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

Nico Franz nico.franz at upr.edu
Wed May 4 17:49:20 CEST 2011

Hello all: I have a few inserted comments, hopefully with some 
clarifying effect:

On 5/4/2011 10:54 AM, Peter DeVries wrote:
> 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.
> 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.
> Are we modeling species or variations in human conceptualizations of 
> species?
>>     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!
> 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.
> Again, Are we modeling species or variations in human 
> conceptualizations of species?
NMF: I believe there is a history of biodiversity database engineering 
that actually led some people, initially in Australia (Greg Whitbread?) 
and Europe (Berendsohn's group) to place more emphasis on modeling human 
conceptualizations of taxa. I understand this happened in the late 80s / 
early 90s. The motivation was, apparently, that no long-term consensus 
seemed available to model a single and sufficiently widely accepted 
taxonomy of, say, Central European vascular plant species or mosses. I 
believe that projects such as the Euro + Med PlantBase 
(http://www.emplantbase.org/home.html) are examples of the persistence 
(success?) of this 20+ year old practice. I think this is the kind of 
background that Steve is referring to.

> 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.
> In the real world taxa are not as clean as some would like to make 
> them out to be.
> Each individual is a unique combination of thousands of separate gene 
> lineages which often do not follow clean monophyletic paths.
> 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.
NMF: The solution of how to properly model things such as species in 
RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, 
ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this 
issue. The examples below are too simple, ignoring for example cases 
such as pro parte synonymy, or a concept ("species") that appears unique 
and monophyletic to one author but (vastly) polyphyletic to another. To 
do an accurate mapping in that latter case (which is not super-common 
but it's real), I think one would have to come down on saying we're 
modeling human conceptualizations. They are not just that, so really 
it's not a strict dichotomy, meaning that by modeling conceptualizations 
we do not have to say "the species only exist on our heads", or "well, 
then anything goes". I agree (sheepishly) that it does come down to what 
the input data look like, and what the expectations are towards just 
accommodating the user community versus pushing them in a particular 

Some of this also on p. 47 of this PDF: 

> /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



Nico M. Franz, Ph.D.
Assistant Professor
Director, UPRM Invertebrate Collection
Department of Biology
University of Puerto Rico
Call Box 9000
Mayagüez, PR 00681-9000

Phone: (787) 832-4040, ext. 3005
Fax: (787) 834-3673
E-mail: nico.franz at upr.edu
Laboratory website: http://academic.uprm.edu/~franz/
UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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