Hi Rich - some comments inline below.
- A well-defined and enumerated set of whole organisms (pod of whales, packof wolves, etc.) documented in nature
What distinguishes well-defined from not well-defined? It sounds like this is relatively clear to you. It's not to me, and to see whether there is broad agreement, these things need to be spelled out. (One benefit from thinking about vocabularies in terms of ontologies is that this forces one to be specific and precise, which can help a lot in surfacing and pinpointing disagreements that need to be resolved.)
The preceding set requires some elaboration. For example, a herbarium
specimen is usually a clipping or other small part of a larger whole plant.
Often multiple clippings from the same individual plant are taken and
preserved as separate herbarium specimens. Should there only be one
instance of this class representing the whole plant? Or should there be
multiple distinct instances of this class, one for each herbarium specimen?
Yes, depending on what roles they play. As you say, a tissue sample can serve as an evidence (as can presumably non-biological entities, too), or may be the specimen being observed.
Similarly, suppose the mammal skeleton and skin in the above list are from
the same individual mammal. Would there be one instance of this class (for
the whole organism), and the Skeleton and Skin be treated as instances of
the Evidence class? Or, should there be two instances (one for the skin,
one for the skeleton)? Or should there be three instances (one for the
whole mammal organism, one for the preserved skin derived from it, and one
for the preserved skeleton derived from it)?
My take is it would depend on what observation you are trying to represent, and hence which instance is the one being observed.
I would like to believe that all instances of Occurrence can be rooted into
one instance of this proposed new class.
You may have meant something different, but just in case, instances aren't rooted, in the subsumption sense, in other instances. Only classes are.
-hilmar
Sent with a tap.