Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
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 direction.
Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852
/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
Regards,
Nico
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@upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/
Steve,
Earlier in the thread you commented that reasoning about taxonomies wasn't your main goal, but that others might be interested in that facet. I wanted to point out that Dave Thau, who was extensively involved in the development of TCS in his role on the SEEK project, did a lot of work on reasoning over biological taxonomies in his dissertation work. He published a number of very useful papers on these experiments in taxonomic reasoning, which are available here: http://wwwcsif.cs.ucdavis.edu/~thau/ -- I find the Ecological Informatics article one of the more approachable of the set, but they all say a lot about the power and pitfalls of reasoning over taxonomies.
Nice work on DSW, and thanks for the effort you've been investing here.
Matt
On Wed, May 4, 2011 at 7:49 AM, Nico Franz nico.franz@upr.edu wrote:
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 thereis 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 direction.
Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852
*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
Regards,
Nico
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@upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
participants (2)
-
Matt Jones -
Nico Franz