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I'm going to go ahead and leave this subject line since its a
convenient way to group related emails. However, this email really
isn't about the material sample proposal (which I support given that
dwctype:MaterialSample seems to me to be well-enough defined and to
have a clear use). <br>
<br>
I wanted to comment on what Rich said about "a robust ontology" and
modeling in our data domain. I feel like the discussion here has
demonstrated that there are a number of groups in our constituency who
have an interest in modeling complex datasets that involve relating
multiple observations/sampling incidents and keeping track of the
relationships among sets of derived objects. So developing a consensus
model is really important if we hope to integrate such datasets and
facilitate "asking questions of the data" which probably will in many
cases mean having the ability to construct queries that will "work"
across these diverse datasets. <br>
<br>
What I have an issue with is equating the development of a consensus
data model with the development of a robust ontology. In a previous
email, Rich hoped that DSW might be harmonized with BCO. I really am
not sure that is possible and is perhaps not even desirable. DSW and
BCO are in my mind apples and oranges. <br>
<br>
Although we've called DSW an "ontology" because it's written in OWL and
uses some of the constraints present in OWL to restrict how the DSW
terms can be used, it really is fundamentally a data model, not an
ontology. The basis of DSW (outlined at
<a class="moz-txt-link-freetext" href="http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels">http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels</a> )
was pretty much laid out in Rich's email
<a class="moz-txt-link-freetext" href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html</a>
based on the ASC model as modified by the discussion of "individual" in
the 2010 discussion. The DSW model says that one to many Events can
happen at one Location, one to many Occurrences can be documented
during one Event, one Individual can be recorded in one to many
Occurrences, etc. The DSW model does NOT define (ontologically) what a
Location, Event, Occurrence, or Individual is (other than in the
documentary text) or how they are related to each other ontologically
(except to say that the class instances can be connected through DSW
object properties, e.g. <dsw:IndividualOrganism instance>
dsw:hasOccurrence <dwc:Occurrence instance>. DSW is designed to
describe (and to some extent restrict) how its users should organize
their data to allow them to aggregate their data with other DSW users
and to allow queries to be constructed that will produce consistent
results across providers.<br>
<br>
In contrast, BCO (browse at
<a class="moz-txt-link-freetext" href="http://bioportal.bioontology.org/ontologies/49826?p=terms">http://bioportal.bioontology.org/ontologies/49826?p=terms</a> ) uses
rdfs:subClassOf, owl:someValuesFrom, and other properties to define how
its classes are related to each other and to restrict what kinds of
resources are allowed to fall within their defined classes. This makes
it very useful for clearly defining what classes are in an ontological
sense, but it's not a particularly efficient way of organizing class
relationships in a database. For example, if you wanted to explain how
an identification process was related to an organism, you could say
that an identification process is a subclass of a process, which is a
subclass of an occurrent, which is a subclass of an entity, which has
the subclass continuent, which has the subclass independent continuent,
which has the subclass material entity, which has the subclass object,
which has the subclass organism or virus or viroid. If you wanted to
do some kind of logical reasoning about organisms or identification
processes, this would be great, but if you wanted to relate an
Identification instance with an IndividualOrganism instance in a
database, you would be better off just using
<dws:IndividualOrganism> dsw:hasIdentification
<dwc:Identification> than stringing a connection between the two
class instances using the eight or so subClassOf relationships that
connect <identification process> instances with <organism or
virus or viroid> instances. The latter would not be "de-normalize
until it works".<br>
<br>
I think we clearly need a mechanism for defining and clarifying the
relationships among material samples, organisms, specimens, material
entities, populations, etc. and BCO or something like it is probably
the best way to do that clearly. But I don't think that the resulting
ontology is going to be a data model like DSW or ASC. I think a
consensus ontology and a consensus data model would both be very
useful, but I don't think they will or should be expected to be one and
the same thing.<br>
<br>
Steve<br>
<br>
Richard Pyle wrote:
<blockquote cite="mid:004401ce5db6$ba3f8880$2ebe9980$@bishopmuseum.org"
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Thanks
Ramona;<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Actually,
the basic elements of our data mode precede DwC by quite a bit. What
we’ve tried to do, however, is mold the data model to be more
compatible with DwC, to make the task of mapping for data export &
exchange that much easier. Of course, DwC is not (and is not intend to
be) a data model in any sense of the word; however, it’s impossible to
avoid representing core elements of a bona-fide data model within DwC.
This is especially true when it comes to each of the “ID” terms (and
doubly-especially true when the “ID” terms correlate to class terms).
The existence of an “ID” term implies that some class of object exists
to which an “ID” value is applied. The “ID” value itself is never
useful data/metadata – it is just a way to reference a data record that
(presumably) contains properties that can be expressed as data/metadata
for the object represented by the “ID” value.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">This
was all well-understood when the original DwC was being drafted; but as
it evolved into its current iteration (with the addition of all the
“ID” terms), it has been drawn ever more (in some ways subtly, and in
some ways not-so-subtly) in the direction of a data model.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Of
course, what we all (desperately!) need is a robust ontology that fits
our world. The task is not easy in part because our data domain is not
so easily modeled, in part because different sections of our broader
community have different priorities, and in part because there is
always a delicate balance between developing a model or ontology that
is practical and useful for the data providers and consumers, with one
that is robust and detailed and flexible, to allow asking questions of
the data that were never even considered at the time the model/ontology
were conceived. The parallel experience in database modeling is
normalization (as Paul Kirk likes to say: “Normalize until it hurts;
then de-normalize until it works”).<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
original DwC was completely flat. The current DwC moved into the
direction of more complex structures by clustering terms into classes
and sprinkling with “ID” terms. It even tip-toed into RDF-space with
dwc:ResourceRelationship. I think that’s definitely an improvement,
but it still must strike a delicate balance between the needs by some
to represent a robust data model, and the needs by others to have a
simple/practical mechanism to exchange biodiversity data in a standard
form. It will never be all things to all people; but at least it is
enough things to enough people that it represents an important “flag
pole” around which our community has (more or less) successfully
rallied.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Hmmmm….
Now I’ve forgotten what my point was. I guess I was just in a ramblin’
mood. Well….sorry about the bandwidth!<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Ramona
Walls [<a class="moz-txt-link-freetext" href="mailto:rlwalls2008@gmail.com">mailto:rlwalls2008@gmail.com</a>] <br>
<b>Sent:</b> Thursday, May 30, 2013 6:05 PM<br>
<b>To:</b> Richard Pyle<br>
<b>Cc:</b> Jason Holmberg; TDWG Content Mailing List; John Deck;
Robert Whitton<br>
<b>Subject:</b> Re: [tdwg-content] New Darwin Core terms proposed
relating to material samples<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Jason,<br>
<br>
Thanks for sharing how you have been using the Darwin Core terms. I am
intrigued by the data structure you have developed. It is quite
interesting how both you and Rich have adapted the DwC to fit your
specific needs. While I am often troubled by the vagueness of DwC, I
guess in some ways it is that vagueness allows it to be used in many
different applications. Of course, I don't think vagueness is necessary
for wide application, or a good thing for data exchange, but it does
seem to be working for a lot of different purposes.<o:p></o:p></p>
</div>
<p class="MsoNormal">Ramona<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Thu, May 30, 2013 at 3:07 PM, Richard Pyle
<<a moz-do-not-send="true" href="mailto:deepreef@bishopmuseum.org"
target="_blank">deepreef@bishopmuseum.org</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Hi
Jason,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Many
thanks for this input. If I understand you correctly, then you are
using “Encounter” as equivalent to what we have been using “Occurrence”
for. That is, by our definition, an “Occurrence” is the instance
representing an intersection between an Event (i.e., where, when, who,
etc.) and what we have been calling an “Individual” (i.e., what); and
the properties we attach to the Occurrence are the “how” bits
(including things like size, etc.).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In
my mind, the essence of an “Individual” is the collective physical
material of the individual. If I see a fish on a reef, its
“Occurrence” on that reef and at that time exists (and is worth
documenting) regardless of whether I took an image of it (what we would
call “Evidence”), or whether I took a tissue sample from it, or whether
I collected and killed the whole damn thing. To me, the “essence” of
the individual – or its occurrence at an event – is unaffected by what
I end up doing to it. By extension, following a hierarchical model of
“individual”, a sub-sample (materialSample) extracted from it is just
another instance of “Individual”. This is why I generally think of
“materialSample” (if it were represented as a class – which it is
currently not propsed for DWC) as a subclass of a broader concept
(e.g., “material”, but what I have naively been referring to as
“Individual”).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">That
part of our model has proven to be very stable and effective for
representing the information as we want it.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Where
it gets complicated is instances of taxonomically heterogeneous objects
treated as a single “individual” – which (in my mind) includes such
things as soil samples.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In
that contect, I see (and agree) with John and others that really it’s a
separate axis of classification from what I have called “Individual”.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I
don’t expect that to make a lot of sense (I barely understand it
myself).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
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<p class="MsoNormal" style=""><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Jason
Holmberg [mailto:<a moz-do-not-send="true"
href="mailto:holmbergius@gmail.com" target="_blank">holmbergius@gmail.com</a>]
<br>
<b>Sent:</b> Thursday, May 30, 2013 11:28 AM<br>
<b>To:</b> Richard Pyle<br>
<b>Cc:</b> Ramona Walls; TDWG Content Mailing List; John Deck; Robert
Whitton</span><o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
<b>Subject:</b> Re: [tdwg-content] New Darwin Core terms proposed
relating to material samples<o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="">Hi everyone.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="">List lurker here. DWC has been a great
inspiration in my work, so I hope I can contribute some small amount of
insight on the "individual" and "material sample" threads. I have no
grand thoughts on the subject, but I can tell you how the DWC has
inspired my own information architecture for open source mark-recapture
software:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""><a moz-do-not-send="true"
href="http://www.ecoceanusa.org/shepherd/doku.php?id=manual:2.0.x:1_overview"
target="_blank">http://www.ecoceanusa.org/shepherd/doku.php?id=manual:2.0.x:1_overview</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="">I felt the very clear need for a
distinct Individual Class and to separate that from the concept of a
sample taken from nature. When reviewing DWC, I interpreted
Occurrence.individualCount to be somewhat contradictory to
Occurrence.individualID, so I created a
one-individual-at-a-point-in-time class called Encounter that reuses
quite a bit of DWC.Occurrence. Occurrence I then broadened to include
the potential for multiple marked individuals.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="">I neither present this as "right" nor
"good" (though they have worked very well for us). I just present it as
a practical example from mark-recapture in which we have tried to
adhere to DWC in order to expose data to GBIF, iOBIS, etc. The concepts
of "material sample" and "individual" are very important to us, and
this is how we have defined them.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="">Cheers,<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="">Jason Holmberg<br>
ECOCEAN Whale Shark Photo-identification Library<br>
<a moz-do-not-send="true" href="http://www.whaleshark.org"
target="_blank">http://www.whaleshark.org</a><br>
<br>
Please consider adopting a shark to support our mission:<br>
<a moz-do-not-send="true"
href="http://www.whaleshark.org/adoptashark.jsp" target="_blank">http://www.whaleshark.org/adoptashark.jsp</a><o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom: 12pt;"> <o:p></o:p></p>
<div>
<p class="MsoNormal" style="">On Wed, May 29, 2013 at 4:13 PM,
Richard Pyle <<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Hi
Ramona,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Yes,
I agree, and thanks. I’ve always felt that there has been a trend
towards trying to push too much “ontology” (or other semantic meaning)
onto DWC terms and classes, when DWC was fundamentally intended to
represent an mechanism for data exchange; not a mechanism to describe
the ontological landscape of biodiversity data. The only reason I
brought this up now (and, I think, why we discussed it in 2010), is
that the term “individualID” in DWC sort of hinted that something like
“Individual” was the “forgotten class” for DWC. I sincerely hope that
BCO and DSW gain more traction (and, ideally, harmony between them)
than earlier attempts at developing ontologies in this space have met –
and clearly that is the right path forward.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">My
main concern for this thread (and the reason I engaged in it), was to:</span><o:p></o:p></p>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">1)</span><span
style="font-size: 7pt; color: rgb(31, 73, 125);"> </span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Find
out the status of the discussions that began in 2010; and</span><o:p></o:p></p>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">2)</span><span
style="font-size: 7pt; color: rgb(31, 73, 125);"> </span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Clarify
where the current materialSample proposal overlaps, or does not
overlap, with that earlier effort.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Steve
has very adequately answered the first question, and you, John, and
others have answered the second, and I’m happy with both sets of
answers.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I’m
sorry for the voluminous exchange, but I felt the discussion was both
important, and very helpful (certainly to me).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0in 0in 0in 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;">
<p class="MsoNormal" style=""><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Ramona
Walls [mailto:<a moz-do-not-send="true"
href="mailto:rlwalls2008@gmail.com" target="_blank">rlwalls2008@gmail.com</a>]
<br>
<b>Sent:</b> Wednesday, May 29, 2013 1:03 PM<br>
<b>To:</b> Richard Pyle<br>
<b>Cc:</b> John Deck; Markus Döring; Steve Baskauf; TDWG Content
Mailing List; Robert Whitton</span><o:p></o:p></p>
<div>
<p class="MsoNormal" style=""><br>
<b>Subject:</b> Re: [tdwg-content] New Darwin Core terms proposed
relating to material samples<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Hi Rich,<br>
<br>
Sorry I didn't mention this sooner, but your emails were also helpful
to me in describing an important and generalizable use case. <br>
<br>
I don't know whether or not the TDWG community is ready to deal with
the level of abstraction we are talking about, but my assessment is
that whether or not they are ready, the Darwin Core is not constructed
to deal with it. That is why (among other reasons) we started work on
the BCO, and perhaps one reason why Steve and others developed DSW. <o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Our goal with the
material sample proposal was not to overhaul DwC, but to work within
the DwC framework to make it more compatible with other standards such
as MIxS. That is why we tried to keep our proposal fairly narrowly
focused.<o:p></o:p></p>
</div>
<p class="MsoNormal" style="">Ramona<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"> <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="">On Wed, May 29, 2013 at 3:21 PM,
Richard Pyle <<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>>
wrote:<o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Thanks,
Ramona – this is an *<b>extremely</b>* helpful email! It helps clear
things up a lot in my mind.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Just
to be clear, what I am looking for is the notion of a defined physical
object (what I think you mean by “material entity”), and I explicitly
mean the material entity itself. Yes, there is information
(properties) that relate to that material entity, but to me that is a
separate issue. What I would like to see clearly defined is the class
representing the material (physical) entity – which seems to me to be a
superclass of what materialSample is intended to represent.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Perhaps
our (TDWG/DWC) community is not yet ready to deal with this level of
abstraction (unfortunately, I absolutely have to, because “Occurrence”
is simply way too overloaded a class for me to use independently of
what I have been calling “individual” and what I have been calling
“Evidence”). In that case, I guess the best thing to do is accept
materialSample as a basisOfRecord for Occurrence and move on. But this
is more or less the same thing that happened the last time we engaged
in this conversation (2 years or so ago), and I was hoping this
conversation about materialSample could leverage progress on the larger
issue.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">As
I’ve said before, the last thing I want to do is confuse or otherwise
slow down the process of incorporating the term “materialSample” into
DWC. It’s just that I saw enough overlap with that “other” issue, that
I was hoping we could find a reasonable pathway forward on both.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Thanks
again for the very helpful comments.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
</div>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0in 0in 0in 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;">
<p class="MsoNormal" style=""><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Ramona
Walls [mailto:<a moz-do-not-send="true"
href="mailto:rlwalls2008@gmail.com" target="_blank">rlwalls2008@gmail.com</a>]
<br>
<b>Sent:</b> Wednesday, May 29, 2013 9:14 AM<br>
<b>To:</b> Richard Pyle<br>
<b>Cc:</b> John Deck; Markus Döring; Steve Baskauf; TDWG Content
Mailing List; Robert Whitton</span><o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style=""><br>
<b>Subject:</b> Re: [tdwg-content] New Darwin Core terms proposed
relating to material samples<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Rich,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="">I now understand more fully what you
are asking for ( a clear definition goes a long way!). A material
sample, as we discussed it at the Kansas and Oxford workshops, does
indeed need to be physically removed from its environment. This is also
the case with the OBI term material sample, which, as a subclass of
OBI:specimen is the output of some collecting process. It is true that
concept of material sample could be defined to include sampling in an
observational sense, but that is not how it is defined at this point.
Based on this, material sample is NOT the term you are looking for or
defined as :<o:p></o:p></p>
</div>
<p><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">"The
category of information pertaining to the physical basis of a sampling,
subsampling, or observational event. In biological collections, the
[SuperclassTerm] is typically a defined group of organisms, a single
whole organism, or a part of a whole organism that is collected or
otherwise documented in nature, and either preserved, destructively
processed, or documented through some form of Evidence (such as images
or reported visual observations)."</span><o:p></o:p></p>
<p> <o:p></o:p></p>
<div>
<p class="MsoNormal" style="">What you have defined is a category of
information (whatever that may be) that pertains to some material
entity. Not the material entity itself, but information about that
entity. The "SuperclassTerm" you refer to in the definition sounds an
awful lot like a material entity from the Basic Formal Ontology, which
is used for defining material sample in OBI and the Bio-collections
Ontology.<o:p></o:p></p>
</div>
<p>Ramona<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"> <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="">On Wed, May 29, 2013 at 11:51 AM,
Richard Pyle <<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>>
wrote:<o:p></o:p></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Many
thanks, John. This is extremely helpful!</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">First
of all, in the context of a distinct term for basisOfRecord, I see
absolutely no problem with adding the term “MaterialSample”. I fully
support your proposal (although if this is simply a basisOfRecord term
to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen,
FossilSpecimen, HumanObservation, MachineObservation; does it need a
defined “ID” term? Do all the others have defined “ID” terms?). </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">However,
I’m excited by this conversation because I think we are very close to
solving a bigger problem (which was the focus of the 2010 discussion on
this list around “IndividualOrganism”).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">This
bigger problem involves the need for a defined “concept” (I’m
hesitating to say “class”), and an associated “ID”, in dwc that refers
to the physical/material basis of an Occurrence. We don’t yet have a
term for this concept in dwc (“IndividualID” hinted at the need for
one, but that term was not well-defined, and the term itself seems to
cause confusion). As Steve Baskauf and I have both been advocating for
the establishment of new class in dwc for exactly this purpose, I just
want to make sure that we’re on the same page about what each concept
is. The more I understand about what you need for “materalSample”, the
more convinced I am that both of our needs can be met with the same
concept.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I
am perfectly happy to adopt the term “MaterialSample”, but I guess it
all boils down to this: In order for something to be a
“MaterialSample”, must it necessarily be removed from nature? </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">If
the answer is “No”, then I think we can merge the two concepts into one.</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">If
the answer is “Yes”, then I think “materialSample” is best
characterized as a subclass of what Steve and I have been pushing for
(setting aside, for the moment, the additional complexity of
taxonomically homogeneous vs. heterogeneous).</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In
the latter case, I would define the superclass (whatever term is used
for it), along the lines of:</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">"The
category of information pertaining to the physical basis of a sampling,
subsampling, or observational event. In biological collections, the
[SuperclassTerm] is typically a defined group of organisms, a single
whole organism, or a part of a whole organism that is collected or
otherwise documented in nature, and either preserved, destructively
processed, or documented through some form of Evidence (such as images
or reported visual observations)."</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Aloha,</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Rich</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0in 0in 0in 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;">
<p class="MsoNormal" style=""><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> <a
moz-do-not-send="true" href="mailto:jdeck88@gmail.com" target="_blank">jdeck88@gmail.com</a>
[mailto:<a moz-do-not-send="true" href="mailto:jdeck88@gmail.com"
target="_blank">jdeck88@gmail.com</a>] <b>On Behalf Of </b>John Deck<br>
<b>Sent:</b> Wednesday, May 29, 2013 4:01 AM<br>
<b>To:</b> Richard Pyle<br>
<b>Cc:</b> Markus Döring; Steve Baskauf; TDWG Content Mailing List;
Robert Whitton; Ramona Walls</span><o:p></o:p></p>
<div>
<p class="MsoNormal" style=""><br>
<b>Subject:</b> Re: [tdwg-content] New Darwin Core terms proposed
relating to material samples<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<div>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">Since
the original proposal was from a group of folks, we decided to put our
heads together to construct a general response to the various issues
and ideas expressed on this thread. </span><o:p></o:p></p>
<div>
<div>
<p style="margin: 0in 0in 0.0001pt;"> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">John
Deck for Rob Guralnick, Ramona Walls, and John Wieczorek</span><o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">In the
text of the issue submitted for MaterialSample (</span><a
moz-do-not-send="true"
href="https://code.google.com/p/darwincore/issues/detail?id=167"
target="_blank"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">https://code.google.com/p/darwincore/issues/detail?id=167</span></a><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">) we
noted cases where the current basisOfRecord terms pertaining to the
Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen,
FossilSpecimen, HumanObservation, MachineObservation) do not adequately
cover certain cases, including: environmental sample (for metagenomic
analysis), transcriptomes (measuring genes but not taxa), and
destructive samples (e.g. tissues destructively sampled in order to
generate genomic DNA). The term we borrowed from OBI (<a
moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/OBI_0000747" target="_blank">http://purl.obolibrary.org/obo/OBI_0000747</a>)
is broad enough to be utilized across various cases that fulfill our
criteria while still maintaining a consistent, clear and human
understandable meaning. For our purposes, we can think of “Material
Sample” as any type of matter that we can use in order derive further
evidence needed for identifications, and taxa, whether it is
taxonomically homogenous, heterogenous,<span
style="background: white none repeat scroll 0%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
a single individual, </span>sets of individuals, or populations. </span><o:p></o:p></p>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">How is
MaterialSample different from Individual? The intent of individualID
is fairly clear: since an Occurrence represents an organism at a place
and time (per Markus’ email), the individualID term allows us to assign
an instance identifier for a particular organism that can be present in
multiple events. MaterialSampleID, on the other hand, is intended to
allow users to say that the basis of an occurence is a material entity
(i.e. matter) that has been sampled according to some particular
method. Whether or not this material entity is an individual (sensu
individualID in DwC) is an independent axis of classification. As was
already pointed out, there is no restriction on specifying that an
occurence is associated with more than one type, so any occurrence can
have both an individualID and a materialSampleID.</span><o:p></o:p></p>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">We
maintain our position on the proposal for MaterialSample as a value for
the basisOfRecord, with an associated materialSampleID to identify
instances of them. Per Steve’s initial comments, we have already
withdrawn the proposal for a MaterialSample class distinct from that in
the Darwin Core type vocabulary, which should make it easier to
evaluate the implications of what we’re discussing. </span><o:p></o:p></p>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">********************</span><o:p></o:p></p>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<p style="margin: 0in 0in 0.0001pt;"><span
style="font-size: 11.5pt; font-family: "Arial","sans-serif";">NOTES,
MaterialSample from OBI:</span><o:p></o:p></p>
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<span style="font-size: 11.5pt; font-family: "Arial","sans-serif";">OBI
has fairly broad definitions of samples & specimens that are meant
to be utilized across many different scientific activities. Material
Sample is defined as a “<i>material entity that has the material sample
role</i>”, while a material sample role is defined as “ <i>a specimen
role borne by a material entity that is the output of a material
sampling process</i>”, and a material sampling process is “<i>a
specimen gathering process with the objective to obtain a specimen that
is representative of the input material entity</i>”. </span><o:p></o:p></p>
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<p class="MsoNormal" style="">On Mon, May 27, 2013 at 11:59 PM,
Richard Pyle <<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>>
wrote:<o:p></o:p></p>
<p class="MsoNormal" style="">Hi Markus,<br>
<br>
Great question! Particularly because this is exactly the sort of use
case<br>
we designed our model around.<o:p></o:p></p>
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> if you take a tissue sample of the same tree every year, would the<br>
identifier<br>
> in individualID be the same for all of them or be different? WIth
the<br>
current<br>
> dwc:individualID definition it would be the same for all samples.
If I<br>
> understand you correct each sample would have its own "individual"<br>
> identifier in your proposal? It can't see how you can collapse
these two<br>
things<br>
> into one definition.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom: 12pt;">No, that is not how
we would handle it.<br>
<br>
In our model, there would be one IndividualID to represent the tree,<br>
spanning the time period beginning (more or less) when the seed was<br>
germinated, until the time at which the entire physical structure of the<br>
tree was disintegrated. It is an individual tree.<br>
<br>
There would be multiple Occurrence instances, for each time that someone<br>
observed or sampled or otherwise wished to document some condition of
that<br>
tree. All of these Occurrence instances would refer to the same
individualID<br>
value (i.e., the "tree"). In the example above, this means there would
be a<br>
different Occurrence instance for each year that a sample is taken --<br>
because in each case, an assertion that the full tree existed at a
certain<br>
time and place can be made (I understand that trees tend not to move
around<br>
very much, so the Location for each event associated with each
Occurrence<br>
would, in this case, remain the same; but the other Event properties --
such<br>
as eventID, samplingProtocol, samplingEffort, eventDate, eventTime,<br>
startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate,
habitat,<br>
fieldNumber, fieldNotes, eventRemarks -- would be documented
accordingly for<br>
each sampling Occurrence instance).<br>
<br>
Suppose that the tree is visited every month, but only sampled once per<br>
year. In that case, there would be an Occurrence record for every
monthly<br>
visit. In other words, an Occurrence instance exists regardless of
whether<br>
a physical sample was made or not. Any in-situ images made of the tree<br>
would likewise be associated with the specific Occurrence instance, and
each<br>
image would represent a separate instance of "Evidence".<br>
<br>
Now, let's focus on the annual samplings. Every time a new sample is
taken<br>
from the tree, at least one new instance of Individual (with a unique<br>
individualID value) is created to represent the sample. This sample<br>
(individual instance) may be a "gathering" (set of multiple individual<br>
specimens gathered at the same time), or it may be a single specimen,
or it<br>
may be simply a tissue sample intended for destructive analysis. In any<br>
case, it's a new individual instance derived from the "parent"
individual<br>
instance representing the whole tree. In our implementation,
"Individual"<br>
can be hierarchical, such that a whole-organism tree can be sub-sampled
with<br>
many "child" instances of "gatherings" (say, one gathering each year),
and<br>
each gathering may have multiple child "specimen" individuals (e.g.<br>
individual botanical sheets created from the multiple items of a single<br>
gathering), and each specimen may have further "child" subsamples
extracted<br>
for DNA analysis (or whatever), and the hierarchy can continue on down
to<br>
whatever derivatives that people feel a need to keep track of (e.g.,<br>
aliquot).<br>
<br>
The point is, all Individual instances are well-defined physical
objects (or<br>
well-defined sets of physical objects), and they can be arranged in a<br>
n-tiered hierarchy.<br>
<br>
Moreover, each Individual that can be characterized as a "sample" (what
we<br>
refer to as a "CollectionObject") may also have a property value for<br>
"CollectionOccurrenceID" -- which refers to the specific Occurrence
instance<br>
at which the sample was obtained.<br>
<br>
So, for example, if the tree is visited on May 27, 2013 and a specimen<br>
(sample) is taken, then:<br>
1) An Event instance is generated to represent the event where the tree
was<br>
visited;<br>
2) An Occurrence instance is generated, which refers to the new
EventID, and<br>
the existing IndividualID for the whole tree, and includes whatever
other<br>
Occurrence properties are relevant for the tree at the time of this<br>
Occurrence<br>
3) An Individual instance is generated for the specimen, which has a<br>
property value for parentIndividualID that refers to the individualID
for<br>
the whole tree, and a property value for collectionOccurrenceID that
refers<br>
the Occurrence instance where the specimen was collected.<br>
<br>
So, to summarize the answer to your question:<br>
- There are multiple Occurrence instances that refer to the same
Individual<br>
instance representing the whole tree (and, hence can be collapsed to the<br>
same IndividualID value).<br>
- Any Individual can have derivatives that are themselves unique
Individual<br>
instances.<br>
- Individuals are arranged hierarchically, and certain properties can be<br>
inherited up or down the hierarchy, depending on the properties and
their<br>
associated logical constraints.<br>
<br>
At some point, I will assemble a set of other specific use cases, and
how we<br>
manage them through our use of the "Individual" instance (although I
will<br>
probably not use the word "Individual", as this seems to cause too much<br>
confusion in these discussions).<br>
<br>
Aloha,<br>
Rich<o:p></o:p></p>
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<p class="MsoNormal" style="">-- <br>
John Deck<br>
<a moz-do-not-send="true" href="tel:%28541%29%20321-0689"
target="_blank">(541) 321-0689</a><o:p></o:p></p>
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<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
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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>
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