Dean,
I intended to comment on your earlier post but got caught up in other threads and hadn't yet taken the time. I know on at least one previous occasion this issue of mixed aggregations was discussed on the list but I spent about 15 minutes looking for it in the archives this morning and couldn't find it. I remember somebody pointed out some software that allows places within an image to be demarcated (i.e. call the image an aggregation and define spots in it as Individuals). Also, I tried to handle the issue of tokens (or evidence) that are derived from other tokens in my paper (see http://bioimages.vanderbilt.edu/pages/conceptual-scheme-insect.gif for an example) by using sernec:derivedFrom and sernec:derivativeOccurrence (see http://bioimages.vanderbilt.edu/rdf/terms.htm). But I think my approach needs to be rethought in the context of separating tokens from occurrences. I am very keen to work this out, but I really don't thing that piling this onto Individual is the way to do it. I'm in the middle of running and photographing gels at the moment but look forward to continuing the discussion on these points at a later time.

Steve

Dean Pentcheff wrote:

Leveraging off my earlier toss-in of the parent-child collection scheme, let me toss in this observation.

I'll preface it by saying that although it's a situation we deal with in reality, my gut impulse is that it should probably _not_ be accomodated by the "Individual" concept under development.

We have many records for un- or partially-sorted lots of marine invertebrate samples. Often we can make very rough determinations of what are in those lots (e.g., we can see that a jar contains ophiuroids, gastropods, sphaeromatid isopods, red algae, and larval fish). Critically, these are multiple particular and disjunct parts of the taxonomic hierarchy, not just a single "highest containing rank" determination.

It turns out to be super-useful to record that very rough determination because (as alluded to by Rich) we can then appropriately make that jar available to visitors seeking particular taxa (and save them the trouble of grubbing through shelves of jars where we already "know" there's nothing of interest to them).

Right now, we do _not_ conflate this rough determination with a Real Taxonomic Determination (®™ and all that): they are two completely separate fields. So to find all the jars we know have ophiuroids, one does indeed have to search both the real taxonomic determination field as well as the rough-determination (text) field (if one wants to include unsorted lots in the quest).

I'm introducing this case more with the idea that it may usefully help define the outer limits for "Individual" -- something that the "Individual" concept should _not_ accomodate. I can't really wrap my head around how the developing "Individual" concept can usefully be mutilated to accomodate this case.

-Dean
--
Dean Pentcheff
pentcheff@gmail.com
dpentche@nhm.org

On Wed, Nov 3, 2010 at 11:53 AM, Richard Pyle <deepreef@bishopmuseum.org> wrote:

> I think if I'm understanding what John wrote,
> he was going to substitute "taxon" for "species
> (or lower taxonomic rank if it exists)" with
> the understanding that Individual is not
> intended to be used for aggregates of
> different taxa. That would solve this problem, right?

It depends on what you mean by "different taxa". If you are using the word
"taxa" here to imply "species or lower ranks", than I don't think it would
solve the problem. But if you mean it in a generic way, then I'm OK with
that. By "in a generic way", suppose I had a trawl sample or a plankton tow
sample that included unidentified organisms from multiple phyla, all of
which are animals. I should not be prevented from representing this
aggregate as an "Individual", with an identification instances linked to a
taxon concept labelled as "Animalia". This means the contents of the
Individual all belong to a single taxon (Animalia), and therefore it does
not violate the condition excluding aggregates of different taxa. An
instance of Individual so identified would be almost useless for many
purposes, I agree -- but it's easy enough to filter such Individuals out by
looking at dwc:taxonRank of the Taxon to which the Individual was
identified. Also, it's not useless for all purposes, because a botanist
would like to know that s/he doesn't have to look through that sample to
find stuff of interest.

I guess my point is, there should not be any rank-based requirement for the
implied taxon circumscription of an "Individual".

Rich

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