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.
DR
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
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@gbif.org] Sent: Monday, July 05, 2010 3:32 AM To: Markus Döring Cc: David Remsen (GBIF); Richard Pyle; Kevin Richards; tdwg-content@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
- 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.
- 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.
- 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@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org ] On Behalf Of Kevin Richards Sent: Sunday, July 04, 2010 5:44 PM To: tdwg-content@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 nomenclaturaldetails +
accepted name + parent name
Concept + relationship tables that containdetails 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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