Hi Steve,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.
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?
Aaaaaaaaaaaaaah! Please Nico C., don't take this one up!Assuming that there was only one individual organism identified there is really one one species (or hybrid).
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?
Which of these is of primary importance to decision makers and non-taxonomist biologists?
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 direction.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.
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