[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
Wed May 4 15:35:12 CEST 2011
I beg to differ.
Peter DeVries wrote:
> About occurrences.
>
> It is the specimen (individual) that gets identified and it can have
> several identifications.
I do not believe it is a good idea to equate "specimen" with
individual. I have reached the conclusion that a specimen CAN be an
individual if one chooses to type a particular "thing" as both a
specimen and and an Individual but I'm not comfortable with saying that
they are owl:sameAs . It is my opinion, and I think one that was
supported to some extent in the discussion of last Oct/Nov that when we
"identify" some kind of evidence like a a branch cut from a tree we are
really making a statement about what taxon we think the tree represents,
not the branch per se. This is an important distinction, because if we
are identifying the tree, then any branch that is dcterms:partOf the
tree shares that identification. This may seem like an esoteric point,
but it is one that has a fairly significant bearing on how one chooses
to construct a model. I will stop there because I don't want to
re-plough the same ground again. The relevant posts are summarized and
referenced on the DSW pages explaining the IndividualOrganism and
Specimen classes.
>
> 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.
Again, I beg to differ. It was my understanding (again from the
extensive conversation about this in Oct/Nov) that the creation of
multiple Identifications were "preference agnostic". Each
Identification represented an expressed opinion about the concept/TNU
that the determiner asserted that the individual represented. They were
not flagged as "right" or "wrong". In fact, it is possible that there
could be several Identifications by different determiners that asserted
the same concept/TNU, indicating that the determiners agreed with each
other.
>
> Assuming that there was only one individual organism identified there
> is really one one species (or hybrid).
Aaaaaaaaaaaaaah! Please Nico C., don't take this one up!
>
> Different human identifiers make assertions about what that species
> is, those different identifications are then tied to the individual
> organism.
Yes I agree entirely.
>
> In other words it is the specimen that is identified not the occurrence.
Yes, the occurrence was not identified. But I would say the individual,
not the specimen (as explained above).
>
> 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?
Not really, but I think the issue here is that the way you are
conceptualizing specimens, individuals, and identifications is NOT the
same as DSW defines them. So I retract my earlier statement that the
taxonconcept.org ontology and DSW are really the same thing with
different term names .
Steve
>
> - Pete
>
> On Mon, May 2, 2011 at 8:16 AM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu <mailto: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#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:
> 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 <tel:%28615%29%20343-4582>, fax: (615) 343-6707 <tel:%28615%29%20343-6707>
> http://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 <mailto: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
> --------------------------------------------------------------------------------------
--
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) 343-6707
http://bioimages.vanderbilt.edu
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