Steve,<div><br></div><div>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: <a href="http://wwwcsif.cs.ucdavis.edu/~thau/">http://wwwcsif.cs.ucdavis.edu/~thau/</a> -- 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.</div>
<div><br></div><div>Nice work on DSW, and thanks for the effort you've been investing here.</div><div><br></div><div>Matt<br><br><div class="gmail_quote">On Wed, May 4, 2011 at 7:49 AM, Nico Franz <span dir="ltr"><<a href="mailto:nico.franz@upr.edu">nico.franz@upr.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">
Hello all: I have a few inserted comments, hopefully with some
clarifying effect:<div class="im"><br>
<br>
On 5/4/2011 10:54 AM, Peter DeVries wrote:
<blockquote type="cite"><font face="arial, helvetica,
sans-serif">Hi Steve,</font>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">I may have overloaded the term specimen to make
the explanation easier to follow.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">A specimen could be an individual or it could be
part of an individual.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">To some extent you need to think about how these
models will be used.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">If you subscribe to the model that a species is
whatever a taxonomists says it is then it is difficult to make
statements like.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">X% of the world's species will be extinct by 2050.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">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.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">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.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Are we modeling species or variations in human
conceptualizations of species?</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div>
<div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div bgcolor="#ffffff" text="#000000">
<div>
<blockquote type="cite">
<div><font face="arial,
helvetica, sans-serif">Assuming that there was
only one individual organism identified there is
really one one species (or hybrid).</font></div>
</blockquote>
</div>
<font face="arial, helvetica,
sans-serif">Aaaaaaaaaaaaaah! Please Nico C., don't
take this one up!</font></div>
<div><font face="arial,
helvetica, sans-serif"><br>
</font></div>
</blockquote>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">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.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Again, Are we modeling species or variations
in human conceptualizations of species?</font></div>
</div>
</div>
</div>
</blockquote></div>
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 (<a href="http://www.emplantbase.org/home.html" target="_blank">http://www.emplantbase.org/home.html</a>)
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.<div class="im"><br>
<br>
<blockquote type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Which of these is of primary importance to
decision makers and non-taxonomist biologists? <br>
</font></div>
</div>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font face="arial, helvetica,
sans-serif">Part of the problem with various
publications relating to ontologies and taxonomy is that
their species models entail a specific phylogenetic
hypothesis.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">In the real world taxa are not as clean as
some would like to make them out to be. </font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Each individual is a unique combination of
thousands of separate gene lineages which often do not
follow clean monophyletic paths.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">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.</font></div>
</div>
</div>
</div>
</blockquote></div>
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.<br>
<br>
Some of this also on p. 47 of this PDF: <a href="https://journals.ku.edu/index.php/jbi/article/view/3927/3852" target="_blank">https://journals.ku.edu/index.php/jbi/article/view/3927/3852</a><div class="im"><br>
<br>
<blockquote type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif"><i>Aedes triseriatus</i> owl:sameAs <i>Ochlerotatus
triseriatus</i> </font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Others seem to see them as phylogenetic end
nodes which entail a specific phylogenetic history. </font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div>
<font face="arial, helvetica,
sans-serif"><i>Aedes triseriatus</i> distinctFrom <i>Ochlerotatus
triseriatus</i></font></div>
<div><font face="arial, helvetica,
sans-serif"><i><br>
</i></font></div>
<div><font face="arial, helvetica,
sans-serif">If you are primarily interested in
understanding issues of ecology, disease, diversity and
conservation the former model is more appropriate than
the later.</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">Respectfully,</font></div>
<div><font face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font face="arial, helvetica,
sans-serif">- Pete</font></div>
</div>
</div>
</div>
</blockquote>
<br></div>
Regards,<br>
<br>
Nico<br>
<br>
<br>
Nico M. Franz, Ph.D. <br>
Assistant Professor <br>
Director, UPRM Invertebrate Collection <br>
Department of Biology <br>
University of Puerto Rico <br>
Call Box 9000 <br>
Mayagüez, PR 00681-9000 <br>
<br>
Phone: <a href="tel:%28787%29%20832-4040" value="+17878324040" target="_blank">(787) 832-4040</a>, ext. 3005 <br>
Fax: <a href="tel:%28787%29%20834-3673" value="+17878343673" target="_blank">(787) 834-3673</a> <br>
E-mail: <a href="mailto:nico.franz@upr.edu" target="_blank">nico.franz@upr.edu</a> <br>
Laboratory website: <a href="http://academic.uprm.edu/%7Efranz/" target="_blank">http://academic.uprm.edu/~franz/</a>
<br>
UPRM-INVCOL: <a href="http://uprm-invcol-project.tumblr.com/" target="_blank">http://uprm-invcol-project.tumblr.com/</a>
<br>
<br>
</div>
<br>_______________________________________________<br>
tdwg-content mailing list<br>
<a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
<a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
<br></blockquote></div><br></div>