[tcs-lc] Demonstration Dataset

[Richard Pyle]

All:

I spent this evening re-examining the TCS "Demonstration Dataset" on the TCS
Wiki:
http://www.soc.napier.ac.uk/tdwg/index.php?pagename=TCSAndTheLinneanCore

To all the non-wiki folks on this list, I urge you to take a look at this
page, and in particular, download and review the "Timeline" Powerpoint file
(or re-review it if you've looked at it previously).  I would like to
commend whoever created this file, as it very clearly and graphically lays
out a timeline of hypothetical nomenclatural changes, and serves as an
excellent foundation for discussion, to help make sure we're all on the same
page.  Henceforth, I will (whenever possible) draw my hypothetical examples
from this file, rather than create them ad-hoc.

I had looked at this file back when it was first announced, but I didn't
have time to scrutinize it.  I'm glad that I took the time this evening to
review it in more detail, as it helps me understand the TCS perspective in a
nomenclatural context.

I have a couple of questions/comments about the PPT file, which might help
spark/focus additional discussion. My references to slide numbers refer to
actual slide numbers when viewed in Design mode -- not to animation steps
(often several per slide).

Slide 1:
 - Probably trivial, but do the little symbols represent only those
particular specimens examined by each "in" author -- or do they represent
the full scope of individual organisms (living, recently dead, and
yet-to-be-born) on the planet that each author would have included within
each concept circumscription?  I'm assuming the latter, because it is very
unlikely that each author would have access to the same particular set of
specimens.  But then again, from the "Demo_v2.xml" file, it looks like the
symbols represent actual vouchered specimens. Like I said, probably trivial,
but I just want to make sure one way or the other.

Slide 3:
- Need to be really careful with the words "valid" and "invalid" (side-box
for Pyle 1990).  Those words mean different things to different people and
different nomenclatural codes.  In this case "bea" and "cea" would have been
treated by Pyle as incorrect spellings, not as "invalid" names; and "beus"
and "ceus" would considered "correct" spellings of the *same* name (at least
from a zoologist point of view).

Question to Botanists: In this example, would you consider "Aus bea" and
"Aus beus" as "different names", or "different spellings of the same names"?

Slide 4: Whenever a new Code-compliant original description is published,
two concept records are simultaneously created: one that refers to the
concept circumscription intended by the Author ("Original" concept), and the
other is an "empty" concept automatically created to represent the name by
itself, without any specific implied concept circumscription ("Nominal"
concept).  In the PPT file, you provide an implied "link" between each pair
of "Concept" records via the "ID" attribute (e.g., "cl1" and "cl1n"; "cl2"
and "cl2n").  I'm 99% sure that you don't intend the actual ID value to have
embedded within it some sort of self-evident link between an Original
concept and its corresponding Nominal concept -- but could you please erase
my 1% uncertainty with an explicit confirmation of this?

Slide 10: The Codes (at least the ICZN code) would not consider the
gender-corrected "Aus beus" as a "replacement name" to "Aus bea".  Indeed, I
don't think any zoologist would think of these as different "names" -- but
rather as different spellings of the same "name". I don't believe the Pyle
1990 act of noting the corrected spelling would represent either an
"Original" concept, or a "Nominal" concept.  More of a "usage" instance.
Hence, I am either uneasy about: a) creating two different concept instances
for each spelling correction; or b) the way that "Original" and "Nominal"
concept types are defined.  Perhaps it would be appropriate to create only a
new "Nominal" concept for each of the two misspelled names (not sure I would
agree with this), but to me, what distinguishes an "Original" concept from a
"Nominal" concept is that the former has a specific implied concept
circumscription, whereas the latter is purely nomenclatural.  Pyle 1990
never made any assertions about concept circumscriptions for either name,
and therefore should not have an "Original" concept associated with either
(by my understanding, anyway).

On the other hand, if Franz had discovered that Xus Pargiter 2003 was
preoccupied by Xus Smith 1950 (thus Pargiter's "Xus" being a junior homonym
of Smith's "Xus"), then published the replacement name "Zus", it *would* be
appropriate to create a new "Original" concept and a new "Nominal" concept.
But this is a special case, and there are botanical/zoological differences
here (with respect to basionym treatment).

Slide 12: You illustrate "Xus beus" as having a new "Original" concept and
new "Nominal" concept.  This the botanical perspective, but not the
zoological perspective.  There's been a general assumption that the
Zoological perspective would change to accommodate the botanical
perspective, but I think it depends ultimately on how the names data is
ultimately modeled within TCS (i.e., as attributes of Concepts, or as
objects to themselves).  Needs more discussion.

Slide 14: I had been under the impression that "Original" concept was
restricted to Basionyms, true "replacement names", and *perhaps* new
combinations (if the botanists win) -- but not alternate spellings. However,
I get the impression that here a new "Original" concept is created whenever
there is a novel "NameString" (specific string of characters).  Also, I
thought they were created only in cases where an actual concept
(circumscription of specimens) was asserted -- not for purely nomenclatural
acts (without any concept implications).

Slide 15: Because Pyle never made any statements about the
shape/size/position of the concept circumscriptions associated with the two
names he was correcting, I don't see why there should be any "SEC Pyle"
instances.

- Also, I think there is an error in the box for TCrev19 -- shouldn't that
be "Aus cea Fry 1989", instead of "Aus cea Archer 1965"? Also, what's with
the "BFry"?  Is that a botanical author code?


Regarding the "Demo_v2.xml" file:

- Why don't any of the Species-rank names have Relationships?  Are there no
reciprocal "is type of" or "is child of" relationships?

- Does <Relationship type="has type"> mean "Has type species."?  If so, I
understand why cl1 has this relationship, but why is it repeated for ca1,
cf1, ct1, etc.  Is this only because these are "Revision" concepts, and in
each case the author re-affirmed the type species of the genus?  Or will
*all* concept instances of Aus L. 1758 contain a copy of this connection
with the type species?  This is an example of something that is a property
of the *name* "Aus", not of every single Concept instances of "Aus".

- For TaxonConcept cp5 (original concept of "Xus beus (Archer 1965) Pargiter
2003"), there are "Relationships" with ct2 and cf3.  Does their
representation here (instead of as a RelationshipAssertion)?  Is this
because relationships stated by Pargiter 2003 himself about his own concepts
belong within his TaxonConcept instance, and RelationshipAssertions are for
"third-party" relationship assertions? (Is this effectively the definition
distinction between Relationships and RelationshipAssertions? I.e., between
intra- and inter-publication relationship statements?)


General question about "Original" vs. "Nominal" concept:
Intuitively, it makes sense to me that if you're going to go to the trouble
of automatically creating a Nominal Concept for every Original Concept, then
the Nomenclatural information should be embedded within the "Nominal"
version, and that should be the unit of exchange for nomenclators.  It seems
intuitive to me that a "Nominal" concept would be a container for "all the
name stuff".  I think an "Original Concept" should be used for a true
concept -- the concept that was asserted by the Author(s) of the original
description of the name.

Also, we need more discussion about what sorts of "name changes" should
warrant the creation of a new "Original" concept and/or "Nominal" concept.

If the TCS group would find it useful, I could offer a real-world set of
examples in fishes that offer a set of particularly thorny nomenclatural
issues.  I would begin with a PPT file similar to the abstract one in
"TimeLine", except I would replace it with real values. Would that be
worthwhile?

One final note:  I may be the only one to recognize the irony, but anyone
who really understands my Taxonomer model should recognize that the approach
taken in Taxonomer is congruent with the position that I am currently
arguing *against*.  If I lose this debate, then Taxonomer wins because it
will be much closer in fundamental structure to what Jessie/Nico are arguing
in favor of (i.e., that "Original Concepts" can be used as a representative
"handle" to track nomenclatural information). At the very least, this should
confirm that the logical foundation for my position in this debate is pure!
:-)

Aloha,
Rich

P.S. I've added the relevant bits above to the Wiki at:
http://www.soc.napier.ac.uk/tdwg/index.php?pagename=TCSAndTheLinneanCore

Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://www.bishopmuseum.org/bishop/HBS/pylerichard.html