GUIDs for Taxon Names and Taxon Concepts

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Mon Nov 14 13:18:57 CET 2005

Thanks, Roger.

Yes, I was waiting for commentary on my use of "explicitly implied"....

> "explicitly implied"  is actually contradiction in terms:

Agreed -- but I couldn't think of a different term to express what I meant.
Rather than grasping for alternate expressions, let me explain it with an

Suppose a book made clear and unambiguous references to "Ditrichum
cornubicum Paton".  And then, in the text account directly underneath, there
is a paragraph that makes reference to "D. cornubicum".  Because this has an
abbreviated genus name, it is technically not the same character
text-strings as "Ditrichum cornubicum".  However, the contextual placement
represents an "explicit implication" (oxymoron that it may be) that "D." is
intended as an abbreviation of "Ditrichum".  It is "explicit" in the sense
that it is unambiguously following traditional taxonomic practice of genus
abbreviation.  It is "implied" in the sense that nowhere did the authors
actually state that "D." is intended as an abbreviation for the genus name

But the point is, even though "Ditrichum cornubicum" represents a different
character string from "D. cornubicum", they would not constitute different
"NameStrings", and hence would not warrant different NameUsage GUIDs. There
are, of course, similarly "explicitly implied" abbreviations for trinomials.

Another example would be if a documentation instance (e.g., a book) listed a
species heading as "Aus (Xea) bus", where "Xea" is intended as a subgenus.
If, in the body of the text underneath this heading, the name "Aus bus" or
"A. bus" is used, it would be "explicitly implied" that these are intended
as short-hand abbreviations for the "full" NameString, "Aus (Xea) bus".
Thus, only one GUID for this documentation instance.

There are other examples as well, and all introduce *some* degree of
ambiguity -- but as I said before, NONE of the solutions are completely free
of ambiguity.

> I don't actually see a great deal of disagreement here.
> We are debating between only two alternatives.

Really??  Which two?  I assume you mean "one kind of GUID" for taxon
objects, vs. "two kinds of GUIDs".  But earlier Rod Page had proposed three
different "levels", with GUIDs for all three.  Others seemed to like to
three-level approach, but some slightly re-defined what the three levels
ought to be.  I pointed out at least 8 different "units" of a name, not all
of which could be unambiguously pidgeonholed into either a "TaxonName"
object or a "TaxonConcept" object. You advocate two kinds (levels? types?
domains?) of GUID for taxon objects (i.e., Name & Concept).  Personally, I
think the ultimate goal should be as you describe: separate GUID
domains/kinds/types for TaxonNames vs. TaxonConcepts.  But Rod Page and
others contributing to this thread have convinced me that this might be
reaching for too much at this stage of the game.  Thus, I am comfortable
with the idea of establishing one domain/kind/type of GUID within the
taxonomy realm, that is the most flexible and unambiguous of them all, and
which can serve as a "stepping-stone" and/or surrogate to a future
informatics world where we have an unambiguous distinction between a
"TaxonName" object and a "TaxonConcept" object. Importantly, establishing
GUIDs for usage instances now does not carry the risk that they will be
rendered useless in the future, because I think there will always be value
in identifying unique NameUsage instances.

> Perhaps what we should do is each put together a page on the
> wiki expounding either of the approaches. It will be easier
> for some one coming along later to get up to speed on
> the arguments and add to them. We then have both cases clearly
> stated and we can see which one a consensus builds around.

I agree with this, and took a hasty first stab at it with "Scenario 5" on
the page you created:

If I can find time, I'd be happy to expand it on a dedicated page, using a
real-world example (maybe a PDF excerpt of a representative documentation
instance).  I'd be happy to provide the PDF example, if you wish.

> This way we can move on to other stuff without having
> to make a decision on this one right now.

I don't think anyone is being prevented from starting a new thread of
discussion -- that can happen anytime independednt of this discussion.

> I'll probably not get my page finished till later in the
> week as I have other commitments - but certainly by Friday.

O.K., if you pick a real-world PDF example that we can both model, I'll
follow whatever template you create.  Or, if you'd like me to provide a PDF
real-world example, I can easily do that as well.


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

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