steve.baskauf at vanderbilt.edu
Tue Aug 24 07:16:43 CEST 2010
1. The definition of dwc:individualID is an identifier for "an
individual or named group of individual organisms...". Thus by this
definition a small population of organisms of the same species found
together can be considered an individual even if they are not biological
individuals. The definition of individual is a functional one that
facilitates the common circumstance you describe where a collector
collects "duplicates" that aren't really duplicate individuals but are
considered to reliably be from the same species because the members of
the population are in close proximity and (hopefully) the collector took
care to collect only biological individuals of the same species.
2. If it is discovered that a sheet has individuals of two species, a
curator would undoubtedly create two records for the two species on the
sheet. I can't imagine the curator would try to somehow cram the
metadata for the specimens of both species into the same record unless
the curator had some kind of special way of dealing with "specimens"
that were actually themselves collections of species. The fact that the
occurrences described in the two records were on the same piece of paper
would not really be relevant other than that they would have the same
collection date, collector, etc. in the same way as would two specimens
of different species collected on the same day by the same collector
placed on two different papers.
3. I do not see why cataloging the two different parts of the same
organism as separate specimens would be any problem at all. I've
collected from the same tree in different seasons to get leafy stems and
then winter twigs. They are two dwc:Occurrences, each with its own set
of metadata properties, and its own identifier that happen to be from
the same individual. People who do mark/recapture or repeated
observations of live organisms have multiple Occurrences from the same
individual all the time.
4. The issue that you bring up about the problem of different
determinations based on different specimens is not a problem if the
determinations are associated with the individuals rather than with the
Occurrences (i.e. specimens) as I suggest in the paper (see Fig. 8 on
p.30). If the assertion is made that the individual from which the
first specimen is derived is owl:sameAs the individual from which the
second specimen is derived, then a client capable of drawing inferences
from RDF (e.g. a 'bot gleaning biodiversity metadata from many
institutions to build a large database) will apply determinations linked
to either of the individuals to both of them (since they are known to be
the same entity). All of the determinations applied to the (now
singular) individual will be associated with both specimens through the
relationship of each specimen to its source individual (i.e. its
dwc:individualID property). Users of the resulting database would be
able to examine for either specimen the entire set of determinations
associated with the (formerly separate) individuals. They could assess
the temporal order of the values of the determination's
dwc:dateIdentified properties (i.e. which is most "current") and assess
the weight to place on a particular determination based on the identity
of the determiner (dwc:identifiedBy property). You say that the holders
of the original duplicates would not be interested in the determination
based on the acorn. Really? If the specimens and the acorn came from
the same tree, the curators certainly ought to be interested because the
tree couldn't simultaneously BE two different species (even if it had
This suggested solution isn't intended to address all kinds of
associations, just the case of duplicates. Some one else can take that
one on... :-)
Bob Morris wrote:
> 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
> <steve.baskauf at vanderbilt.edu> wrote:
>> 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
>> is an image of an acorn from the same tree:
>> as the bark image
>> I won't say more here as I have written more extensively on this approach in
>> Biodiversity Informatics 7:17-44
>> (https://journals.ku.edu/index.php/jbi/article/view/3664). 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).
>> Bob Morris wrote:
>> http://rs.tdwg.org/dwc/terms/index.htm#associatedOccurrences carries
>> this description:
>> Identifier: http://rs.tdwg.org/dwc/terms/associatedOccurrences
>> Class: http://rs.tdwg.org/dwc/terms/Occurrence
>> 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
>> 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?
>> 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
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.
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
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