[tdwg-content] tdwg-content Digest, Vol 20, Issue 17
Steve Baskauf
steve.baskauf at vanderbilt.edu
Thu Nov 4 17:03:05 CET 2010
Comment inline
Dean Pentcheff wrote:
> 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.
For clarification, in cases like #1, we ARE allowing one-to-many
relationships between "composite" Individuals and Identifications as
long as those Identifications represent differences of opinion about the
common taxon, or refinements to a lower taxonomic level (e.g. I'm not
capable or don't have time to determine the lowest taxonomic level
common to all of the biological individuals in the jar, but later I am
able to find that out). What we AREN'T allowing is for subsets of the
composite "Individual" that belong to different lower level taxa to be
identified to those taxa without first separating them into different
Individuals. I think I'm stating the principle that Rich laid out
correctly.
>
> 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.
This is where having something like individualScope would help. There
could be one model, but it would require (I think) a metadata term to
differentiate between case #1 and case #2.
Steve
>
> -Dean
> --
> Dean Pentcheff
> pentcheff at gmail.com <mailto:pentcheff at gmail.com>
> dpentche at nhm.org <mailto:dpentche at nhm.org>
>
>
> On Wed, Nov 3, 2010 at 3:39 PM, Richard Pyle
> <deepreef at bishopmuseum.org <mailto: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
>
>
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--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
http://bioimages.vanderbilt.edu
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