[tdwg-content] New Darwin Core terms proposed relating to material samples

[Richard Pyle]

Hi Markus,

Great question!  Particularly because this is exactly the sort of use case
we designed our model around.

> if you take a tissue sample of the same tree every year, would the
identifier
> in individualID be the same for all of them or be different? WIth the
current
> dwc:individualID definition it would be the same for all samples. If I
> understand you correct each sample would have its own "individual"
> identifier in your proposal? It can't see how you can collapse these two
things
> into one definition.

No, that is not how we would handle it.

In our model, there would be one IndividualID to represent the tree,
spanning the time period beginning (more or less) when the seed was
germinated, until the time at which the entire physical structure of the
tree was disintegrated.  It is an individual tree.

There would be multiple Occurrence instances, for each time that someone
observed or sampled or otherwise wished to document some condition of that
tree. All of these Occurrence instances would refer to the same individualID
value (i.e., the "tree").  In the example above, this means there would be a
different Occurrence instance for each year that a sample is taken --
because in each case, an assertion that the full tree existed at a certain
time and place can be made (I understand that trees tend not to move around
very much, so the Location for each event associated with each Occurrence
would, in this case, remain the same; but the other Event properties -- such
as eventID, samplingProtocol, samplingEffort, eventDate, eventTime,
startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat,
fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for
each sampling Occurrence instance).

Suppose that the tree is visited every month, but only sampled once per
year.  In that case, there would be an Occurrence record for every monthly
visit.  In other words, an Occurrence instance exists regardless of whether
a physical sample was made or not.  Any in-situ images made of the tree
would likewise be associated with the specific Occurrence instance, and each
image would represent a separate instance of "Evidence".

Now, let's focus on the annual samplings.  Every time a new sample is taken
from the tree, at least one new instance of Individual (with a unique
individualID value) is created to represent the sample.  This sample
(individual instance) may be a "gathering" (set of multiple individual
specimens gathered at the same time), or it may be a single specimen, or it
may be simply a tissue sample intended for destructive analysis.  In any
case, it's a new individual instance derived from the "parent" individual
instance representing the whole tree.  In our implementation, "Individual"
can be hierarchical, such that a whole-organism tree can be sub-sampled with
many "child" instances of "gatherings" (say, one gathering each year), and
each gathering may have multiple child "specimen" individuals (e.g.
individual botanical sheets created from the multiple items of a single
gathering), and each specimen may have further "child" subsamples extracted
for DNA analysis (or whatever), and the hierarchy can continue on down to
whatever derivatives that people feel a need to keep track of (e.g.,
aliquot).

The point is, all Individual instances are well-defined physical objects (or
well-defined sets of physical objects), and they can be arranged in a
n-tiered hierarchy.

Moreover, each Individual that can be characterized as a "sample" (what we
refer to as a "CollectionObject") may also have a property value for
"CollectionOccurrenceID" -- which refers to the specific Occurrence instance
at which the sample was obtained.

So, for example, if the tree is visited on May 27, 2013 and a specimen
(sample) is taken, then:
1) An Event instance is generated to represent the event where the tree was
visited;
2) An Occurrence instance is generated, which refers to the new EventID, and
the existing IndividualID for the whole tree, and includes whatever other
Occurrence properties are relevant for the tree at the time of this
Occurrence
3) An Individual instance is generated for the specimen, which has a
property value for parentIndividualID that refers to the individualID for
the whole tree, and a property value for collectionOccurrenceID that refers
the Occurrence instance where the specimen was collected.

So, to summarize the answer to your question:
- There are multiple Occurrence instances that refer to the same Individual
instance representing the whole tree (and, hence can be collapsed to the
same IndividualID value).
- Any Individual can have derivatives that are themselves unique Individual
instances.
- Individuals are arranged hierarchically, and certain properties can be
inherited up or down the hierarchy, depending on the properties and their
associated logical constraints.

At some point, I will assemble a set of other specific use cases, and how we
manage them through our use of the "Individual" instance (although I will
probably not use the word "Individual", as this seems to cause too much
confusion in these discussions).

Aloha,
Rich