[tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class

Steve Baskauf steve.baskauf at vanderbilt.edu
Mon May 2 15:16:27 CEST 2011


OK, Pete, I'm going to try to write the other email that I mentioned in 
the previous one.  This email relates to the actual suggestion that you 
made in the email, that is to use the URIs of the form like: 
"http://lod.taxonconcept.org/ses/mCcSp#Occurrence".  In the RDF that 
defines what this URI means, the URI is described as "A lightweight tag 
that can be used to label occurrences of this species".  What I'm not 
sure about is what exactly one is supposed to do with it.  From the 
example that I was talking about in the previous email 
(http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf), 
this "tag" is the object of the predicate 
txn:occurrenceHasSpeciesOccurrenceTag .  So I guess that it is another 
way that one could query Occurrence records to find out which ones are 
Occurrences of the species having the identifier "ICmLC" (/Boloria 
selene/).  But I'm not sure what the advantage of that is.  The RDF for 
the Occurrence already tells me that the Occurrence has the 
txn:occurrenceHasSpeciesConcept property with object URI 
http://lod.taxonconcept.org/ses/ICmLC#Species .  I can resolve that URI 
and "find out" that the "species concept" (sensu DeVries) is /Boloria 
selene/ .  But if I used the "lightweight tag" I'd also have to resolve 
its URI to find out about it and the RDF for the tag directs me to the 
http://lod.taxonconcept.org/ses/ICmLC#Species URI anyway via the 
dcterms:isPartOf property of the tag.  I guess the point is that if one 
wants to "find out" about the Occurrence, it takes two steps to get to 
the species concept description if I use the tag (first through 
txn:occurrenceHasSpeciesOccurrenceTag, then through dcterms:isPartOf) 
which is no advantage over just getting there in one step (via 
txn:occurrenceHasSpeciesConcept).  If the only point is to have 
something to put in as a search term, then why not just make the 
txn:occurrenceHasSpeciesOccurrenceTag a data property with the literal 
object the string "ICmLC"? 

I suppose that one could say that an advantage of the "lightweight tag" 
approach would be that one is indicating that the particular Occurrence 
is an instance of a class that consists of all Occurrences of the 
species /Bororia selene/.  That seems to be what the intention is.  But 
this seems to be a case of creating many subclasses rather than having a 
general class and assigning it properties that help one to understand 
the nature of the instance of that class.  It requires the creation of a 
class for every species on the planet.  Instead of there being a 
relatively small number of classes that includes the basic kinds of 
resources (Occurrence, individual, Identification, taxon concept) there 
is a class for occurrences of every kind of taxon concept.  Actually, 
there are several classes for every instance of taxon concept, because 
you are recommending that the "lightweight tag" approach be used for 
other types of things as well, such as individuals and (in your 
suggestion below, populations).  There isn't anything intrinsically 
"wrong" with this approach, but with my bias toward preferring "well 
known" types/classes it just seems like a lot to expect consuming 
applications to "understand" what amounts to potentially millions of 
classes that this method would introduce.

I also don't quite understand what a txn:SpeciesOccurrenceTag is 
exactly.  In the RDF that defines the txn:SpeciesOccurrenceTag instance 
for /Bororia selene/ (http://lod.taxonconcept.org/ses/ICmLC#Occurrence) 
the dcterms:description says that it "allow species occurrences to be 
modeled as instances of SpeciesOccurrenceTag".  But that doesn't seem to 
be what is actually occurring.  When the Occurrence instance 
http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurrence 
is described, it is not typed as the lightweight tag (which IS a 
txn:SpeciesOccurrenceTag because of the implicit typing caused by the 
XML container element name).  The lightweight tag URI is the object of 
the txn:occurrenceHasSpeciesOccurrenceTag property, but that doesn't 
make the Occurrence an instance of SpeciesOcurrenceTag as would be the 
case (I think) if the lightweight tag URI were the object of a rdf:type 
property.  Anyway, I'm confused about this.

The other issue that I would raise with this approach is that it brings 
up the same issue that I raised in the other email that I wrote.  It 
essentially puts a burden of anticipating the results of a query onto 
the metadata provider.  If one follows the model of allowing multiple 
Identifications for an organism, then it is possible that someone 
somewhere else might apply their own Identification instance to the 
individual represented in the Occurrence.  As was the case in my earlier 
example, for txn:occurrenceHasSpeciesOccurrenceTag to be useful as a 
thing to be queried, the metadata provider would need to somehow know 
that this additional Identification had been made, and then create 
another txn:occurrenceHasSpeciesOccurrenceTag property for the 
Occurrence instance.  This seems to somewhat at odds with the benefit 
that the Linked Data world has in allowing resources to be created by 
people all over the cloud and then linked rather than expecting a 
centralized authority to do everything. 

Anyway, maybe you can explain what is going on so that I can understand 
it better and maybe explain why this approach is better than just 
creating a few classes and describing their instances by descriptive 
properties. 

Steve

Peter DeVries wrote:
> I am still somewhat puzzled why TDWG seems so opposed to adopting 
> anything that comes from outside a small click?
>
> I was thinking that it would be best to create a separate class that 
> can be used for populations of a species.
>
> This would require adding an additional tag to the TaxonConcept 
> Species Concept Model, which currently includes several tags like entities
>
> http://lod.taxonconcept.org/ses/mCcSp#Species <- The Species Concept 
> for the Cougar
>
> See http://lod.taxonconcept.org/ses/v6n7p.html HTML
>        http://lod.taxonconcept.org/ses/v6n7p.rdf  RDF
>       
>  http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23Species 
> Knowledge Base View (http://bit.ly bit.ly/gMFqR1 
> <http://bit.ly%20bit.ly/gMFqR1>
>  
> The model mints URI's for the following related entities. See RDF. or 
> KB View
>
> http://lod.taxonconcept.org/ses/mCcSp#Image      - An image of a Cougar
> http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a 
> Cougar
> http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar
> http://lod.taxonconcept.org/ses/mCcSp#Taxonomy   - A Basic Taxonomy 
> for the Cougar, one alternative among many potential classifications
> http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI 
> Taxonomy for Cougar, or starting at the lowest available clade
> http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The 
> Original Description of the Cougar, ideally with links to the PDF or 
> BHL URI.
>     
>     
> Here is how a subset of these would relate to the new #Population Tag 
> and related semantic entities.
>
>
> This tag is used an individual organism that that is an instance of 
> the species concept pecies concept RDF.
> This allows you to refer to a individual cougar in a way that is 
> separate from the concept of cougar and retains links to other data 
> relating to that species concept.
>
>
>   <txn:SpeciesIndividualTag 
> rdf:about="http://lod.taxonconcept.org/ses/v6n7p#Individual">
>     <dcterms:title>A Tag for individuals of the species concept Puma 
> concolor se:v6n7p</dcterms:title>
>     <skos:prefLabel>A Tag-like resource that is used to label 
> individuals of the species concept Puma concolor se:v6n7p</skos:prefLabel>
>     
> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Individual</dcterms:identifier>
>     <dcterms:description>A lightweight tag that can be used to label 
> individuals of this species. These allow individual organisms to be 
> modeled as instances of SpeciesIndividualTag</dcterms:description>
>     <dcterms:isPartOf 
> rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Species"/>
>     <wdrs:describedby 
> rdf:resource="http://lod.taxonconcept.org/ses/v6n7p.rdf"/>
>   </txn:SpeciesIndividualTag>
>
> Add a tag for a species population to the species concept RDF.
> This allows you to refer to a population of cougars in a way that is 
> separate for an individual cougar and retains links to other data 
> relating to that species concept.
>
>   <txn:SpeciesPopulationTag 
> rdf:about="http://lod.taxonconcept.org/ses/v6n7p#Population">
>     <dcterms:title>A Tag for populations of the species concept Puma 
> concolor se:v6n7p</dcterms:title>
>     <skos:prefLabel>A Tag-like resource that is used to label 
> populations of the species concept Puma concolor se:v6n7p</skos:prefLabel>
>     
> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Population</dcterms:identifier>
>     <dcterms:description>A lightweight tag that can be used to label 
> populations of this species. These allow populations of a species to 
> be modeled as instances of SpeciesIndividualTag</dcterms:description>
>     <dcterms:isPartOf 
> rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Species"/>
>     <wdrs:describedby 
> rdf:resource="http://lod.taxonconcept.org/ses/v6n7p.rdf"/>
>   </txn:SpeciesPopulationTag>
>
>
> This is the RDF for a population, it has as one of it's parts an 
> individual organism.
> It is typed to indicate that it refers to a population of Cougars.
>
>   <owl:Class 
> rdf:about="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation">
>     <rdf:type 
> rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Population"/>
>     <skos:prefLabel>The population of North American Cougars Puma 
> concolor se:v6n7 </skos:prefLabel>
>     <dcterms:hasPart 
> rdf:resource="http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Individual"/>
>     <wdrs:describedby 
> rdf:resource="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf"/>
>   </owl:Class>
>
> Respectfully,
>
> - Pete
>
> -------------------------------------------------------------------------------------
>
> Pete DeVries
>
> Department of Entomology
>
> University of Wisconsin - Madison
>
> 445 Russell Laboratories
>
> 1630 Linden Drive
>
> Madison, WI 53706
>
> Email: pdevries at wisc.edu <mailto:pdevries at wisc.edu>
>
> TaxonConcept  <http://www.taxonconcept.org/> &  GeoSpecies 
> <http://lod.geospecies.org/> Knowledge Bases
>
> A Semantic Web, Linked Open Data  <http://linkeddata.org/> Project
>
> ---------------------------------------------------------------------------------------
>
>

-- 
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

postal mail address:
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office: 2128 Stevenson Center
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