More GBIF questions (was: ITIS)

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Wed Jun 23 13:26:40 CDT 2004

So many good TAXACOM threads; so little time....

I was off email yesterday (coincidentally, I was upgrading the OS on our
DiGIR provider server that played a role in starting this thread), but I
see some good discussion has followed.  Some comments below.

Wolfgang Lorenz wrote:

> On a side note, two questions:
> 1.) Obviously, since the Rio Convention there have been 
> increased efforts (GBIF, Species2000, UBIO, etc.) to address 
> and solve the 'names problem' (part of the 'taxonomic 
> impediment'), but it seems to me that the logic central role 
> of the Codes (IZCN, ICBN, etc.) has received too little 
> attention, so far.

I tend to agree.  Indeed, in my grand vision of how to solve the
informatics of nomenclature, ICZN/ICBN should play a central/leading

> How do GBIF& allies deal with this part of the 'names 
> problem', which - it seems to me - could be reduced  to an 
> unavoidable minimum if the International Commissions would 
> receive more support from those who have an interest in 
> building global web-based databases, name servers or search 
> engines (even incl. 'Google' etc.).

I COMPLETELY agree with you!  I know that ICZN is proactively trying to
fortify its standing, and I would like to see the taxonomic community
rally around it (and the other codes as well).  These codes stand as a
shining example of international acceptance and conformity in science,
and are incredibly fundamental to all of biology -- yet they are often
taken for granted by the community at large.

> 2.)  >>... The time has CLEARLY come to coordinate these 
> efforts, synergize the work that has already been done... << 
> My impression is that a lot of funding is going to IT 
> solutions while potential content providers are asked to 
> contribute for free to everyone's advantage (see previous 
> discussions).  Any encouraging news on that issue?

My only (admittedly weak) response to that is that scientists (usually)
do what they do in order to add to the body of knowledge available in
the public domain; whereas IT professionals do what they do in order to
make money.  Also, a number of the major content-creation efforts have
been funded by federal dollars. But that side-steps the real issue, on
which I believe that we are in complete agreement -- that the content
providers (like the codes) are under-appreciated, generally, and need
more robust support.  Speaking as a taxonomist who earns his living
doing mostly IT stuff, I can say with great certainty that the taxonomic
expertise required to research original descriptions to generate
reliable content is a VASTLY rarer (and more valuable) commodity than
the skills required to create the IT solutions to these problems.

Rod Paige wrote:

> I suspect the way forward is to adopt the tools and mindset 
> of the Open Source software community. Have open databases of 
> names that people can annotate (i.e., report "bugs"). The 
> bugs themselves can be seen by (and commented on by) 
> everybody. Hence, the error mentioned by Richard Petit (the 
> type species of the genus Cancellaria being attributed to 
> Pilsbry, 1940 instead of to Linnaeus, 1767) would be visible 
> for all to see (and comment on).

To which I respond, Yes, YES, and YES!!!   This is *exactly* how I think
the way forward should be.  Doug Yanega has made similar arguments on
this and other lists, which is why I tried to bait him into this

Meredith Lane wrote:

> More important to this discussion, however, is your last 
> question "who is to do this (using databases in innovative 
> ways to sort out nomenclature)"?  Seems to me that the answer 
> is another question: Who has always done the work of sorting 
> out nomenclature?  It's just that now there are some new 
> tools to help (and speed up the process), which it seems a 
> good idea to use.

To which I respond, again, Yes, YES, and YES!!!  We need to work
towards, as Meredith describes it, a "meta-GSD" (I would prefer "GTD",
as the need applies to all ranks of taxonomic names; not just species).
This doesn't mean that ITIS, Species 2000, IPNI, Catalog of Fishes,
etc., etc. should be thought of as obsolete -- absolutely not!  What it
does mean is that technology and the internet provide us with tools that
would allow all of these "primary GTDs" to synchronize with each other
where they overlap in scope, and more importantly, to propagate updates
and corrections to each other automatically and *instantly*.  When you
study the technological, political, and sociological landscape, the most
realistic path to this (from my perspective) would be for a high-clout
collaboration (e.g., between GBIF, TDWG, and the IC_N commissions, and
possibly SEEK) to serve as a "hub" around which all of the data content
providers could rally.  The taxon "names" data (harking back to my
earlier "Part 1" post that lacked a Part 2) should transition into the
public domain, with free public accessibility and robust feedback
mechanisms; and the aforementioned content providers (ITIS, SP2K, IPNI,
etc.) should be seen more as primary (but not exclusive) editors of the
names data, and perhaps more importantly, serve more as taxonomic
*CONCEPT* providers, all plugged into the public domain names resource,
and all following the lead of the SEEK effort to develop tools for
managing taxonomic concepts. A critical aspect of all this is that the
people who have slaved for so long thus far to generate the existing
content absolutely NEED to be adequately acknowledged for their
extremely important contributions.

The logistical cornerstone of all this comes back to the idea of GUID's
and (dare I say it in public?) the "Registration" of taxonomic names.
This is all basically the same rant I had planned to burden this list
with in the previous thread, and this thread has given me the
opportunity (and the inspiration) to revisit it.

Meredith Lane also wrote:

> At present, we 
> estimate that *on average* for every valid, accepted 
> scientific name, there are two synonyms. This means that 
> there are 3 X 1.75 million species names out there that need 
> to be listed, sorted and "cleaned up".

Indeed; but it goes beyond this.  We also have to think about the
estimated 10-30 million or so names that have yet to be established for
the as-yet undescribed species of the world.  It would be a real shame
if the historical average of 3 names per later-accepted species
continued (do we really need 100 million names for 30 million species?)
One way to reduce (certainly not eliminate) such over-description is to,
as Meredith has already described, provide a service to access all
existing names. It is this goal about which I preach.

Mary Barkworth wrote:

> The operative phrase here seems to be "*will* be made 
> possible". Having just gone to the GBIF Web site and looked 
> under standards, many seem to be under development. 

Yes, but this is a reason to compliment and thank GBIF; not scorn it.
That such tools are still in the development stage -- and not yet a
functional reality -- can be blamed primarily on the quirky, somewhat
eccentric nature of the taxonomic community; not on any sort of failure
on the part of people who have tried to get us where we need to be (like
ITIS, SP2K, IPNI, GBIF, etc.)  I mentioned in an earlier post that I
could "just smell it" that we were close.  What I meant by that is that
I am seeing all around me a convergence of the here-to-fore somewhat
disconnected data resources.  I'm not just talking about ITIS/SP2K/IPNI,
etc.; I'm also talking about specimen data, made available online
through the wondrously elegant (and wholly under-appreciated) DiGIR
protocol.  No, we're not there yet.  But if/when we do get there, it
will be thanks largely to the passionate efforts of the people behind
the ITIS/SP2K/IPNI/GBIF/SEEK/uBIO/CoF/etc/etc/etc efforts.

Enough....for now....


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

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