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

[Paul Murray]

On 16/11/2010, at 9:05 AM, Steve Baskauf wrote:

Again, my coming from a computing background rather than a scientific one:

> 'We can argue about the properties and tokens later; first we need to nail
> down the "essence" of an Individual.'
> 
> I actually disagree strongly with this statement.  I have tried to stay 
> out of the current thread about the future course of the TDWG ontology 
> because it isn't my something that I know much about.  But I think I am 
> leaning to the side of those who suggest that we create use cases first 
> and then see how the ontology can be developed to facilitate those use 
> cases.

I suspect that a useful question is not so much "what is an individual", but "what kinds of thing might we want to treat as an individual".

It seems clear that you have a SingleIndividual - a "monogenetic" (whatever the correct term is) free-living multicelluar organism: a tree, an ant. And you have CompositeIndividual - a colony of spiders, a bee's nest or anthill, a breeding pair, a family of humans. You also have things like an algal bloom or a disease outbreak, where the individuals are single-celled but you sample populations of them.

* Individuals can be part-of composite individuals - either lifelong or not. 
** Tokens taken from an individual are also tokens of any individuals it is part-of (?).
** An individual can serve as its own token - a living or preserved whole specimen - much as a word like 'foo' can serve as its own name. 
* Individuals can be known to be genetically related to other individuals. (parent/child/hybrid, colonies being split)
* Individuals can be found in association with other individuals (aphids in an ants nest, parasites, a pride of lions that follows some particular herd).
* Composite individuals are not necessarily single species: aphids in an ant's nest again
* Taxa, perhaps, are not the same as clades. Again: an ants nest with aphids - we can identify an ants nest as a nest of western red ants without thereby saying that all individuals in the nest are of the same species.
* An individual is usually bounded by place and (almost always) time - exceptions include things like permanent bird colonies
 
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.
* Individuals may be identified (Actually ... it's the tokens that are identified.)
* 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

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.

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.



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