Bob Morris<br>
<br>
<br>
<br>
On Thu, Jul 14, 2011 at 2:41 AM, Richard Pyle <<a href="mailto:deepreef@bishopmuseum.org">deepreef@bishopmuseum.org</a>> wrote:<br>
> My turn to disagree (strongly, in this case). It's not an instance of a<br>
> taxon, it's an instance of an Organism. A taxon is merely a non-factual<br>
> (i.e., opinion-based) attribute of an organism, secondarily associated via<br>
> an Identification instance.<br>
><br>
> I could probably be comfortable with "OrganismInstance"; but in that case,<br>
> why not just "Organism" as Paul suggested? Isn't "Instance" sort of implied<br>
> by all the classes?<br>
><br>
> I am certainly open to debate about where the "upper boundary" of an<br>
> instance of this class, and I agree that "population" could be interpreted<br>
> more as a low level of "taxon", rather than a high level of "organism". But<br>
> I certainly don't think that instances of this class should be limited to a<br>
> singular organism. Would a coral head then constitute thousands of<br>
> instances of this class? Surely such colonies could be collapsed into a<br>
> single instance of this class. And the same would likely also be useful for<br>
> colonies of insects (ants, termites, bees, etc.), as well as small groups<br>
> (pack of wolves, pod of whales, etc.); not to mention a specimen "lot" in a<br>
> Museum collection.<br>
><br>
> I agree it should have only *one* taxon, but that there should be no upper<br>
> limit on the rank of this taxon. If more than one taxon is identified, then<br>
> there needs to be a separate instance of this class for each identified<br>
> taxon. But this only applies when multiple taxa are acknowledged -- it does<br>
> NOT restrict multiple taxa being linked to the same instance via multiple<br>
> identifications when there is a difference of opinion about what the correct<br>
> taxon identity should be. In other words, an instance of this class may be<br>
> identified as "A" *or* "B", but could not legitimately be identified as "A"<br>
> *and* "B" simultaneously (except, perhaps in the case of hybrids, but that's<br>
> another situation altogether).<br>
><br>
> More later.<br>
><br>
> Aloha,<br>
> Rich<br>
><br>
>> -----Original Message-----<br>
>> From: <a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [mailto:<a href="mailto:tdwg-content-">tdwg-content-</a><br>
>> <a href="mailto:bounces@lists.tdwg.org">bounces@lists.tdwg.org</a>] On Behalf Of Gregor Hagedorn<br>
>> Sent: Tuesday, July 12, 2011 10:09 AM<br>
>> To: Steven J. Baskauf<br>
>> Cc: <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
>> Subject: Re: [tdwg-content] New terms need resolution: "Individual"<br>
>><br>
>> > represent a single taxon. I think that Individual is probably not a<br>
>> > good name due to confusion with the technical use of that term<br>
>> elsewhere.<br>
>><br>
>> TaxonInstance seems to me to be perhaps most precise.<br>
>> Personally I have a problem merging individual with population, since<br>
>> population -> metapopulation -> subspecies form a continuum in my<br>
>> understanding. But I am quite willing to be pragmatical :-)<br>
>><br>
>> Gregor<br>
>> _______________________________________________<br>
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><br>
><br>
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><br>
><br>
<br>
<br>
<br>
--<br>
Robert A. Morris<br>
<br>
Emeritus Professor of Computer Science<br>
UMASS-Boston<br>
100 Morrissey Blvd<br>
Boston, MA 02125-3390<br>
IT Staff<br>
Filtered Push Project<br>
Department of Organismal and Evolutionary Biology<br>
Harvard University<br>
<br>
<br>
email: <a href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a><br>
web: <a href="http://efg.cs.umb.edu/" target="_blank">http://efg.cs.umb.edu/</a><br>
web: <a href="http://etaxonomy.org/mw/FilteredPush" target="_blank">http://etaxonomy.org/mw/FilteredPush</a><br>
<a href="http://www.cs.umb.edu/~ram" target="_blank">http://www.cs.umb.edu/~ram</a><br>
phone <a href="tel:%28%2B1%29%20857%20222%207992" value="+18572227992">(+1) 857 222 7992</a> (mobile)<br>
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</blockquote></div><br><br clear="all"><br>-- <br>
------------------------------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>1630 Linden Drive<br>Madison, WI 53706<br>
Email: <a href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept</a> & <a href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge Bases<br>
A Semantic Web, <a href="http://linkeddata.org/" target="_blank">Linked Open Data</a> Project<br>--------------------------------------------------------------------------------------<br>
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