names vs. "names" (was: Names for BioDiv Informatics)

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Tue Feb 8 13:56:26 CST 2005

Hi Nico,

Having corresponded at some length with David Remsen (and others at uBio)
off-list (in response to this, as well as previously), I've come to better
understand where they are coming from, and find myself in increasing
agreement with their approach.

Many of us have been approaching the informatics infrastructure of taxonomy
with taxonomists' blinders on.  I really believe that the "second taxonomic
impediment" (most of which consists of miscommunication & misunderstanding)
as described by Dave is largely responsible for why we are not currently
much further along in opening the floodgates of taxonomic/biological
information flow via the internet.

Like you, my greatest concern is with the *process* -- and I believe this is
also shared by the folks at uBio.  And I am increasingly of the realization
that the process must acknowledge the difference between a "taxon", and a
name that is applied (by whatever rules or standards or lack thereof) to
represent that taxon.  It is true that taxonomy depends on nomenclature.
But the point here is that nomenclature is not dependant upon taxonomy.
Indeed, name entities, in the context of Linnean nomenclature, are defined
and governed by articles set forth in Codes of nomenclature.  Taxon
(=concept) entities, on the other hand, are defined by individual
taxonomists, and are governed by no one (as it should be).

When I read Dave's description of the "three layers", it very clearly mapped
in my mind to:

Layer 1: Lists of text strings that have been used to represent organisms
(uBio's focus)

Layer 2: Code-compliant Linnean Name entities (the focus of the LinneanCore

Layer 3: TCS and related activites

I don't believe there necessarily must be any particular chronology to these
three layers -- they can all be developed concurrently.  HOWEVER!  We can
avoid a lot of unnecessary wasted time if the players in each of these
domains works closely with the others.

I wish I had more time to elaborate more on this, but it's a particularly
busy period right now...


Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at

> -----Original Message-----
> From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU]On
> Behalf Of Nico Mario Franz
> Sent: Tuesday, February 08, 2005 1:30 PM
> Subject: Re: names vs. "names" (was: Names for BioDiv Informatics)
> Dear Dave:
>    This was an insightful post. I also liked that you stressed that yours
> is a strategy for a library service. Biodiversity researchers or
> taxonomists can ill afford separating nomenclature and taxonomy any
> more than is already the case. For them, I think, a priority might be
> to build an infrastructure that can capture the taxonomic PROCESS over
> time, rather than trying to achieve comprehensive "at this moment in
> 2005" lists of names which no expert judgments and research goals
> attached to them.
> Cheers,
> Nico Franz
> "At the library/taxonomy meeting in London this past
> weekend, we made a reference to a “second taxonomic
> impediment.”  This is the lack of clear separation between
> nomenclature and taxonomy both within and between
> technological implementations.  Compilations of the two
> are based on entirely different rate-limiting steps."
> [...]
> "This separation allows the compilation of known recorded
> names, the application of the codes, and the enterprise of
> taxonomy to proceed independently."

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