[tdwg-content] New Darwin Core terms proposed relating to material samples

[Richard Pyle]

Hi Gregor,

Again, I think we need to pin down the concepts before we spend too much
time thinking about what the terms should be.  I understand that it's
difficult to discuss the concepts without the terms, but focusing on the
terms first is like putting the cart before the horse.  Perhaps we should
follow Chuck's advice and use latin terms or some other kinds of labels that
do not come with so much baggage -- so we don't attach too many
pre-conceived notions.  The only terms in this space that have "standard"
definitions are "Individual" (as inferred from dwc:individualID) and
"CollectionObject" (from historical definitions in the MVZ/ASC models).  The
DSW terms are also useful and well-defined, but are not as well established
as standards.

All of the terms you propose ("Sample", "Unit", etc., as well as a number of
others such as "item" and "object") were very-much in consideration when we
were thinking about these things, but all of them have similar levels of
weaknesses to other term options (most people think of a "unit" as a term
applied to units of measure, and "Sample" implies the collection or removal
of something from nature). We eventually went with "Individual" because it
is already defined in DWC (though not well defined).

But let's see if we can have a discussion first about the different concepts
we are talking about.  Can we nest all of these ideas under a single
superclass?  Or do we need different top-level classes to
define/distinguish:

- Biological things from non-biological things;
- Collected/extracted things from things that are observed/documented
in-situ;
- Things that are taxonomically homogeneous from things that include
taxonomic heterogeneity?

Also, to what extent are the things we want to discuss best represented as a
nested hierarchy?  For example, if an aggregate (school, colony, herd,
etc.), has multiple specimens collected at the same time, and then some of
those specimens have parts/tissues removed from them, and then some of those
tissues have subsamples taken or destroyed for analysis.....  are those all
instances of the same class of thing related via parent/child hierarchy?  Or
is each step a separate class of thing?  If the latter, how many classes of
such things do we need?

I used the word "thing" as much as I could to avoid the term-baggage issue;
but another term that I have found useful in these conversation is "Object".
As I wrote to Chuck off-list, the top-level superclass might be thought of
as "physicalObject"; under-which some of these other concepts (e.g.,
"biologicalObject" and others) can be represented either as subclasses, or
as key properties of instances within the superclass.

Aloha,
Rich

> -----Original Message-----
> From: Gregor Hagedorn [mailto:g.m.hagedorn at gmail.com]
> Sent: Sunday, May 26, 2013 7:37 PM
> To: Richard Pyle
> Cc: Steve Baskauf; John Deck; TDWG Content Mailing List; Robert Whitton;
> Walter G. Berendsohn; Anton Güntsch
> Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
> material samples
> 
> > "population" or "taxon" -- things get very messy.  During the previous
> > discussion, it seemed that everyone agreed that "taxon" was too broad
> > and not useful for our purposes; whereas "colony", "school", "herd",
> > etc. were absolutely necessary (lest we need to treat every polyp on a
> > coral head as a separate database entry, and many use cases involve
> > treating herd/pod/flock as an important unit to be able to track in
> > exactly the same way that "individuals" are tracked -- which is why
> > the definition of dwc:individualID is as it is). The border-line term
> > is "population" -- which is cleary below the realm of taxon, but
> > perhaps a bit too vauge and poorly defined to be regarded as the same
> class as an individual.
> 
> Yes, and I am also thinking of metapopulations, just for fun...
> 
> I understand that we need an operationally defined term with a particular
> use case. Primarily I agree with Chucks observation that an important
point is
> that we believe to understand what an individual is, both in biology and
in
> informatics and philosophy, so I just want to warn about the use of this.
> Secondarily I do believe we need to define it in a way that the upper
limit of
> the set we want to refer to becomes clear, at least operationally. I was
> missing that.
> 
> WIth respect to the operational usefullness of a term that does not
> distinguish between part, individual, set of taxonomical homogeneous OR
> heterogeneous samples (you excluded tax. heterogeneous, which would
> exclude lichens, most plants (mycorrhiza!) or any other symbiosis like us
> humans with our skin and intestine microbes) I have two proposals:
> 
> Broadly the term "sample" implies not necessarily physical sampling, you
can
> sample observations or data. A sample is a subset of a
> (statistical) population, selected under operational rules and encompasses
> the individual and part. Think of sampling music.
> 
> The other term is unit. What you describe has been discussed extensively
in
> the CDEFG and later ABCD papers and standard and the term
>    "Unit"
> was chosen for as far as I understand exactly the concept you are looking
for.
> Perhaps that can be followed, if we accept that these are not "natural"
units,
> but operationally defined units (think of OTU, oper. tax. units). Unit was
> chosen in ABCD because it applies both in a sampling context, in an
analysis
> context, and in a collection curation context.
> 
> Apologies should I repeat something already discussed previously.
> 
> Gregor