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

[Nico Cellinese]

Hi Pete,

> Hi Steve,
> 
> I may have overloaded the term specimen to make the explanation easier to follow.
> A specimen could be an individual or it could be part of an individual.
> To some extent you need to think about how these models will be used.
> If you subscribe to the model that a species is whatever a taxonomists says it is then it is difficult to make statements like.
> X% of the world's species will be extinct by 2050.
> If you mean a species as defined by the concept documented at this URI which is supported by these specimens, images, and DNA then you are on firmer ground.

I would have stopped here! If someone wants to point to a series of objects to indicate his own concept of a "species", then that's ok. That's a convention we can work with.

Everything else you talk about below seem to be a confused mashup of "species" as a taxon and "species" as ranks.

> Species in the natural world do a pretty good job recognizing those individuals that are appropriate mates. In other words members of their own species.

Really?  Maybe in animals but everywhere else I don't think so!  And what about asexual organisms?  I guess they do not deserve the status of "species".  So, the biological species concept you are referring to can't be universally applied = not a good concept to use for ALL organisms, right?

> Are we modeling species or variations in human conceptualizations of species?

Is there anything else out there besides the human conceptualization of species?  Do we have an absolute concept of what a species represent? Last time I checked we have been arguing about this for the past century and more.  Species defined by the 25+ species concepts out there can't possibly be real.  They are defined by human conceptualization = artificial.  The only think we can clearly try to discern are clades and often those clades may correspond with someone's concept of a species.  In other words, you can take the rank of species and point it at a node that define a taxon.  Or you can take the rank of species and point it to an assemblage of lineages, regardless if that assemblage represents a monophyletic group or not.  Traditionally recognized species are most likely polyphyletic anyways.

> I stick with this. Assuming you don't have a hybrid individual. That individual is one species. The fact that human may disagree on what species it is a human issue.

What do you really mean by individuals?  Are species created by the gods and we just can't figure out what they meant? Human issue? We, humans came up with this impossible to define concept. Individuals are just that: individuals. The individuals = species hypothesis has been argued in the literature and is not an accepted notion by far (note: I am not saying I agree or disagree, this is just another non-absolute concept).  But maybe you don't mean it that way.

> Again, Are we modeling species or variations in human conceptualizations of species?

Your statement is recursive. You have an idea of species that is above all of the other variations on the theme. I don't understand what you mean and that's why I think there is a confusion between the usage of "species" as a taxon and "species" as an arbitrary rank.

> Which of these is of primary importance to decision makers and non-taxonomist biologists? 
> Part of the problem with various publications relating to ontologies and taxonomy is that their species models entail a specific phylogenetic hypothesis.

Even in the lack of a phylogenetic framework, every species is a hypothesis. When we lump and split we generate hypotheses. A new name points to a new hypothesis.  Adding a new genus to a family or a new species to a genus refines and modifies the original hypothesis.

> In the real world taxa are not as clean as some would like to make them out to be. 

In fact, the only way we can discover a little more clarity is through phylogenies. When it comes to low level taxa, population studies help a lot too.  

> Each individual is a unique combination of thousands of separate gene lineages which often do not follow clean monophyletic paths.

But as you stated above you equate individuals with species.  if that's correct, then you admit that individuals can be polyphyletic, and as such do we really care about polyphyletic entities? As such you admit that species as you define them are artificial.

> I would argue that most of those who work with species related data see them as useful typological constructs which in general follow the biological species model.

I actually don't and I can name many others who don't. The rank of species may be useful to many as communication tool but the way it is applied vary a lot.  The biological species concept is not widely accept and certainly not followed by the vast majority as you indicate.

The only think we can really achieve from an informatics standpoint is to reconcile objects (specimens, images, sequences, descriptions, etc.etc.) with the many names that may have been associated with those and leave the rest (philosophical masturbation) to the users. Reconciling names with concepts, given the nature of the concepts and the idiosyncratic way that names have been historically used, is a Quixoterian challenge.

Cheers,
Nico



> 
> Aedes triseriatus owl:sameAs Ochlerotatus triseriatus 
> 
> Others seem to see them as phylogenetic end nodes which entail a specific phylogenetic history. 
> 
> Aedes triseriatus distinctFrom Ochlerotatus triseriatus
> 
> If you are primarily interested in understanding issues of ecology, disease, diversity and conservation the former model is more appropriate than the later.
> 
> Respectfully,
> 
> - Pete
> 
> On Wed, May 4, 2011 at 8:35 AM, Steve Baskauf <steve.baskauf at vanderbilt.edu> wrote:
> 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> 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".  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
>>>  
>>> 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  &  GeoSpecies Knowledge Bases
>>> 
>>> A Semantic Web, Linked Open Data  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
>>     
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> Email: pdevries at wisc.edu
>> TaxonConcept  &  GeoSpecies Knowledge Bases
>> A Semantic Web, Linked Open Data  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
>   
> 
> 
> 
> -- 
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries at wisc.edu
> TaxonConcept  &  GeoSpecies Knowledge Bases
> A Semantic Web, Linked Open Data  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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