[tdwg-content] [Re: [tdwg-tag] class design, generalization, L(O)D] [SEC=UNCLASSIFIED]

[Steve Baskauf]

Paul,

What you have described here is actually very close to what I have asked 
for as the definition of Individual  
(http://bioimages.vanderbilt.edu/pages/full-model.jpg for the 
diagrammatic view, defined at 
http://code.google.com/p/darwincore/issues/detail?id=69 , comment 10).

Paul Murray wrote:
> ...
> So, a taxonomy of "Individual". Your use cases seem (to me) to be:
>
> * An individual is a thing that may have several specimens (tokens) taken from it, potentially from several different CollectionEvents.
>   
Except that tokens need not only be specimens, they may be anything that 
provides evidence that the Occurrence happened.  There may also be no 
tokens if the Occurrence is an observation.  The Darwin Core class would 
be Event rather than CollectingEvent.
> * Individuals may be identified (Actually ... it's the tokens that are identified.)
>   
Yes, exactly!  As I am defining Individuals, one learns about them 
through Occurrences.  You infer the individual's taxonomic identity 
either through examination of the evidence ("tokens" such as specimens, 
images, DNA sequences) or the organism (colony, etc.) itself, in which 
case it has an Occurrence record that is an observation with no token).  
As I have suggested earlier, a property of Identification that would be 
very useful would be one that links the Identification to the evidence 
(tokens) on which it is based.  We infer taxonomic identity through 
tokens, knowing that if the several tokens are from the same Individual, 
all Identifications based on any of these tokens apply to the Individual.
> * Some kinds of individuals are "monogenetic" (or whatever the correct term is) and can be identified as belonging to a taxon (clade?) with a scientific name
>   
I'm not sure what monogenic means, but the definition simply says a 
single taxon and does not specify what that is.  One does not need to 
know what the taxon is, as one or more Identifications can be applied at 
a later time.
> You could treat a coral outcrop as a single composite individual, even having a taxon named "warm south-pacific nodular atolls" - assuming that that kind of coral outcrop is a common one. You could treat a jar of coral fragments as coming from that individual, and to treat the individual fragments as specimens of sub-individuals that you can identify to species. That seems reasonable.
>   
We have agreed that this is allowable under the definition under 
discussion.  If one discovers that the individual is composed of 
multiple taxa at a lower level (such as species), those 
"sub-individuals" can be given separate identifiers and assigned 
Identifications at that taxonomic level.
> The problem would seem to be that you could also do the same trick with a jar of seashells collected at some beach - to treat "the population of sea-shells on shelley beach" as an individual. That seems a little ... illegitimate, as sea-shells are free living in a way that coral is not. I'd suggest that it's probably not worth trying to stop people abusing the notation in this way. Some things will have to remain judgment calls on the part of the dataset curator.
>   
Well, this gets at the difference between what I wanted originally, and 
what we have now in allowing Individuals to be at higher taxonomic 
levels.  In order to allow for reasoning that asserts that an 
Identification which is applied to one Individual also applies to an 
Individual which is discovered to be a duplicate, one has to have a way 
to know that the Individual is taxonomically homogeneous at a low enough 
taxonomic level for taxonomists to consider them "duplicates".  This is 
a bit hard to define, but as a practical matter taxonomists create 
"duplicates" and distribute them to other herbaria and museums as such 
routinely.  It is a judgement call they make all the time.  Whatever 
criteria they use would be my criteria for what an Individual would be 
allowed to be.  However, I have relented on this point so that 
Individuals can be defined at higher taxonomic levels as long as there 
is some way (like a term such as individualScope) that can be used to 
indicate when an Individual is scoped at the level where a taxonomist 
would call it a "duplicate".  Such Individuals would probably include 
coral colonies but not jars of sea shells.

Steve

-- 
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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