[tdwg-content] DwC taxonomic terms

[Richard Pyle]

Greetings,

I only just now subscribed to this list, and I apologize for not coming into
the discussion earlier.  I've just finished reading this complete thread in
the archives, and I want to make a few comments while it's frseh in mind (as
fresh as one's mind can be at 3:30am). I will expand (expound?) some more
tomorrow.

I understand the desire to stick with familiar terms; but in the case of
taxonomy, "familiar" can be a bad thing.  Several critical words (e.g.,
"name", "concept", "taxon", etc.) mean slightly (sometimes not so slightly)
different things to different people.  As such, relying on the term itself
to inform users of what the term represents (without referring them to the
definition) can lead to disparate applications of the term in provided
datasets. In my mind, it's better to use a less-familiar term that requires
users to consult the definitoion, to reduce the chance of misapplication;
rather than save the end user the trouble of consulting the definition by
trying to use a familiar term that is definied differently by different
people.  Too much opportunity for a person to jump to the wrong conclusion
about what content is expected in association with a particular term.

One of the biggest complaints I had about TCS 1.0 was the distinction
between "name" and "concept".  It was always my intent to try to suppress or
eliminate this distinction in TCS 2.0; so I'm less eager than Stan is to
cling to the terms as they exist in TCS 1.0.

Don't get me wrong -- I have been wrestling with data modelling of taxon
names and taxon concepts since about 1990, so I am *VERY* familiar with what
people mean when they distinguish names from concepts.  But at an
informatics level, I think Markus was absolutely right when he defined the
"usage" as the most granular (and convenient) data object you can use to
refer to either taxon concepts or taxon names.  Our community has struggled
with what to call this "thing" for a long time.  Walter called it "Potential
Taxon".  I first started calling it "TaxonRef" (short for "Taxon Reference",
based on pretty-much the same logic Dave Remsen alluded to).  Then I started
calling it "Assertion" (sensu:
http://systbio.org/files/phyloinformatics/1.pdf). James Ytow had something
similar called "Appearance"; but after years of conversations with him, we
finally established that his "Appearance" was something slightly different
(actually more granular).  Others have called it a "Treatment" or "Taxon
Treatment".

In developing GNUB, we finally settled on "TaxonNameUsage", because that was
both explicit, and generic (and also wouldn't likely be confused with
anything else in our field).  Yes, it's cumbersome, but I think it
represents the right balance of self-describing but without potentially
disparate preconceived notions.

The definition is the usage or application of a taxon name within a
particular documented context.  "Documented context" is mostly published
literature, but can also include any other forms of documentation, such as
correspondence, unpublished manuscripts, single-copy documents such as field
notes, specimen identification tags, etc.  This is the core unit of
information that GNUB will index and assign shared GUIDs to.  I am
absolutely convinced that it will become the standard currency for
referencing taxon names and concepts.

The point that Markus was trying to make is that a TaxonNameUsage instance
carries both an implied (or explicit) taxon concept circumscription, and
also the nomenclatural metadata associated with how that circumcription was
labelled (i.e., the "name").  This doesn't mean it's ambiguous, because it
is what it is: a discrete Usage Instance.  The difference is in what set of
metadata is harvested from the identified Usage Instance. For example,
consider:

1. Aus bus Smith 1950 sec Smith 1950
2. Aus bus Smith 1950 sec Jones 1960
3. Xus bus (Smith 1950) sec Brown 1970

We have one species epithet, and three TaxonNameUsage instances (TNUs).  #1
is the original taxonomic description of the species "bus", which was
originally combined with the genus "Aus".  This has both a name part (Aus
bus Smith 1950), and an implied taxon concept (sec Smith 1950).  If I
resolve any of these TNUs for nomenclatural information, I get a genus name,
species epithet, an author, and a year.  If I resolve them for taxon concept
information, I get all the name bits plus the according to stuff ("sec"
stuff); plus any other taxon concept information that is resolvable through
that particular usage instance. Thus, whether you're interested in the
nomenclature or the concept circumscription, you get both (explicitly) from
referencing a TNU instance.

I'm too tired to write any more now, but I plan to expand on this tomorrow,
with specific reference to the DwC terms and in the context of GNUB.

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
  and Associate Zoologist in Ichthyology 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