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Rich,<br>
Thanks for clarifying that "individual" as you are using the term
corresponds to dsw:IndividualOrganism rather than THeE. I didn't read
carefully enough. With regards to the term "Individual", as you note,
its origin is from the term dwc:individualID. The original DwC term
addition proposal was to create the term dwc:Individual to follow the
pattern of the other ID terms in DwC. When Cam and I were writing DSW
in Web Ontology Language (OWL), we realized that "individual" had a
particular meaning in OWL: it effectively means "instance". So that
made creating a class called dsw:Individual particularly confusing.
For that reason, Cam suggested dsw:IndividualOrganism to indicate that
we were talking about individuals sensu organisms rather than
individuals sensu OWL. As you know, we never intended for it to apply
only to individual organisms. <br>
<br>
I think that pretty much everybody agrees that "individual" is a
confusing term name for a number of reasons. If at some point there is
a DwC term which corresponds to what we are talking about
(TaxonomicallyHomogeneousEntity, THoE, or whatever), the solution may
be to deprecate dwc:individualID and change it to
dwc:taxonomicallyHomogeneousEntityID or whatever corresponds to the new
class name with "ID" tacked on the end. For convenience, in this email
I'll refer to "Individual" with the understanding that it's not a good
name.<br>
<br>
Although there is potentially significant overlap between the proposed
dwc:MaterialSample class and Individual, I think that there are at
least two ways that they differ significantly. One is that I'm pretty
sure that there is no requirement that a dwc:MaterialSample must be a
biological material (i.e. derived from a living thing). I think that
it's pretty clear from what Rich has said that Individual (to include
the range from tissue samples up to herds) must consist of biological
materials. The other is that a material sample must be physically
sampled (i.e. removed from the environment and subjected to some kind
of processing). An important feature of an Individual (at least to
me!) is that it can be observed, photographed, or recorded without
necessarily having all or part of it being removed from its environment
and subjected to processing. My reading of the definition of
dwc:individualID (<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/index.htm#individualID">http://rs.tdwg.org/dwc/terms/index.htm#individualID</a> )
is that the "individual or named group of individual organisms" (e.g.
"Orca J 23") might be observed repeatedly without physical sampling.
The definition of dwc:individualID says "resampling", but I think
"sampling" there was being used more broadly than just "physically
removing part or all of the organism". I've been thinking about
whether it is a problem for DwC type vocabulary terms to overlap.
There is nothing in the current definitions of the type vocabulary
terms that require its classes to be disjoint. I think it is possible
that something could be both a dwctype:PreservedSpecimen and a
dwctype:FossilSpecimen, and if dwctype:MaterialSample is accepted as a
term there would undoubtedly be things that were both
dwctype:PreservedSpecimen and dwctype:MaterialSample. So I don't think
it is necessarily a problem if there is overlap between
dwctype:MaterialSample and an Individual class. Certainly RDF allows a
resource to have two (or more) rdf:type declarations.<br>
<br>
With regards to Ramona's objection "Making one root class to cover lots
of different types of entities is poor ontological practice", I would
just note that Darwin Core is "glossary of terms ... intended to
facilitate the sharing of information about biological diversity"
(<a class="moz-txt-link-freetext" href="http://www.tdwg.org/standards/450/">http://www.tdwg.org/standards/450/</a> ) and that the mission of TDWG in
general is to "Develop, adopt and promote standards and guidelines for
the recording and exchange of data about organisms"
(<a class="moz-txt-link-freetext" href="http://www.tdwg.org/about-tdwg/">http://www.tdwg.org/about-tdwg/</a> ) and not ontology building per se.
So in the context of TDWG and Darwin Core, the primary criterion for
judging a proposed term is whether it effectively facilitates the
sharing and exchange of information about biological diversity, and not
whether it fits well into an ontology. Don't get me wrong - I'm fully
in support of ontology-building as a means to clarify the relationships
among entities of interest to TDWG. What I'm saying is that there will
probably be terms in DwC that have a utilitarian purpose in promoting
data exchange that will never be part of an ontology. It is possible
(perhaps likely) that Individual will be such a term. It was once
described as "more of a database join than a real thing" (or something
like that) which is perhaps an overstatement because it does correspond
roughly to a certain set of real things. But I think its purpose is
really more for linking sets of resources that have shared properties
and shared connections to identifications, observations, etc.<br>
<br>
Steve<br>
<br>
Richard Pyle wrote:
<blockquote cite="mid:007701ce5aa2$33933410$9ab99c30$@bishopmuseum.org"
type="cite">
<pre wrap="">Hi Ramona,
I apologize for the long emails, but this stuff is complex and unfortunately
requires lots of words (to avoid - or at least minimize - misunderstanding).
I will try to keep my responses to your points short.
</pre>
<blockquote type="cite">
<pre wrap="">Using the word "individual" to describe collections of organisms -
whether they are taxonomically homogenous or heterogeneous - makes no
</pre>
</blockquote>
<pre wrap=""><!---->sense.
</pre>
<blockquote type="cite">
<pre wrap="">Yes, I know it is just a label, but seriously, just make a better label.
</pre>
</blockquote>
<pre wrap=""><!---->
Yes, I agree. But it's what we already have in DWC
(<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/index.htm#individualID">http://rs.tdwg.org/dwc/terms/index.htm#individualID</a>) I have no problem
using a different term, but before we choose terms, we should first define
what the concepts are.
</pre>
<blockquote type="cite">
<pre wrap="">A single organism and a collection of organisms are fundamentally
</pre>
</blockquote>
<pre wrap=""><!---->different things.
Actually, not really different things. Many natural history collections
maintain their specimens as "lots", which may have a single individual
specimen, or multiple specimens. Regardless of whether it's a single
specimen or multiple specimens, the basic properties are the same (same
collecting event, sme taxonomic identification, and many other identical
properties). This becomes especially true for colonial organisms (like
corals, where the "individual" could be interpreted as a single polyp). It's
also true for other use cases we deal with that are outside the DWC/TDWG
scope.
</pre>
<blockquote type="cite">
<pre wrap="">If you need a class that can cover both of them under certain
</pre>
</blockquote>
<pre wrap=""><!---->circumstances,
</pre>
<blockquote type="cite">
<pre wrap="">you need to use a logical definition to define the circumstances (just
</pre>
</blockquote>
<pre wrap=""><!---->like the
</pre>
<blockquote type="cite">
<pre wrap="">class material sample does by using the criterion of having a material
</pre>
</blockquote>
<pre wrap=""><!---->sample role).
</pre>
<blockquote type="cite">
<pre wrap="">In order to do this, you also need to have separate classes for individual
</pre>
</blockquote>
<pre wrap=""><!---->organism
</pre>
<blockquote type="cite">
<pre wrap="">and collection of organisms.
</pre>
</blockquote>
<pre wrap=""><!---->
We have tried to do this by distinguishing instances as "Lot" or "Whole
Organism" -- which could be thought of as distinct subclasses (though again,
they generally share the same properties). The same is true for tissue
samples, and other "parts".
</pre>
<blockquote type="cite">
<pre wrap="">I agree whole-heartedly with the need to clearly track stakeholders needs
for different classes of things, using a logical system to decide how
</pre>
</blockquote>
<pre wrap=""><!---->these
</pre>
<blockquote type="cite">
<pre wrap="">things relate to one another, examining alternative systems for creating
the classes of things, and testing them against use cases (Steve's points
</pre>
</blockquote>
<pre wrap=""><!---->1-4).
</pre>
<blockquote type="cite">
<pre wrap="">This is precisely what we are trying to do with the bio-collections
</pre>
</blockquote>
<pre wrap=""><!---->ontology
</pre>
<blockquote type="cite">
<pre wrap="">(BCO). The suggestion to use the term material sample came out of just
such a process. It is important to remember that the stakeholders include
more than just the community using DwC.
</pre>
</blockquote>
<pre wrap=""><!---->
It seems we are all in full agreement on these points. In my case, I am
especially in agreement with the last point, as much of our thinking has
been independent of the TDWG/DWC thinking, but still keeping that set of
use-cases in mind.
Aloha,
Rich
.
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 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) 322-4942
If you fax, please phone or email so that I will know to look for it.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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