[tdwg-content] Background for the Individual class proposal. 3. Should an Individual also be a Collecting Unit?

[Kevin Richards]

I have several comments / questions on all this:

The "Individual" debate seems to me like we are discussing very similar things, just trying to clarify the subtleties of the class/term.  Tell me if I am wrong but it seems like Steve's idea for the Individual more closely resembles a many-to-many joining table in a database (ie doesn't serve much use other than connecting two tables/classes together - and doesn't normally relate to a "real world" type of object).  Whereas it seems Rich's idea is to relate it more to "real-world" objects, such as samples, re-samples, etc, to allow tracking and connectability of the observed/collected/processed individuals.  I think in a "model" we need to try to define the real world object types and relationships, then we apply that model to an instantiation of that model which will tend to contain more structure, such as joining table type classes.

Another comment is on how RDF works (RDF domains in particular, and the benefit of defining the domain, or having no domain).  It thought we removed the rdf domain restrictions off the DwC classes to allow more flexible use of the DwC terms.  So this is obviously an important requirement.  So my question really is, would it be possible to do both?  I.e. is it possible to have terms that can be defined as having a certain domain, then equivalent terms that are not part of the domain - I know this would complicate things immensely, but I do wonder if other communities using RDF have encountered similar problems and have found a way to do this??  We could perhaps have SimpleDwC that defines a bunch of terms that have no domain, that have "rdf links" to terms defined in a FullDwC that defines all classes and the properties of each class - this seems flexible to me and I thought this was one of the benefits of RDF - i.e. the links/mappings etc???  Another way to look at this could be to develop DwC as a UML model - no RDF defined, then have several implementations of the DwC model for specific use cases (this would make Roger happy  :-)) - but I'm not sure how this will work with respect to the full advantages of using RDF - eg reasoning - i.e. we probably need to define the full model in RDF to make full use of RDF features.

Another comment is on the placing of your useful posts, Steve.  Do you think you could do some of these as blogs that could be commented on.  We can then link to blogs from google repositories, wikis, etc.  Otherwise they may disappear into the mailing list archives (I know I have said this before, but it still bugs me).  It seems to me you have a lot more time to spend on this stuff right now than a lot of us - being a predominantly voluntary community, the effort that can be put into discussions and activities by the community members is very sporadic.  I personally would like more time to spend on this stuff, but have other tasks that are more demanding.  Also, due to the sporadic nature of the effort in the TDWG community, I think a lot of people are getting left behind - especially with the large amount of content that is submitted to the mailing list - but I DO NOT want to curb your enthusiasm at all!  Just thinking there might be a better place to store them??  Thanks for your efforts on these topics Steve, it is certainly valuable.

Kevin

-----Original Message-----
From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Steve Baskauf
Sent: Sunday, 14 November 2010 5:26 a.m.
To: tdwg-content at lists.tdwg.org
Subject: [tdwg-content] Background for the Individual class proposal. 3. Should an Individual also be a Collecting Unit?

In the first and second installment of this series, I have tried to show
that the class Individual as I have proposed it is a central part of a
fully denormalized Darwin Core model.  It's connective role allows for
one-to-many relationships between itself and both the Occurrence and
Identification classes (see
http://bioimages.vanderbilt.edu/pages/full-model.jpg).  I have also
pointed out that in that role, it has very few properties.  The reason
for this is described in detail on p.26 of my Biodiversity Informatics
paper (https://journals.ku.edu/index.php/jbi/article/view/3664), but in
summary the only way we can actually find out anything about an
individual organism is through some kind of observation or collection,
which is exactly what happens in an Occurrence.  Thus things that we
"know" about Individuals generally are directly or indirectly associated
with Occurrences, not with the instances of Individual themselves.

Rich has suggested that we should consider whether some properties that
are currently properties of Occurrence should be moved into the proposed
Individual class.  It is good to think about this, because we do want to
have an economy of classes and terms (no point in having two classes for
something when one would do), and because the mental image that we have
about an individual organism does include aspects of both the proposed
Individual class and the part of the ASC diagram called "Collecting
Unit".  There are a number of ways of approaching this problem.  The
first approach, which is the way the discussion developed on the email
list, is to just try moving terms from Occurrence to the proposed
Individual class and to see whether that would "work" or not.  As the
discussion progressed, I began to feel increasingly uncomfortable with
this process, but wasn't sure why.  After I went back to the ASC
diagram, it became clear to me what was the problem was.  I believe that
the question is really being framed incorrectly.  What I have proposed
for the class Individual is precisely what I have described in the
previous posts: for it to serve as a node connecting Occurrences to
Identificaitons.  What I think Rich wants to recognize is the section of
the ASC model called Collecting Unit and the boxes below it: Unsorted
Lot, Lot, Specimen, and Specimen Component (I'm not sure exactly what
"Derived Object" is - maybe things like images of specimens?).  If I am
correct in understanding what Rich wants, then the question boils down
to: can or should my proposed class be the same as (or possibly include)
the section on the ASC diagram called Collecting Unit.  I think that I
have a pretty clear idea in my mind what Individual as I have defined it
means, so my task has been to try to understand what exactly is a
CollectingUnit and what properties should it have.  The I can approach
the question of congruence with "my" Individual.  If all things that we
would want to fold within CollectingUnit share properties that can be
placed within the Individual class, then they are congruent and should
be the same thing.  If some or most properties that we want to fit
within CollectingUnit don't fit the defined purpose of the Individual
class, then they should be two separate classes.

Because the ASC model was developed by the museum community, I think
that its creators were primarily concerned with handling dead
specimens.  However, as Rich has correctly pointed out, the distinction
between dead and living CollectingUnits is probably artificial.  Rather,
both living and preserved specimens may be instances of the same class
which have a different value for some "live/dead" property (see
http://code.google.com/p/darwincore/issues/detail?id=91).  So for the
moment, I'm assuming that a CollectingUnit can be either living or
preserved.  The case of preserved specimens is fairly straightforward.
The have their origin in a single Occurrence that happens at a single
Event (what I called a "resource creation event" in my Biodiversity
Informatics paper).  Living specimens are more complex.  They may
originate when the whole organism is collected from the wild and moved
to a zoo or botanical garden (John's wildebeest calf).  In that case
there is a clear "resource creation event" if we call the living
specimen a resource that is distinct from the organism when it was in
the wild.  In some cases, the living specimen is born in captivity,
grown from a seed, or propagated vegetatively from a cutting.  In that
case, there is also a definable event when the living specimen
originated.  What was really driving me crazy was this:
http://bioimages.vanderbilt.edu/vanderbilt/7-314
The Bicentennial oak is a tree that is growing in Vanderbilt's
arboretum.  It seemed to me that it was a living specimen because it is
now a part of a collection of trees (the arboretum).  But it is over 230
years old and Vanderbilt itself is only 137 years old. So clearly nobody
captured, moved, or planted it to make it a part of the arboretum.  For
a while I tried to define it out of being a living specimen, but then I
realized that the thing that made it different from other old trees that
are standing around Nashville is that it has been accessioned.  In other
words, when the tree was claimed as a part of the arboretum, assigned an
identifier (7-314), and added to the arboretum database, it became a
living specimen in addition to being just a normal tree.  The event of
calling the tree a part of the arboretum, assigning it an identifier,
and adding it to the arboreutm database is the Occurrence that marks the
creation of the thing "living specimen".  At that point it can have any
attribute that other Occurrences have and it is then capable of serving
as evidence for the Occurrence because anybody can examine it at will.
The "claimed as a part of the arboretum" part is important, because I
can go out into the woods and collect information about a tree there,
assign it an identifier, and add it to my database, but that doesn't
make it a living specimen because I don't assert that I have any control
over it or that I can guarantee anyone that I can verify its status at
will.  If I band a bird and release it, I have assigned it an identifier
and hopefully will be able to track it over time, but I can't claim it
is a living specimen because I don't claim to exert control over it.
That's different from John's wildebeest calf which is in a pen and be
observed at will.  It is similar to a maize plant in a field in Iowa
which was cultivated by a human, but has no curator who is making sure
that it can be found again and that it won't be harvested and ground up
into wildebeest food without his or her knowledge.

If I think about all of the kinds of things that I would like to put
into the spot on the ASC diagram labeled "Collecting Unit" (including
things like the Bicentennial Oak that was never "collected" by anybody),
the one thing that they all seem to have in common is this aspect of
being "accessioned".  So I would assert that in a general model,
"AccessionedUnit" would be a better name than "CollectingUnit".  Some of
the terms that I think should come out of Occurrence (such as
preparations and disposition) could apply to any AccessionedUnit.

So that brings me back to the question of whether this thing that I'm
calling AccessionedUnit (which is sitting in the spot on the ASC diagram
where Collecting Unit was originally) can or should be considered the
same as what I have proposed to be the class dwc:Individual.  The
decision on this should not be made based on what we "think" an
Individual should be, but rather on what we need it to be to fulfill the
role that we have assigned it in our model.  With that in mind, it might
be better for the moment to change the name dwc:Individual to
dwc:ResamplingUnitHavingDetermination because that is what it needs to
do according to its current definition and location in the model diagram
(I'm considering resampling to be the documentation of multiple
Occurrences).  The question them becomes: should AccessionedUnit be
considered the same as ResamplingUnitHavingDetermination because they
share the same properties (i.e. are described by the same terms)?  To me
the answer is clearly "no".  It is very likely that an AccessionedUnit
will never be associated with more than one Occurrence (i.e. be
resampled), particuarly if it is dead and has been put in a museum
collection.  It is possible that the thing referred to by an
AccessionedUnit might be documented by multiple Occurrences if it is
alive (like the Bicentennial Oak), but that is not an intrinsic property
of an AccessionedUnit in the same way that preparations or disposition
would be.  On the other hand it is also quite clear that many
"ResamplingUnitHavingDetermination"s will never become accessioned.
That would include the banded bird, a tree photographed in the forest,
or a whale observed swimming in the ocean.  The longer I think about
this, the more convinced I am that making a distinction between
AccessionedUnit and ResamplingUnitHavingDetermination is the best course
of action.

Having made a decision about this based on functional need and shared
properties, it is still helpful for me to try to develop a mental image
of what these two things are.  In my mind, I imagine the
ResamplingUnitHavingDetermination (which I will henceforth return to
calling dwc:Individual) to be an entity having a homogeneous taxonomic
identity.  It has some moment when it came into existance as a living
thing (by being born, planted, or founded) although we will never know
when that moment was unless an Occurrence happens that allows us to
document that Event.  The Individual remains an entity as long as it has
the potential to be documented as an Occurrence.  That doesn't
necessarily means that it must be alive.  But if it decomposes, or is
preserved and put into a collection, it no longer is capable of being
resampled (i.e. documented by an Occurrence).  Thus a fossil that is
dead for a million years and is sitting in some stratum still fits my
mental image of an Individual.  If it gets chipped out of the rock and
put in a museum, there would no longer be any point in documenting
another Occurrence for it since there would be no useful Location or
GeologicalContext information to be gained from that.  A roadside
population of herbaceous plants having homogenous taxonomic identity
would be an Individual from the first time it was capable of being
sampled (when it was founded) and would end being an Individual when it
was extirpated by some road construction crew and was no longer capable
of being documented by an Occurrence.  A wolf pack would be a similar case.

My mental image of AccessionedUnit is an entity that comes into
existence when some human person or institution takes control of it,
assigns it an identifier, and keeps records of it.  I think I would
never see it as coming to an end.  Even if it is lost or destroyed, it
would continue to exist as long as the person or institution maintains
its record.  It would just have dwc:disposition "lost" or "destroyed".
It could be a dead, preserved specimen in a jar or glued to a sheet of
paper, a living wildebeest calf in a zoo, or even a field sampling plot
in a park as long as the park exerts control and ownership over it and
maintains records about it.  It could not be any wild, free-ranging
animal or plant.  It could not be roadkill left on the side of the road
to decompose.  It could not be a photograph of a wildebeest calf in the
zoo, or the sound recording of the wildebeest calf's grunt. It COULD be
a tissue sample from the wildebeest calf or from the roadkill.  The
critical thing is that it is a physical artifact originating from a
living thing that has been cataloged and placed under human control.  I
think this is the kind of thing that Rich wanted to be able to define
when he wanted to broaden the definition of Individual.

For any entity having an origin as a living thing (in my mental image),
its status as an Individual is independent of its status as an
AccessionedUnit.  If the entity is removed and preserved in its entirety
(fish killed and put in a jar of formaldehyde), it ceases to exist as a
dwc:Individual and begins to exist as an AccessionedUnit.  If a branch
is removed from a tree or one plant pulled from a roadside population to
become specimens, the removed part becomes an AccessionedUnit while the
dwc:Individual continues to exist.  In the case of the Bicentennial Oak
or a permanent sampling plot, the entity simultaneously exists as both
an AccessionedUnit and a dwc:Individual.  In terms of metadata records,
the establishment of any AccessionedUnit is an Occurrence (grouped under
the Individual) having a property of recordedBy.  Whether or not
subsequent Occurrences are possible for the Individual depends on
whether the act of creating the AccessionedUnit has rendered subsequent
sampling irrelevant.

I agree with the point that was made previously that no specific
taxonomic level should be placed in the definition of Individual.  That
would allow for the possibility that Individuals could contain several
different lower level taxa as long as the Individual is homogeneous at
the taxonomic level at with the determination is applied.  I am open to
suggestion for how this could be accomplished.  Somehow there needs to
be a value for a term like "individualScope" that allows one to make the
kind of inferences about duplicates that I described previously.  Maybe
one controlled value for "individualScope" should be "DuplicateLevel"
meaning that the Individual is homogeneous in taxonomic identity to the
level at which a taxonomist would collect multiple specimens and call
them duplicates.  That would get us out of the problem of deciding
whether the several grass stems we collect and send off to different
herbaria are actually the same biological individual or clones connected
by underground stems.  Other possible levels could be
"BiologicalIndividual" for things known to be single biological
individuals, and "Heterogeneous" for things that are know or suspect to
be mixtures of lower level taxa but for which it is convenient to assign
a determination at a higher taxonomic level at which we know the mixture
to be homogeneous.

For AccessionedUnit, I think there should also be an
accessionedUnitScope term.  I defer to the museum people on this, but
the boxes in the ASC diagram (unsorted lot, lot (presumably
homogeneous), specimen (presumably one biological individual), and
specimen component) could be a starting point.  The "partOf" and
"hasPart" properties could be used to related AccessionedUnits that are
related to each other.  Relating these various levels of
AccessionedUnits to levels of Individual above "DuplicateLevel" is going
to be tricky, but if people want to do this, I'm sure there is a way to
represent the relationships in RDF.

THE BOTTOM LINE
I believe that the proposed definition for the DwC class Individual
should stand as it is (i.e. as a node to connect multiple Occurrences to
multiple Identifications).  To allow Identifications for Individuals
that are homogeneous at higher taxonomic levels, we also need a term
like dwc:individualScope.  I believe that there needs to be a separate
class that represents what I've described here as "AccessionedUnit"
which also has some kind of scope property.  I am not going to propose a
name for this thing or propose what properties belong with it.  Rich and
the herbarium/museum/botanical garden/zoo people need to decide and
propose that.  AccessionedUnit then becomes one of several types of
evidence that can be used to support an Occurrence, with
dctype:StillImage, dctype:Sound, dctype:Text as other possibilities.
Darwin Core does not need to define their properties and types since
others (MRTG, DCMI) have already done so.  We then need two more terms:
one to relate the evidence to the Occurrence and one to relate the
Occurrence to the evidence (I would suggest "hasEvidence" and
"isEvidenceFor" as possibilities).  If we can do these things, I think
we could say that a general (i.e. denormalized enough to satisfy
everyone who is dissatisfied at the present moment) Darwin Core model is
"complete" to the "left" of Identification on the
http://bioimages.vanderbilt.edu/pages/full-model.jpg diagram.  I'm not
going to touch the Taxon side right now.

Whether or not action is taken on creating a class for what I'm calling
"AccessionedUnit", there is no reason to hold up action on my Individual
class proposal if people agree with the points I've made here.

Steve

--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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