[tdwg-content] tdwg-content Digest, Vol 20, Issue 17

Wed Nov 3 21:26:37 CET 2010

Hi Dean,

I agree with you -- but the question is, would you want to require that your
"rough sorts" create Individual instances on a 1:1 basis with taxa at the
rank of species or lower?  I was using the "Animalia" example as an extreme
case.  In the real world, it's more like you describe.  That is, it's
usually realtively easy, and extremely useful, to pre-sort such lots down
tot he level of, say, family, and then generate instances of Individuals
accordingly.  But the implication of the "species" requirement would be that
you'd have to guestimate how many distinct species are represented in the
lot, then generate an Individual instance for each one of them.  This, I
think, would not be so easy in many cases.

I guess in your case you've divided Indentifications into two subclasses:
"real", and....err...."artifical"? "temporary"? "provisiolnal"?

I'm not sure that's a solution that will work for most data
providers/consumers (i.e., defining subclasses of Identifications), so it
may not be ideal to "go there" in DwC.

I guess what I'm still struggling with is why species-level identifications
are somehow fundamentally different from higher-rank identifications
(fundamental enough that the scope of the Individual class is constained by
them).  Especially when it's easy enough to filter out the
higher-than-species-rank Identifications in cases where you want to exlcude
them.

I think what we're circling around is something to the effect of: "An
individual should be circumscibed/scoped in such a way that it can be
Identified to a single Taxon".  I'm just saying there should be no
constraints on the scope of that taxon.

For example, let's take the example of a lot that includes ophiuroids,
gastropods, isopods, algae, and fish larvae.  I think there is consensus
that we would *not* want to establish a single Individual instance that has
multiple and concurrently legitimate Identification instances applied to it.
In other words, we don't want an Individual instance that has one
Identification instance for "ophiuroid", one for "gastropod", one for
"isopod", one for "algae", and one for "fish", all simultaneously and
legitimately applied to the single Individual instance. Stated another way,
we don't want to allow for an Identification instance to apply to only part
of an Individual -- an Identification instance should apply to the *entire*
Individual.

So, in this example, we either would want no Identification instance at all
applied to the aggregated lot, or if we really wanted an Identification, the
best we could do (depending on the kind of algae) would be "Eukarya".  But
if you want to acknowledge that there are five different subsets within that
lot, then you generate five "child" Individual instances, each of which has
a single legitimate Identification instance to its respective higher-rank
taxon.

So, I think what we're really after here is that, when there are multiple
Identification instances linking an instance of Individual to more than one
distinct Taxon, these should always be mutually exclusive -- they should
never be simultaneously legitimate (i.e., they should never apply to
different "parts" of a single Individual instance).

Looking at the big picture....we seem to agree that the maximum scope of an
Event instance in terms of place is "Planet Earth" (for now, anyway); the
maximum scope for time is "any window of time since there has been life on
the planet" (i.e., up to 4 billion years or so).  We have discussed the
ideal of establishing scoping metadata for both place (e.g.,
coordinateUncertaintyInMeters, coordinatePrecision), and Time (not yet
defined in DwC).  I think the same logic should apply to Indetifications.
That is, the scope of Taxon that can be assigned to an Individual via an
Identification should span anything from "forma" (or whatever the most
precise taxon identification there is),  all the way up to Domain (or even
simply "Life").  DwC:taxonRank already serves as a rough guide to defining
the scope of any particular taxon Identification (with apologies to
Nico-the-other-one).

So the point is, I think the general rule for DwC should be "maximum
flexibility for allowing breadth of usage, with sufficient metadata to allow
for filtering to more restrictive usage".

I'm guessing that most of that doesn't make much sense....sorry for that.

Aloha,
Rich

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: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html

________________________________

	From: tdwg-content-bounces at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Dean Pentcheff
	Sent: Wednesday, November 03, 2010 9:52 AM
	To: tdwg-content at lists.tdwg.org
	Subject: Re: [tdwg-content] tdwg-content Digest, Vol 20, Issue 17

	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 (RT 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 at gmail.com
	dpentche at nhm.org

	On Wed, Nov 3, 2010 at 11:53 AM, Richard Pyle
<deepreef at 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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