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I have quoted below part of an email which has been sitting in my inbox
for a month. It been stuck there because there was a statement in it
that (in my mind) needed clarification. In John Deck's email, he says
"...since an Occurrence represents an organism at a place and
time...". What I am wondering is whether there is actually a consensus
that an Organism represents an organism at a place and time.<br>
<br>
Caveat: I use "individual organism" here in a general way that probably
includes more than individual organisms. But that is a different
issue, so let's not rehash that in this thread.<br>
<br>
The history of the discussion of the meaning of Occurrence is
extensive. You can find my attempt to summarize it at:
<a class="moz-txt-link-freetext" href="http://code.google.com/p/darwin-sw/wiki/ClassOccurrence">http://code.google.com/p/darwin-sw/wiki/ClassOccurrence</a> so I won't
repeat that here. In a nutshell, it seems to me that people have used
dwc:Occurrence in three general ways:<br>
<br>
- to indicate that we know from aggregate records that a taxon occurs
or ever occurred, in a particular geographic area (the "checklist"
meaning of Occurrence)<br>
- as a broad term that includes both preserved specimens and
observations (the "superclass" meaning of Occurrence)<br>
- as a join between Events and individual organisms [database
description]/as a node connecting Event instances to instances of
individual organisms [RDF description]/as a tuple of (individual
organism,Event) with properties to connect it to the individual
organism and Event [computer science description] (the "node" meaning
of Occurrence). <br>
<br>
It has been noted that the "checklist" meaning of Occurrence is related
to Occurrence as a primary unit of data gathering ("superclass" and
"node" meanings; see history reference for details) but the "checklist"
meaning is probably the least likely to be considered a consensus view,
so I'm going to ignore it for the moment. The "node" meaning of
occurrence corresponds to what is described by John Deck (quoting
Markus Döring) in his email below. It is also the view taken by
Darwin-SW and is reflected in Rich Pyle's emails (related since
Darwin-SW was influenced by Rich Pyle's emails!). However, although it
isn't explicitly stated as such, the Darwin Core standard as it
currently stands really reflects the "superclass" meaning. I was
involved in a conversation with John Wieczorek a few months ago which
was on the topic of "fixing" dwc:Occurrence (i.e. getting rid of the
ambiguity surrounding it). In that conversation, I confirmed with John
W. that as things stand currently, Darwin Core effectively considers
dwc:Occurrence to be a superclass of PreservedSpecimen and
Observation. So to me it does not seem that there actually is a
consensus about what dwc:Occurrence means. Is an Occurrence the
*thing* that documents the presence of an organism at a place and time
("superclass" meaning), or is the Occurrence an *abstract resource*
connecting organisms to place/time with the thing itself as
documentation for the abstract resource ("node" meaning)?<br>
<br>
In order to "fix" Occurrence by clarifying its meaning, it seems to me
that there are two courses of action:<br>
<br>
1. Declare clearly that Occurrence is a superclass of PreservedSpecimen
and Observation and create a new term for the more abstract "organism
at a place and time".<br>
2. Declare clearly that Occurrence is an organism at a place and time
and that it is NOT a superclass of PreservedSpecimen and Observation. <br>
<br>
The second course of action would be the easiest from the standpoint of
making a change to the standard. However, it might be the worst from
an implementation standpoint because of the thousands (millions?) of
specimen records that are typed as Occurrence. <br>
<br>
If we can clarify these two uses of Occurrence, then the terms
currently listed in DwC under the dwc:Occurrence class could be
separated among the two "kinds" of Occurrence. Terms related to the
recording of the presence of an organism at a time and place
(dwc:recordedBy, dwc:behavior, etc.) would be separated from terms
related to the specimens themselves (dwc:preparations, dwc:disposition,
etc.). This may not seem like a big deal for flat specimen records,
but it would be very helpful from the standpoint of advancing the use
of DwC in RDF to clarify the types of resources that these terms can
serve as properties of. <br>
<br>
I would be interested in hearing some discussion about concrete steps
that could be taken to "fix" Occurrence. The "best" solution would
probably be to create a robust consensus ontology that includes
Occurrence. However, that is not likely to happen on the timescale of
a year or less. Given that this issue has dragged on for at least two
years already, in the interest of moving forward it would be good to
take some kind of decisive action in the near term. <br>
<br>
Steve<br>
<br>
-------- Original Message --------
<table class="moz-email-headers-table" border="0" cellpadding="0"
cellspacing="0">
<tbody>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">Subject: </th>
<td>Re: [tdwg-content] New Darwin Core terms proposed relating to
material samples</td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">Date: </th>
<td>Wed, 29 May 2013 16:00:35 +0200</td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">From: </th>
<td>John Deck <a class="moz-txt-link-rfc2396E" href="mailto:jdeck@berkeley.edu"><jdeck@berkeley.edu></a></td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">To: </th>
<td>Richard Pyle <a class="moz-txt-link-rfc2396E" href="mailto:deepreef@bishopmuseum.org"><deepreef@bishopmuseum.org></a></td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">CC: </th>
<td>Markus Döring <a class="moz-txt-link-rfc2396E" href="mailto:m.doering@mac.com"><m.doering@mac.com></a>, Steve Baskauf
<a class="moz-txt-link-rfc2396E" href="mailto:steve.baskauf@vanderbilt.edu"><steve.baskauf@vanderbilt.edu></a>, TDWG Content Mailing List
<a class="moz-txt-link-rfc2396E" href="mailto:tdwg-content@lists.tdwg.org"><tdwg-content@lists.tdwg.org></a>, Robert Whitton
<a class="moz-txt-link-rfc2396E" href="mailto:whittonr@gmail.com"><whittonr@gmail.com></a>, "Ramona Walls" <a class="moz-txt-link-rfc2396E" href="mailto:rlwalls2008@gmail.com"><rlwalls2008@gmail.com></a></td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">References: </th>
<td><br>
</td>
</tr>
</tbody>
</table>
<br>
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content="text/html; charset=Windows-1252">
<div dir="ltr"><span
id="docs-internal-guid-3724c683-f092-4b6d-9cdc-ec765aac9a3c">
<p style="line-height: 1.15; margin-top: 0pt; margin-bottom: 0pt;"><span
style="font-size: 15px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; vertical-align: baseline;">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></p>
<p style="line-height: 1.15; margin-top: 0pt; margin-bottom: 0pt;"><span
style="font-size: 15px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; vertical-align: baseline;"><br>
</span></p>
<p style="line-height: 1.15; margin-top: 0pt; margin-bottom: 0pt;"><span
style="font-size: 15px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; vertical-align: baseline;">John
Deck for Rob Guralnick, Ramona Walls, and John Wieczorek</span></p>
<br>
...<br>
<br>
<span
style="font-size: 15px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; vertical-align: baseline;"></span>
<p dir="ltr"
style="line-height: 1.15; margin-top: 0pt; margin-bottom: 0pt;"><span
style="font-size: 15px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; vertical-align: baseline;">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</span><br clear="all">
</p>
</span></div>
<div class="gmail_extra">
<div>...<br>
<br>
</div>
</div>
<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>
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