[tdwg-content] Producing a global taxon register (was: ITIS TSNID to uBio NamebankIDs mapping)

Richard Pyle deepreef at bishopmuseum.org
Sun Jun 5 19:14:35 CEST 2011

> * a GTR - global taxon register - is something else entirely, at least
> if the term is taken literally. It would be indispensable if the purpose
> "to index all usages of all names in all sources" is to be realized.

Yes, that would be nice.  But as Tony indicated, that would be impractical
for the foreseeable future.  Especially when you consider that "all sources"
encompasses not only "all publications" (including popular books and
magazine articles, newspaper articles, etc., etc.), but also all unpublished
sources (museum specimen labels, field notebooks, personal correspondence,
etc., etc.).  The GNUB model is designed to accommodate any & all of these,
but a proactive attempt to populate it to that extent would represent an
unrealistic amount of effort.

However, an enormous benefit would be achieved it a select subset of "all
usages of all names in all sources" was targeted.  For example, the first
priority for populating GNUB will be:

> a complete nomenclatural index
> (inventorying all nomenclatural acts), 

And the next step would be:

> moving towards
> lists of currently accepted names 

That is, capturing the specific usage instances for each that reflect a
modern taxonomic landscape.  Of course, there is more than one
interpretation of the "modern taxonomic landscape" (i.e., different opinions
about how to structure the HCAL). Therefore, you need a spectrum of modern
usage instances to capture all of the popular HCAL perspectives.

> Names and taxa are quite different things and they are interconnected
> in a complex way.

I don't think that the interconnection is all that complex.  In the same way
that nomenclature and biology intersect at the type specimen, names and taxa
intersect at the Taxon Name Usage instance.  The analogy is reasonably good.
A scientific name is "anchored" to the biological world through the type
specimen. Likewise, a taxon concept is anchored to a name through a taxon
name usage instance.  Not all taxon name usage instances rise to the level
of an explicit or implicit taxon concept definition.  However, all taxon
concept definitions exist in the form of a Taxon Name Usage instance.

The problem, as Tony alluded to, is that TNU instances are so abundant that
it can be overwhelming to contemplate the TNU universe in its entirety.
Dave Remsen referred to TNUs as the "individual molecules" of taxonomy. When
we look at a physical object, we don't think of it in terms of an assemblage
of individual molecules; we abstract it to the entire object.  This is why
we have so many databases that focus on the HCAL -- it's much more direct to
capture the entire object (in this case, taxon concept), than to enumerate
all of the molecules that comprise it.  

But unlike physical objects and their constituent molecules, there are
"special" TNUs that stand out from all the rest.  Capturing a few of these
"special" TNUs will allow us to get most of the benefit in representing the
parts of the taxon concept we're interested.  As already noted, these
"special" TNUs include all the relevant nomenclatural acts for all of the
names that have been associated with that taxon concept, as well as the main
concept definitions (e.g., published taxonomic treatments that may or may
not carry nomenclatural acts with them).  In other words, unlike trying to
describe a physical object by enumerating its individual molecules, we can
capture the majority of our interest in taxon names and concepts by
enumerating only a small fraction of the TNUs (i.e., the aforementioned
"special" ones).


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

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