[tdwg-content] Taxon Concept dilemma

Hilmar Lapp hlapp at nescent.org
Mon Jul 5 16:48:08 CEST 2010

Actually this sounds a lot similar to ontology evolution best  
practices. For example, for OBO ontologies*, changes of a class label  
do not trigger an ID change. Changing the class definition (except for  
typographical corrections), however, does, even if the label stays the  
same. I.e., the ID is for the definition, not the label (term name).  
If classes are moved to a different parent, it will trigger an ID  
change too because it will inevitably mean a change of the definition.

Just a thought that occurred to me - not sure this is useful here :-)


(*) I don't know actually whether such ontology engineering best  
practices exist for the TDWG ontologies too.

On Jul 5, 2010, at 9:31 AM, David Remsen (GBIF) wrote:

> 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
>>> Please consider the environment before printing this email
>>> Warning: This electronic message together with any attachments is
>>> confidential. If you receive it in error: (i) you must not read,
>>> use, disclose, copy or retain it; (ii) please contact the sender
>>> immediately by reply email and then delete the emails.
>>> The views expressed in this email may not be those of Landcare
>>> Research New Zealand Limited. http://www.landcareresearch.co.nz
>>> _______________________________________________
>>> tdwg-content mailing list
>>> tdwg-content at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content

: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

More information about the tdwg-content mailing list