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

[Dean Pentcheff]

I'm going to revisit this tomorrow morning, to be able to think carefully
about the prior postings on this. But a quick reply to this posting (which
had the advantage of crossing my desk when I was painfully in need of a
distraction from what I was doing).

I think there may be a useful distinction to be made between these two cases
which match Rich's most recent cases 1 and 2+3):

1. A jar of mixed semi-identified organisms from known-to-be disjunct taxa
(e.g. two molluscan genera, a green alga, and some fish larvae).

2. A jar of one or more organisms collectively identified down to a single
taxon of any rank (e.g. a jar full of ophiuroids only, all of which may or
may not be the same species, but they're all "known" to be ophiuroids).

Without (yet) wrapping my head around this entirely, I think I agree with
Rich that we definitely find it useful to be able to search taxonomically
for higher level taxa as well as searching for species. Without being able
to do so, we are forced to ignore all instances that are not identified to
species, and that's just not a happy solution.

I've made the claim that we sometimes find it interesting to be able to
search taxonomically for (actually, to find) records that describe the
mixed-taxon case #1 above. However, without allowing a one-to-many
relationship between "Individual" and a determination, I don't see how to
accomodate it in a straightforward scheme, and nor do I think it is
necessarily a good idea to do so.

Unless a simple solution presents itself to me, I'm willing to accept the
idea that my case #1 and case #2 cannot be folded into one tidy model.

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


On Wed, Nov 3, 2010 at 3:39 PM, Richard Pyle <deepreef at bishopmuseum.org>wrote:

>
> Here's the thing:
>
> What is fundamentally different between this statement:
>
> > If someone wants to document that they have a jar full
> > of different individuals of several species taken from
> > a particular place and time then perhaps that should
> > be modeled as a separate kind of thing.
>
> ...and this statement:
>
> > If someone wants to document that they have a jar full
> > of individuals from several different populations of
> > the same species taken from
> > a particular place and time then perhaps that should
> > be modeled as a separate kind of thing.
>
> ...and this statement:
>
> > If someone wants to document that they have a jar full
> > of different individuals of the same species taken from
> > a particular place and time then perhaps that should
> > be modeled as a separate kind of thing.
>
> My point is that DwC should not single out "species" as being a special
> kind
> of Taxon, that is allowed to participate in certain kinds of relationships
> that other ranks (or or even rankless) taxa are not allowed to participate
> in.  There have been endless debates about the "specialness" on Taxacom,
> and
> to my knowledge, none of those debates have ended in any sort of consensus
> other than "agree to disagree".  Let's not "go there" in DwC.  Let's treat
> relationships with taxa in a completely rank-agnostic way.
>
> > Eventually one of the jars will be opened and
> > something will be identified to species.
>
> Maybe the "somethings" will all be identified to the same species, and
> maybe
> they'll all be identified to different species.  When we get to that stage,
> if more than one taxon is represented within what was previosuly regarded
> as
> a single Individual, then we generate new Individual instances that
> correspond to the different taxon identifications, and tag them accordingly
> with their own Identifications (maintaining, of course, the approproiate
> "derived from" relatioships among the Individuals).
>
> > They will want to relate that specimen back
> > to the jar it came from.
>
> Yes, definitely!  We certainly want to have a mechanism to address Dean's
> point about Individuals derived from Individuals, whether it be a
> parent-child sort of derivation, or something more general, is a topic for
> another thread.
>
> > However, do we want these collection sets
> > to show up in a search of species occurrence records?
>
> If we want to do a search of "species" occurrence records, then we add the
> appropriate filter to the search that limits the results according to
> dwc:taxonRank.  But we shouldn't constrain the underlying architecture to
> prevent people from doing a search of genus occurrence records, or family
> occurrence records.
>
> > I also question the utility of analyzing
> > occurrence records at clades higher than species.
>
> Really?  In the coral-reef fish world, there are some fasinating
> biogeographic patterns where certain families only occur at continental
> localities, and others that occcu only at oceanic insular localities.  When
> I do queries of, say, larval fish holdings -- where species-level
> identifications are ahrd to come by, but family-level identifications are
> comparatively easy (e.g., a jar of 50 formalin-fixed larval specimens may
> all be reliably be identified to the same family, but may be
> unidentifieable
> ot species) -- I sure would like to know if the larvae of certain insular
> families occur at contiental regions (and vice versa), because that would
> be
> informative of the likely mechanisms behind the family-level geographic
> distributions.
>
> This is just an example I came up with off the top of my head just now.  I
> seriously doubt that it is especially unique -- I'm sure there are other
> kinds of biogeographic questions one would like to ask of our collective
> data, that overalp with situations where identifications may be reliable
> only to the higher-rank level.
>
> > Species are assumed to be made up of population
> > of interbreeding individuals,
> >
> > But what is a genus vs, a subgenus, vs a tribe?
>
> Again...these debates have happened ad-nauseum (almost literally) on
> Taxacom, and I think it would be unwise to clutter DwC with presumptions
> about the outcomes of these unresolved debates (or worse, repeat the
> deabtes
> on this forum).  By its fundamental nature, DwC is accomodating to a broad
> spectrum of user needs.  Why restrict its utility to a subset of needs --
> especially when the subset can be accomodated by adding appropriate filter
> criteria (e.g., in this case, via dwc:taxonRank)?
>
> > If these higher clades were somewhat stable and
> > had some agreed on understanding then this might
> > make sense.
>
> In many groups they do.
>
> > There is no clear reasoning behind why one clade
> > is a family in Mammals and a clade of similar
> > age is a genus in Beetles.
>
> Perhaps not.  But within Mammals, or within Beetles, or within fishes, they
> might have more useful meaning.
>
> But that's not the point.  The real point is that non-trivial amounts of
> data exist in our domain that prevents reliable assessments of aggregated
> organisms to be cirumscribed within the same species-rank taxon concept,
> but
> there are many reasons why we want to be able to assign reliable
> higher-rank
> taxon identifications to these aggregates. As such, if an Identification is
> a tuple of Individual and Taxon, then not only do we want to allow
> Idetifications to link to higher-rank taxa, but we don't want to be forced
> to restricting such links to be used only in cases where we have confidence
> that the members of an instance of Individual reliably fall within a
> species-rank taxon cocnept, even if they are not labelled as such.
>
> I just re-read the preceeding paragraph, and it makes my head spin; so
> apologies in advance to the dizzy among us....
>
> Aloha,
> Rich
>
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20101103/65f0ff66/attachment.html