[tdwg-content] Taxon Concept dilemma

[Richard Pyle]

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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