[tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
Peter DeVries
pete.devries at gmail.com
Tue May 3 20:32:14 CEST 2011
Hi Steve,
About occurrences.
It is the specimen (individual) that gets identified and it can have several
identifications.
See
http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Focs.taxonconcept.org%2Focs%2Ff522444a-2dd9-400e-be59-47213ef38cb9%23Identification_0001
bit.ly http://bit.ly/fCGZdY
<http://bit.ly/fCGZdY>You simply need to markup your own RDF that references
that specimen and create your own identification.
There can be several different alternative identifications:
1) Different name but same species - That would be the same concept.
2) Different name and a different species.
3) Same name different species - The identification should be tied to a
resolvable concept so a different species under the same name would have a
different concept URI
There is an issue with occurrence records that we saw with one of the
initial TDWG BioBlitz RDF Versions.
There were multiple identifications but there was no way of indicating which
was the preferred.
Assuming that there was only one individual organism identified there is
really one one species (or hybrid).
Different human identifiers make assertions about what that species is,
those different identifications are then tied to the individual organism.
In other words it is the specimen that is identified not the occurrence.
If your additional identification RDF links to the specimen then it will be
linked to the occurrence so someone can browse from the occurrence and look
at the identification history of the specimen.
Does, this answer your question?
- Pete
On Mon, May 2, 2011 at 8:16 AM, Steve Baskauf
<steve.baskauf at vanderbilt.edu>wrote:
> 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"<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#Occurrenceis 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%23SpeciesKnowledge Base View (http://bit.ly
> bit.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
>
> 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:
> VU Station B 351634
> Nashville, TN 37235-1634, U.S.A.
>
> delivery address:
> 2125 Stevenson Center
> 1161 21st Ave., S.
> Nashville, TN 37235
>
> office: 2128 Stevenson Center
> phone: (615) 343-4582, fax: (615) 343-6707http://bioimages.vanderbilt.edu
>
>
--
------------------------------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/> &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/> Project
--------------------------------------------------------------------------------------
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