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As I was stuck in traffic this morning I was thinking about my response
to Bob's comments. In retrospect, I should have simply said that
indicating that specimens are duplicates by assigning their
dwc:individualID property to the same URI is really not just one
option, but rather that it is the semantically correct thing to do. <br>
<br>
Assume that we are assembling a database of RDF triples about taxonomic
names and their authors. We discover URI#1 whose metadata asserts that
a foaf:Person has the rdfs:label "L.". If we know of URI#2 whose
metadata asserts that a foaf:Person has the rdfs:label "Carl Linnaeus",
it would be correct to assert that URI#2 is owl:sameAs URI#1. Anyone
who was aware of this assertion through knowledge of our database and
who trusted the veracity of the assertion would then know that both
URIs referred to the same person because the labels "L." and "Carl
Linnaeus" actually refer to the same person. <br>
<br>
In contrast, assume we are assembling a database about specimens at
various institutions. We discover URI#3 for a dwc:Occurrence of
dwc:basisOfRecord="PreservedSpecimen". We realize by some means that
this specimen is a "duplicate" of a dwc:Occurrence of
dwc:basisOfRecord="PreservedSpecimen" having URI#4 and located in
another institution. Despite the colloquial use of the word
"duplicate", it would not be correct to assert that URI#4 is owl:sameAs
URI#3 because the resources represented by those two URIs are NOT the
same thing. They are different pieces of dead tissue in different jars
or pasted to different pieces of paper. If we think of what curators
mean by "duplicate" it has exactly the meaning that both duplicates
were collected from either the same individual organism (in the case of
a large organism like a tree) or from the same small population of
organisms (all members of the same species) such as a clump of grass,
ants in the same colony, etc. Given the definition of dwc:individualID
as referring to a "an individual or named group of individual
organisms", assigning the two Occurrences the same value for their
dwc:individualID property semantically describes "duplicates" exactly.
Curators might not like this way of describing "duplicates" because
it's not the way they are used to talking about them, but in the Linked
Data world it is our job to correctly describe relationships using
existing predicates. We don't make up a new term if there is already
one available that will do the job.<br>
<br>
This relationship may seem more apparent if one considers an example
that involves dwc:Occurrences of a different type. I enjoyed looking
at <a class="moz-txt-link-freetext" href="http://www.whaleshark.org/">http://www.whaleshark.org/</a> yesterday. In this library, users report
dwc:Occurrences of the proposed type
dwc:basisOfRecord="DigitalStillImage". The database assigns
identifiers (not URIs but they could be someday) to individual whale
sharks and associates the dwc:Occurrences with the Individuals (i.e.
the equivalent of providing a value for dwc:individualID for the
dwc:Occurrence). By using pattern recognition software, the project
matches spot patterns and with luck can reach the conclusion that an
Individual represented in a particular dwc:Occurrence is the same as
the Individual documented by another dwc:Occurrence. It is abundantly
clear in this circumstance that the correct thing to do is to assert
that the Individual represented in the first dwc:Occurrence is
owl:sameAs the the Individual represented in the second dwc:Occurrence
if the Individuals had previously been assigned different identifiers,
or just to assign the second dwc:Occurrence the same value for
dwc:individualID as the first dwc:Occurrence if a second identifier
hadn't already been assigned to the Individual. <br>
<br>
The point here is that from a semantic point of view, there is no
difference in what is being done in the case of linking duplicate
specimens in different herbaria and in linking images that were taken
of the same whale shark. In both cases, two dwc:Occurrences are
related in a certain way because they have the same value for
dwc:individualID. Multiple observations/mark recapture might be used
to establish where individuals move or how they behave, recognition of
duplicate specimens might be used to update identifications, track
relationships among herbaria, or anything we want. We do not have to
imply some particular fitness of use when we assert that relationship
and we should not invent terms for a particular fitness of use when we
have generic terms that already describe the relationship. <br>
<br>
Thus I say that it is wrong to invent some other term to represent a
relationship that can be clearly and unambiguously expressed using
existing terms. One of the beauties of the Darwin Core standard is
that it simplifies the vocabulary needed to express equivalent
relationships by having a generic class (dwc:Occurrence) that can
represent kinds of things that are distinguished by typing them with
values for dwc:basisOfRecord such as PreservedSpecimen,
HumanObservation, or DigitalStillImage. So lets not move backwards by
proposing to invent some new terms that will only apply to herbarium
specimens.<br>
<br>
Steve<br>
<br>
Bob Morris wrote:
<blockquote
cite="mid:AANLkTim5RE9wdhn_+stkJbv=tP1TEsoC1Ec65mU0Y0iv@mail.gmail.com"
type="cite">
<pre wrap="">Good idea, but it suffers from the same fate as might
associatedOccurrences (not previously mentioned because I was after
some clarification in principle, with the herbarium duplicate sheets
only one current case of interest): I need to follow whatever the
community practice is of regarding a sheet as part of a duplicate set
distributed by the original collector. I'm told by the people at the
Harvard University Herbaria that "duplicate" usually, but not always,
means from the same organism and same collection event---occasionally
people used to put several organisms on the same sheet, raising the
possibility that they are not even the same taxon. Worse, the
different parts of the same organism might be catalogued as separate
specimens. In this case, an assertion that they are from the same
individual might be true and understandable, but the utility of that
assertion depends on your purpose. Consider a use case in which one
set of traditional duplicates all have a determination that is out of
date, but another specimen---say your acorn collected later from the
same tree---has a current determination. For purposes of notifying
duplicate holders that a new determination has been made to the
original, the later acorn may not be interesting. This means that for
this use, a distributed query of the form "find all records with the
same dwc:individualID" is not as useful as "find all records with the
same dwc:eventID".
Also, as Mark writes, it doesn't address any other associatedOccurrences.
More generally, we are working on annotations of data records.
Probably what the real issue here is that associatedOccurrences is an
assertion about organisms, and we are making assertions about
occurrence data.
On Mon, Aug 23, 2010 at 3:07 PM, Steve Baskauf
<a class="moz-txt-link-rfc2396E" href="mailto:steve.baskauf@vanderbilt.edu"><steve.baskauf@vanderbilt.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Bob,
It seems to me that the most semantically clear way to indicate in a
machine-readable way that two herbarium sheets are duplicates would be to
assert that they have the same dwc:individualID. individualID is defined as
"An identifier for an individual or named group of individual organisms
represented in the Occurrence" so asserting that two occurrences represent
the same individual or named group of individual organisms pretty much
exactly describes what duplicate specimens are. I use this same approach to
indicate that
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/baskauf/67307">http://bioimages.vanderbilt.edu/baskauf/67307</a>
is an image of an acorn from the same tree:
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/ind-baskauf/67304">http://bioimages.vanderbilt.edu/ind-baskauf/67304</a>
as the bark image
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/baskauf/67312">http://bioimages.vanderbilt.edu/baskauf/67312</a>
I won't say more here as I have written more extensively on this approach in
Biodiversity Informatics 7:17-44
(<a class="moz-txt-link-freetext" href="https://journals.ku.edu/index.php/jbi/article/view/3664">https://journals.ku.edu/index.php/jbi/article/view/3664</a>). You can also
look at the RDF associated with those GUIDs to see what I mean. Solving
this problem is also one of the reasons I have proposed adding the class
Individual to DwC (i.e. so that the individuals that are the object of
dwc:individualID can be rdfs:type'd using a well-known vocabulary and
therefore be "understood" by linked data clients).
Steve
Bob Morris wrote:
<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/index.htm#associatedOccurrences">http://rs.tdwg.org/dwc/terms/index.htm#associatedOccurrences</a> carries
this description:
associatedOccurrences
Identifier: <a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/associatedOccurrences">http://rs.tdwg.org/dwc/terms/associatedOccurrences</a>
Class: <a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/Occurrence">http://rs.tdwg.org/dwc/terms/Occurrence</a>
Definition: A list (concatenated and separated) of identifiers of
other Occurrence records and their associations to this Occurrence.
Comment: Example: "sibling of FMNH:Mammal:1234; sibling of
FMNH:Mammal:1235". For discussion see
<a class="moz-txt-link-freetext" href="http://code.google.com/p/darwincore/wiki/Occurrence">http://code.google.com/p/darwincore/wiki/Occurrence</a>
Details: associatedOccurrences
My questions:
a. Are the names of the associations, and/or the syntax of the value
meant to be community defined?
b. If no to a. , where are those definitions? If yes, Have any
communities defined any names and syntax? I am especially interested
in "duplicate of" in the case of herbarium sheets."
c. (May share an answer with b.) Is there any use being made by anyone
in which associatedOccurrences is designed to have machine-readable
values. If yes, where?
Thanks
Bob
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 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) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
</blockquote>
<pre wrap=""><!---->
</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:
VU Station B 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) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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