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Thanks for the various replies. I'm going to try to respond to several
of them in this one. I realize that these lengthy replies may
overwhelm some readers. However, I will beg your collective indulgence
because I've got a proposal on the table for adding Individual as a
Darwin Core class. It appears that the submission process is moving
forward and you can consider this as the "pleading of my case" for why
that addition is desirable (and in my opinion) necessary.<br>
One point which I think has permeated the Darwin Core discussions since
I've started following them is that DwC is designed to facilitate many
uses. Although somebody might use Occurrence records to make dots on a
distribution map, somebody else might be using the same records to
track the movement of the individual organism as it swims around the
sea. Somebody else may just be using the location and time metadata to
demonstrate that the photo that they took places the organism in a
reasonable location for the species they assert they have
photographed. Another person may be using the location and time
metadata to indicate that two species co-occurred at the same location
at the same time. Darwin Core will be functioning well when it allows
occurrence records to do any of these things or possibly all of these
things at the same time. The case that I'll try to make here is that
mostly allows these things, but lack of an Individual class is making
it difficult to do some of them. I will illustrate with a couple
The first one is the problem of tracking an individual over time. As
Rich correctly points out, the "new" Darwin Core standard has the term
dwc:individualID which is designed to facilitate exactly this kind of
thing. In a previous thread when we discussed the appropriate use of
the xxxxID terms, I believe that there was a consensus that using them
as "idrefs" (I can't remember the technical database term for this, I
mean when an item in a record points to the identifier of another
record) was appropriate. In a flat "table-based" database system, you
would just have a table of records (i.e. rows) for some kind of
"thing" with a column heading of "xxxxID". You would place the
the related other thing in that column. In the case of
dwc:individualID, the rows would be occurrence records and the entry in
the individualID column would be the identifier for the individual. In
RDF, you would make
statements asserting the relationship between the thing and the other
thing. For example, if you wanted to say that a dwc:Identification
asserted that something was a particular dwc:Taxon, you could make the
statement in RDF that [identification] dwc:taxonID [taxon], where
[identification] and [taxon] are instances of those two classes that
have been assigned some kind of (hopefully gobally unique)
identifiers. In the case of asserting that a number of occurrence
records track the same individual over time, in RDF, I would for each
occurrence make the statement [occurrence] dwc:individualID
[individual]. That's great and I can (and do) do that with Darwin Core
as it exists. The problem that I face is that in RDF any time that one
makes a statement about a resource (I'm switching to that term because
"thing" is to vague) using an identifier for it (in the form of a URI),
the identifier must dereference (resolve? sorry Bob!) to produce
metadata about the resource. So when I assign a URI to an individual
organism a semantic client should be able to retrieve information about
the individual. One of the fundamental pieces of information that a
client should (according to the TDWG GUID applicability statement) be
given about a resource is what type of thing the resource is. This is
called the "rdfs:type" of the resource. The TDWG Applicability
statement (recommendation 11) says that resources identified by a GUID
"should be typed using the TDWG ontology or other well-known
vocabularies". I hate to be cynical about this, but I don't have
confidence that the TDWG ontology will be ready to use in my lifetime.
The only "well-known" vocabulary that I know of that will work for this
purpose at the moment is Darwin Core and the Darwin Core classes are
just right for
typing all of the kinds of resources I want to talk about (occurrences,
taxon, identifications, etc.) EXCEPT for Individuals. I think that
dwc:individualID is the only one of the xxxxID terms that refers to a
type of thing that doesn't have a class defined for it, hence my
request to add Individual as a class. At the TDWG meeting, somebody
(Roger maybe?) commented that there isn't anything that would stop me
from creating my own URI for an Individual class. That is absolutely
true and I already did that
doesn't make my term "well known". I want Individual to be a class in
Darwin Core so that people other than me know what it means. There is
no way that I can currently follow the "rules" for GUIDs and RDF on
this, and anybody in the future who uses dwc:individualID in RDF is
going to face this same problem (i.e. anyone who wants to track
individuals over time).<br>
In the case of putting "dots on a map" to show the distribution of a
species, the case is simple if the occurrences are specimens where the
whole dead organism is collected. It is not so simple with other types
of occurrences. Let me illustrate with an example. There is currently
precisely one known individual of Crataegus harbisonii in nature. I
have given this individual the URI
. I have
approximately 62 images of that individual at
. Each one
of these images represents an occurrence in that I pressed the shutter
on my camera at different times for each one. Ron Lance has collected
tissue from this tree for grafting purposes and now has an occurrence
basisOfRecord="LivingSpecimen" in his arboretum in North Carolina.
Andrea Bishop of the Tennessee Dept of Environment and Conservation has
seeds collected from the tree - I'd call the collection of those seeds
an occurrence record. I'm pretty sure that there are one or more
specimens from this tree in herbaria (although I'm not sure where). So
my question to Marcus and others at GBIF is: how many dots will you put
on your map for this tree? 65 (one for each occurrence) or 1 (one for
each individual)? I think the answer should be one, but it isn't clear
to me how a data aggregator is going to achieve the goal of having one
dot per individual if the basic unit "dot creation" is an occurrence
rather than an individual. At the present moment, this question seems
like a moot point because most records in big databases like GBIF are
based on one specimen (or observation) per record of an individual, but
that won't necessarily be the
case in the future if people take multiple live organism images,
perhaps also at the same time they collect a physical specimen. I
anticipate that one response to this
question will be to call each imaging bout one "observation" having a
number of dwc:associatedMedia references. That collapses the number
of occurrence records considerably, but not down to one. I took images
of that tree on at least three separate instances over the course of a
year and Ron collected his graft tissue years before that. There is
simply no way to reduce the number of occurrences for this tree to one,
nor should we want to. A possible use of multiple occurrence records
(i.e. my first point above) of this sort might be to establish how long
individuals of Crataegus harbisonii live and each occurrence record
(whether separated by years or by the seconds between shutter clicks)
is a part of the record that we should be able to (and want to)
preserve. Another use would be to track a non-sessile organism (e.g. a
whale) in both time and space. In that case, the record on a map for
an individual would be some kind of curve rather than a dot. But in
any case, recognizing the existence of an entity that I'm calling an
Individual facilitates these broader uses of occurrence data and it's
really hard for me to see how that is going to happen if we ONLY have
occurrences as separate entities. Response Markus? How does GBIF deal
with whale tracks or multiple banded bird observations for a single
The third compelling reason for recognizing the existence of
Individuals as a resource type is that it is the best way to maintain
the linkage between multiple occurrences of the same individual and
identifications. (In the oversimplified examples I gave earlier, I
applied a scientific name directly to an individual. In actual
practice, I relate individuals to identifications and then relate the
identifications to taxa.) Again, to illustrate with a real-life
example, when Bruce Kirchoff was developing his Woody Plants of the
Southeastern US learning software, he asked a taxonomist to go through
the images of mine that he was using for the project to verify that
they were identified correctly. My old website just threw together all
images of a particular species onto one page without regard to the
individuals from which they originated (e.g.
out that I had carelessly misidentified a vegetative Sambucus racemosa
ssp. racemosa individual as Sorbus americana. The taxonomist asked me
which of the various bark, twig, leaf, etc. images were from the same
plant and the only way I could find out was through the laborious
process of looking for images with similar time/date values and my hand
written field notes. It was a nightmare finding all of the particular
image records that needed to have their identifications fixed and then
correcting them. On my new website (e.g.
then click on Quercus
chrysolepis), the images are connected to the individual from which
they originated. If I discover by looking at a particularly
informative image that I have misidentified the individual, I only need
to add an updated determination (i.e. identification) to that
individual's record and automatically all images from that individual
are displayed with the correct name and are placed on the correct
species page. Now imagine a situation that is larger and even more
complicated than this (think a Bioblitz). Herbarium curators and live
plant photographers are working together to document the flora of an
area. Multiple images and multiple specimens may be collected from the
same individual. The images may go one place and the specimens may go
to several herbaria (if "duplicates" are distributed). It's possible
that people might come back to the same individual later to photograph
or collect fruit having initially seen flowers. Suppose on down
the line a taxonomist looks at one of the specimen duplicates and
the initial identification was wrong (or maybe just wants to assert an
alternative opinion about the identity). If the record is based on
that individual, then all that is required is for the annotating
taxonomist to add a determination (i.e. dwc:Identification) to the
Individual's record and poof! all images and duplicate specimens have
that opinion associated with them. In contrast, if all of these
separate occurrence records are not tied together via the Individual,
and if each individual occurrence record has its own determination,
nobody is possibly going to ever track down and correct every one.
Granted, the scenario that I've suggested is contingent on the
existence of a large scale database that can connect metadata across
institutions, but exactly that kind of thing is what projects like the
US Virtual Herbarium and our Live Plants Imaging group are trying to
create. Let's enable this by making it possible within Darwin Core to
have a record structure that is Individual-based.<br>
I recognize that many "specimen-based" organizations aren't really
going to care one whit about this. That's fine. In their databases
and personal XML schemas they can ignore Individuals as it is their
prerogative. But when we build RDF templates, I believe strongly that
for the benefit of those of us who care about the broader applications
of occurrences those templates should use individuals to connect (one
or more) occurrences and (one or more) identifications. For those with
a technical bent, you can see how I have done this for an herbarium
specimen by looking at the page source RDF of the example
those of a non-technical bent, just look at the webpage that shows up
when you click on the link. It looks just like any other web page for
a specimen and you don't even have to know that the underlying RDF
supports using Individuals as a grouping mechanism.<br>
In summary, I think we need Individual as a DwC class to enable
understandable rdfs:typing of records of individuals and to create a
context in which instances of individuals can be placed (i.e. people
would assign and use identifiers for individuals when they document
occurrences). These instances (and their assigned URI GUIDSs) would
allow for "connecting" identifications and occurrences in a more
meaningful way. I am not suggesting that the occurrence be dethroned
as the center of biodiversity records. Assuming that the xxxxID terms
end up being moved out of the various classes and into the record-level
terms area as was suggested recently, I think that there are really
only about two terms that should be put into a new Individual class:
the other new term I have proposed (individualRemarks) and
establishmentMeans (but that is the topic of another email). It may
seem odd to suggest a adding a class that has very few terms in it, but
if you follow my reasoning above you will hopefully understand why I
have done so. <br>
I hope that the discussion (and
criticism!) will continue. Again, I'm interested in hearing
Richard Pyle wrote:
<pre wrap="">In many cases, a specimen is created by killing an organism and gluing it
<pre wrap=""><!---->to a
<pre wrap="">piece of paper (if it's a plant) or putting it in a jar (if it's an
<pre wrap="">It is natural to ask the question "what kind of species is the specimen?".
<pre wrap="">We can look at the specimen and make a statement like [specimen]
dwc:scientificName "Drosophila melanogaster" and it pretty much makes
<pre wrap="">However, in the new Darwin Core standard, we have a broader category of
"things" (a.k.a. resources) that we call Occurrences which include
<pre wrap="">but which also includes observations and probably all kinds of things like
<pre wrap="">images, DNA samples, and a whole lot of other things. If we try to apply
the same kind of statement to other kinds of Occurrences besides specimens
<pre wrap="">we immediately run into problems. If we say that [digital image]
dwc:scientificName "Drosophila melanogaster" we are making a nonsensical
statement. The digital image can have properties like its photographer,
its format, its pixel dimensions, etc. but the image itself does not have
<pre wrap="">scientific name. The scientific name is a property of the thing that was
photographed. It makes even less sense if we are talking about
<pre wrap="">An observation is a situation where somebody observes an organism.
The observation can have properties like the observer, the location, etc.
However, if we say [observation] dwc:scientificName "Drosophila
<pre wrap="">we are saying that that act of observing has a scientific name.
That is an incorrect statement. So the general statement [Occurrence]
dwc:scientificName "Drosophila melanogaster" does not make sense when
applied to all possible types of Occurrences. Rather, the organism
that we are observing is the thing that has a scientific name.
OK, I admit that I have not been following this list as closely as I should
have -- especially during the latter half of 2009. But I have to
ask....seriously....is this the level of misunderstanding that still exists
in our community?
Perhaps I'm the idiot here, but it has *always* been my understanding that
the "thing" (I hesitate to use the word "basis") of an Occurrence instance
is *always* the organism (or set of organisms, or impression of an organism
in the case of fossils). If the organisms were captured and preserved in a
Museum, then we call it a specimen. If the organisms were only witnessed
and not captured, we call it an observation. Everything else (including the
physical specimen) is just layers of evidence to support the existence and
taxonomic identification of the organism within the Occurrence. When
photons reflected off the outer surface of an organism find their way
through a lense and onto some mechanism for recording said photos (either a
human retina and neurons in the brain, or sheet of celluloid, or digital
image sensor and memory stick), it's still the organism that the photons
reflected off of, which represents the "thing" of the Occurrence to which
metadata apply. Same goes for vocalizations transmitted through pressure
waves in the air onto some recording device (ear/brain, or microphone/tape).
So while it's certainly true that a media object such as a 35mm slide or
digital image file does not itself have a scientificName (then again, some
of my old Kodachromes have enough mold on them that they might....), said
media objects are *not* the Occurrence itself -- they merely represent
evidence of the occurrence. Even a specimen in a jar is not the Occurrence
itself. The Occurrence occurred when the specimen was captured (e.g., 400
feet deep on a coral reef). A specimen in a jar on a shelf in a Museum is
no longer the "Occurrence"; it is the evidence of the Occurrence.
When I assign a GUID to an Occurrence record that lacks a voucher (i.e., an
"Observation"), I'm certainly not trying to identify the act of observation;
I'm identifying the organism that was observed, at the time and place that
it was observed.
For what it's worth, if I only have a still or video image of an organism
(e.g., <a class="moz-txt-link-freetext"
href="http://www.youtube.com/watch?v=GVTd11q3Ppc">http://www.youtube.com/watch?v=GVTd11q3Ppc</a>; taken by Rob Whitton, who
some of you met at TDWG this year), and didn't collect the specimen, I
create an Observation record, and link the image to it as associatedMedia.
I would never assign a taxon name to the video clip -- only to the "content
item" of the video that represents an organism, serving as the basis of an
<pre wrap="">The specimen is an occurrence of the individual organism.
The image is an occurrence of the individual organism.
The observation is an occurrence of the individual organism.
I would say in all three cases that the presence of an organism at a place
and time was the Occurrence. Specimens, images, and reported observations
are merely the evidence that the occurrence existed (and to varying degrees,
can also allow for subsequent interpretations of taxonomic identification).
<pre wrap="">These statements may seem odd because we are used to
thinking of an Occurrence being an occurrence of the
"species" but it's not really.
I completely agree. The occurrence was the organism at a place and time.
The "species" is merely the taxon concept that someone identified the
organism as belonging to. The scientificName is merely the label that
someone applied to the taxon concept. In other words, the scientificName is
really a property of the Taxon Concept, and the Taxon Concept is the subject
of an identification event, and the identification event was applied to the
organism, which itself represents the basis of an Occurrence. But very few
people go to the trouble of creating that full chain of relationships, so as
a short-hand, the scientificName is often treated as a direct property of
the occurrence (collected or observed organism). I think this short-hand is
perfectly fine in the context of DwC, but only as long as people understand
the implied chain of linked entities. If we start to forget what's really
going on, then we run into trouble.
Which, I guess, was the whole point of Steve's post.
What concerns me, though, is that we're not (yet?) already beyond this.
<pre wrap="">This point becomes more clear if we look at a situation where several
types of occurrence records are collected from the same individual.
Let's say that we capture a bird, photograph it, collect a feather from
<pre wrap="">collect a DNA sample and band it and let it go. Later somebody sees the
band and reports that as an observation.
How do we connect all of these things?
Two Occurences: The first one when it was captured, photographed, and
relieved of a feather. The second when it was observed at a later date.
<pre wrap="">Do we create an identifier for the specimen (the feather)
and then say that the image and the DNA sample came from it?
We create an identifier for the first Occurrence, capture the
specimen-relevant metadata of the preserved feather, and track the DNA
sample via associatedSequences.
<pre wrap="">That would be wrong. We could take an image of the feather,
but that would be a different thing from an image of the bird.
It's certainly different from an image of the whole Bird, but that doesn't
preclude us from including both bird and feather images among
associatedMedia for the first Occurrence.
<pre wrap="">We didn't get the DNA sample from the feather, we got it
via a blood sample from the bird.
I don't see that as a problem, because the feather is only the evidence of
the bird at the place and time (i.e., the first Occurrence). Thus, the
sequence can still be included as part of the associatedSequences for the
<pre wrap="">The band observation is not an observation of the feather,
or the image or the DNA sample. It's an observation of
the bird which was never any kind of specimen living or dead.
The bird is an individual organism and that's what we need to call it.
Agreed -- it forms the basis for the second Occurrence record (later date).
The two Occurrence records can be cross referenced, either via a shared
individualID, or via associatedOccurrences.
<pre wrap="">Right now we don't have anything in Darwin Core that can
be used to rdfs:type the bird, which is why I proposed Individual
as a Darwin Core class.
As someone else alluded to earlier in this thread, there are near-infinite
ways that we can slice & cluster biodiversity data. I think there are some
cases where "individual" makes a lot of sense as a class (banded birds,
managed organisms in zoos and curated gardens, whale and shark observation
datasets, plant monitoring projects, etc.). But I think the notion of
"Occurrence" makes more sense at this point in biodiversity informatics
history, because the vast majority of datasets can be organized in this way
realtively painlessly, and because the majority of questions being asked of
these data revolve around presence of organisms identified to taxon concepts
occurring at place and time.
<pre wrap="">I could say these things more clearly in RDF, but since
because many members of the audience of this message
aren't familiar with RDF/XML they would probably zone
out and the point would be lost.
Myself among them. Thank you for presenting it in the less-efficient
English Prose form.
<pre wrap="">The point is that we need to have identifiable classes of "resources"
(the technical name for "things" like physical artifacts, concepts,
and electronic representations) for all of the things that that we
need to describe and inter-relate in the Darwin Core world.
Right now, we are missing one of the important pieces that we need,
which is a class for the Individual. If we are satisfied with creating
an RDF model that only works for specimens and one-time observations,
then we probably don't need Individual as a Darwin Core class. On the
other hand, if TDWG and GBIF are really serious about creating a
system (Darwin Core and RDF based on it) that can handle other types
of Occurrences like multiple images of live organisms, observations
of the same organism over time, and multiple types of Occurrences
collected from the same organism, then this capability should be built
into the system from the start. When I got back from the TDWG meeting,
I was all excited about trying to use Darwin Core Archives with my
live plant image collection. However, it quickly became evident
that it could not work because Occurrences were at the center of the
diagram rather than Individuals. So unless something changes, we
are already embarking on the process of locking out these other
Well...I certainly agree with you that we need *clear* documentation on what
these classes are intended to represent. I had *thought* it was clear that
an Occurrence was as I have outlined above. But like I said, I'm perfectly
willing to accept that I'm the idiot in this case, and am completely out of
phase with the rest of the community.
As to whether or not we need to define a class for Individual, I'm not so
sure that's entirely necessary. I guess DwC is already primed for it
href="http://rs.tdwg.org/dwc/terms/index.htm#individualID">http://rs.tdwg.org/dwc/terms/index.htm#individualID</a>) -- but I'm not sure
what properties would apply to such a class that are not already covered in
DwC. Pronbably the next intieration of DwC would move some of the
properties of the Occurrence class (catalogNumber, individualCount,
preparations, disposition, associatedSequences, previousIdentifications)
over to the Individual Class, at which point the Occurrence becomes the
intersection of an Individual and an Event.
But let me ask: how would you scope "Individual"? (see my previous rants on
this list in recent days) Would it be restricted to a particular individual
organism? Or, would it be extended to include specified groups of organisms
(as dwc:individualID already does)? What about populations? Taxon Concepts?
<pre wrap="">I hate to sound like a broken record (do we have those any more?),
but read my paper on this subject.
I've had gotten through the first few pages, and intend to finish soon. But
it's much more fun to write emails about this stuff..... :-)
Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
Associate Zoologist in Ichthyology
Dive Safety Officer
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: <a class="moz-txt-link-abbreviated"
<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.
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>