[tdwg-content] Taxon Concept dilemma

David Remsen (GBIF) dremsen at gbif.org
Tue Jul 6 03:27:49 CEST 2010

Hi Rich

I think I didn't select my words carefully enough and in fact your  
description is inline with what I was saying and is more clear.


On Jul 5, 2010, at 4:44 PM, Richard Pyle wrote:

> Hi Dave,
> I agree with #1 and #2, but I can't think of an example for #3 that  
> doesn't
> fall into your #2 (assuming we're in agreement that taxonID =
> circumscription).
> You already mentioned the circumstance of a replacement name, wherby  
> the
> protonymID changes but the circumscription remains the same.  Another
> example is that a nomenclaturist might discover an older name than  
> the one
> most people use for the concept.  In that case, the circumscription  
> remains
> the same (because if the older name replaces the current name, by  
> definition
> the protonymID for the older name falls within the circumscription
> represented by the current name), but the older ("senior")  
> protonymID (and
> hence the terminal epithet) changes. Thus, in this case, the name  
> chages but
> the circumscription remains the same (your #2).
> A more commom example of what I think you mean by #3 is that the
> circumscription represented by protonymID 1 is subjectively  
> synonymized with
> the circumscription represented by protonymID 2, which results in a  
> new
> circumscription (the union of the original two) that didn't previously
> exist, and hence requires a new taxonID.  I agree that a new taxonID  
> is
> needed, but this isn't so much a case where a new taxonID is needed
> *because* a name changed.  Rather, a new concept was defined  
> (causing the
> need for a new taxonID), and as a result the name that was originally
> applied to one of the concepts (i.e., that represented by protonymID  
> 1)
> changes. Stated another way; the set of organisms included in the  
> original
> circumscription represented by protonymID 1 are now represented by
> protonymID 2.  Of course, the original set of organisms contained  
> within the
> original circumscription represented by protonymID 2 are still  
> represented
> by protonymID 2.
> But the point, is, I can't see any example of where a name change  
> *causes*
> the need for a new taxonID. I only see a (partial) name change as the
> *result* of a newly defined (combined) taxon concept.  Maybe this is  
> just
> semantics; but I would rephrase your #3 as "Two different concepts
> represented by two different names are synonymized, causing the need  
> for a
> new taxonID, which is represented by only one of the original two  
> names."
> I definitely agree with your point about the higher taxonomy  
> (including
> genus placement) not affecting the circumscription; and hence if
> taxonID=circumscription, then there would be no need for a new  
> taxonID when
> the higher clasification or genus combination changes.  But I'm not  
> sure
> everyone agrees with this.
> Rich
>> -----Original Message-----
>> From: David Remsen (GBIF) [mailto:dremsen at gbif.org]
>> Sent: Monday, July 05, 2010 3:32 AM
>> To: Markus Döring
>> Cc: David Remsen (GBIF); Richard Pyle; Kevin Richards;
>> tdwg-content at lists.tdwg.org Mailing List
>> Subject: Re: [tdwg-content] Taxon Concept dilemma
>> Is it worth listing properties that do or do not impact the concept
>> Scientific Name presents as least three cases
>> 1. The name doesn't change at all but the circumscription does,
>> warranting a concept change (a new taxon ID)
>> If you recall the case of Vireo solitarius I used in the 13
>> June mail,  the same name refers to different
>> circumscriptions.  One method for distinguishing these is
>> based on the (to borrow from RIch's
>> terminology)  "protonym count" of the material included in the
>> circumscription.    There are some problems with this (unintended or
>> temporally-based omissions) but it provides one pretty good
>> basis for making gross comparisons.
>> 2. The name changes but this, in itself, does not warrant a
>> concept change (a new taxonID) because the circumscription
>> does not change.
>> When a species is transferred from one genus to another,
>> there is no direct impact on circumscription.  Thus, if two
>> names share a common
>> protonymID,  there may not be a need to change the taxon ID.
>> In this
>> case,  we are back to 1 above.
>> 3. The name changes and this, in itself, requires a new taxonID.
>> If a taxon is renamed and the new name does not share the
>> same protonymID as the previous name, it should be given a
>> new concept
>> ID.   There may be exceptions to this (for replacement names
>> perhaps?)
>> but surely the rule of priority would only result in this
>> case if the circumscription (concept) changed.
>> Higher taxonomy
>> Is it generally agreed that higher taxonomy does not, in
>> itself, impact the concept (circumscription) and therefore
>> different classifications of a taxon are not criteria for a
>> concept identifier change?
>> - David
>> On Jul 5, 2010, at 3:53 AM, Markus Döring wrote:
>>> Rich, Kevin
>>> as one of the main supporter of the taxonID the final decision what
>>> stable piece of information it reflects to me sits with the
>>> publisher/author of the data.
>>> The problem Kevin describes is very common and comes down to the
>>> difficulty to describe what information really is stable in
>> taxonomy.
>>> The name may change, the classification, the textual
>> description, the
>>> distribution and its probably impossible to automatically
>> tell whether
>>> anything significant has changed or if only small
>> "corrections" have
>>> been done. Even for humans its a challenge to compare
>> several textual
>>> descriptions and decide whether its the same thing or not. I guess
>>> this is where some people see the conceptID to come into
>> play to give
>>> some long term stability - but I still dont see much gain
>> in another
>>> ID if you cannot tell what pieces of the information behind
>> that ID is
>>> stable over time. I still believe with scientificNameID and
>> taxonID we
>>> are well equipped to deal with our data. I tend to think
>> someone who
>>> publishes the data should have a good thought about how they assign
>>> and change taxonIDs and try to announce what they consider stable,
>>> what is versioned or what can change anytime without changing the
>>> meaning, i.e. the ID. But I would assume this might be
>> different for
>>> different databases focussing on different aspects of taxonomy in
>>> particular.
>>> For purely automatically aggregated data in Checklist Bank
>> I decided
>>> to assign stable taxonIDs to entire lexical group of names that at
>>> least have one qualified name, i.e. with proper authorship. The
>>> classification, the spelling and authorship of the preferred,
>>> representive name for that group might change - but at
>> least you have
>>> some definition of stability which is really hard to define.
>>> For lexical name groups that only contain bare canonical names I am
>>> assigning volatile IDs right now, as these might
>> dramatically change
>>> with more knowledge about them. I dont know if this could
>> also apply
>>> to Kevins problem - do you treat the same, qualified name
>> in multiple
>>> concepts? If thats the case then surely you need something else to
>>> define a stable taxonID.
>>> Markus
>>> On Jul 5, 2010, at 9:26, Richard Pyle wrote:
>>>> This is why I'm very uncormfortable with the entire notion of
>>>> "taxonID".  The main reason I'm pushing so hard for
>>>> taxonNameUsageID's (ala GNUB) is that these are the
>> "atoms" (as Dave
>>>> R. calls them) of both nomenclature *and* most existing concept
>>>> definitions.  If we can get permanent and widely
>> shared/re- used IDs
>>>> on these "atoms", then we can assmble the complex molecules from
>>>> them.  Someone's notion of a taxon concept then becomes a set of
>>>> TNUID's.  I have mixed feelings about branding these sets with
>>>> permanent GUIDs; but if we did, this is what I imagine
>> taxonID in DwC
>>>> would (ultimately) represent.  If we want to archive the sets for
>>>> posterity, then we can certainly brand them with IDs.  But
>> I tend to
>>>> think these can instead by dynamic services, that assemble
>> the sets
>>>> either algorithmically, or through the fingertips of experts.
>>>> So...I guess before we do anything, we need to get a
>> common sense for
>>>> what is intended to be represented by taxonID.  I suspect
>> my own view
>>>> is not shared by all (or even most).
>>>> Rich
>>>> From: tdwg-content-bounces at lists.tdwg.org
>>>> [mailto:tdwg-content-bounces at lists.tdwg.org
>>>> ] On Behalf Of Kevin Richards
>>>> Sent: Sunday, July 04, 2010 5:44 PM
>>>> To: tdwg-content at lists.tdwg.org
>>>> Subject: [tdwg-content] Taxon Concept dilemma
>>>> Hello all,
>>>> I have an issue that I would like some comment on…
>>>> We have some data that covers Taxa, Names and Concept
>> relationships.
>>>> Eg
>>>> -          A Taxon table that contains the nomenclatural
>> details +
>>>> accepted name + parent name
>>>> -          Concept + relationship tables that contain
>> details about
>>>> the name + references where the name has been used in a taxonomic
>>>> sense (ie not nomenclatural information) – this is specifically a
>>>> link between the Name and a Reference
>>>> We have fairly permanent Ids for the Taxon Name
>> (nomenclatural) and
>>>> the Concepts, but I now what to consider the ID to cover the whole
>>>> Taxon (ie the Nomenclatural data + taxon rank + parent name +
>>>> accepted name, etc, as “we” understand them).  (Probably
>> equivalent
>>>> to the taxonID in Dwc)
>>>> The problem is this tends to be much more dynamic data –
>> ie, in this
>>>> particular case we have aggregated data from a variety of
>> providers
>>>> and are in continual revision of this data - as we revise the data
>>>> the details such as the accepted name may change – this
>> troubles me a
>>>> bit, because this could be seen as fundamentally changing the
>>>> definition of the object behind the taxonID.  However, I
>> suspect this
>>>> is a common case that people find themselves in – ie
>> revision/tidying
>>>> of aggregated datasets must be quite common.
>>>> I would prefer to NOT change the taxonID every time we revise that
>>>> data (taking the angle that these changes are corrections,
>> so are not
>>>> changing the object itself).
>>>> Should it be OK to have an object type like this, that is
>> likely to
>>>> change, but keep the ID permanent for it – ie accept that
>> some object
>>>> types are quite dynamic?
>>>> The only other option is to maintain a hideous version
>> audit trail,
>>>> that probably hinders the use of the data more than it
>> benefits the
>>>> end user by providing “stability”.
>>>> Any thoughts?
>>>> Kevin
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