[tdwg-content] Of Evidence and Individuals (Was Plea for competency questions)

[Richard Pyle]

Hi All,

I, too, am just back from an extended trip with limited internet access, and
am catching up on this discussion.

I think Steve's two recent posts are extremely helpful -- for me in
particular. I very-much like the way he's framed the discussion around
"competency questions" (however correctly the term is applied).

I started off giving a detailed reply to the "Individual"
(="BiologicalEntity") class post, but then decided to read through the
"Evidence" post as well; and this lead me to deleting everything I had
written and start from scratch.

In summary, I largely agree with most of what Steve says in both posts, but
I'm still more than a little bit nervous about the distinction between the
two new proposed classes.  In particular, this passage from Steve's post
about the "Evidence" (="CollectionObject") class freaks me out a little bit:

> So then what IS an actual individual organism like the wildebeest calf?  
> It is a BiologicalEntity if it has been documented as an Occurrence or 
> assigned an Identification.  It is a CollectionObject if it was 
> collected for a zoo, or shot and mounted in a museum.  Or it can be 
> both simultaneously if it is both documented and collected.  If none 
> of these things were done, then it's neither a BiologicalEntity nor a 
> CollectionObject - it's simply a wildebeest calf.  Define the 
> class/type of the thing by the properties that you wish to assert for 
> it (or the competency questions that you can answer for it).

I think I get where you are coming from here, but I'm very queasy about this
notion that the same "thing" (a mass of flesh & bones) can be represented as
an instance of two different DwC classes, depending merely on what
attributes about the "thing" are emphasized.  For example, during my recent
trip to South Africa, we took the opportunity of one of our non-diving days
to visit a game park where we saw (among other things), numerous wildebeest
(coincidentally enough).  I took video images of these wildebeest with my
GPS-enabled camera, and therefore documented the presence of a specific
individual wildebeest at a particular date and time. Clearly there is a
dwc:Occurrence record there, so it's certainly a BiologicalEntity (by your
definition; i.e., documented as an Occurrence and assigned an
Identification).  But does a Game Park constitute the same thing as a zoo?
There are electric fences around the perimeter of the park, so I'm inclined
to think so.  Is it also a CollectionObject? Would this be an example of
something that is both?

The more I think about it, the less confident I am that we really need
*both* new classes.  With such potential overlap between them, should we not
simply generalize them both into the same class, and provide whatever
properties are known/relevant in a DwC instance of it?

You said that the CollectionObject class is fully capable of doing much of
what I want to accomplish with my vision of "Individual".  Could I not say
the exact same thing that a broader definition of CollectionObject (i.e.,
one that doesn't attempt to distinguish the disposition of the same mass of
flesh & bones in the context of human-mitigated captivity/preservation vs.
nature) could be fully capable of accomplishing what you want to accomplish
with Individual?  Namely, the three competency questions you established for
the "Individual" (=BiologicalEntity) class.

> An actual single, live organism can serve both as a unit for 
> resampling and "attachment" of Identifications, AND as an 
> organizational unit that is part of and which has parts that are 
> biological samples.  Some other entities, such as cohesive pack/herds 
> and clonal organisms can also serve both purposes.  Other entities 
> cannot: it doesn't make sense to resample dead organisms or pieces of 
> organisms,

I guess it depends on what you mean by "resample".  Surely a tissue sample
can be removed from a dead organism, and used for DNA sequencing that can
lead to a new Identification instance.  I agree that a dead organism cannot
represent the basis for future Occurrence instances, but I don't really see
the relevance of that.

> Personally, I would like for the third function ("inferring 
> duplicates"; linking multiple Identifications to the same entity and 
> being assured that all Identifications of the same Individual would 
> apply to all artifacts associated with that Individual) to be 
> accommodated by the definition,

I definitely support this, and on this basis, I am willing to abandon my
earlier defense for what you would call taxonomic heterogeneity.  I still
feel the need to not limit the rank at which a taxon identification may be
applied, but I am ready to abandon my original notion that a rock with
multiple phyla of organism attached should ever be represented as a single
instance with Identification "Animalia".  In other words, I've come around
to your perspective on this.  I think the power of implied "taxon
identification inheritance" that you advocate in your function #3 overrides
my advocacy for taxonomically heterogenous organisms to be lumped together
with the same instance of the class.

Thus, I now agree with you on the following:

> When I used that term, I intended for it to mean that the entity is 
> believed to be homogeneous to the lowest possible level in the way 
> that one knows that two branches from the same tree or two parts of 
> the same clonal organism are guaranteed to have the same taxonomic
identify at every level.

So, from my perspective, we can put that part of the debate to rest.

> This email is now at or has exceeded the length of an email that many 
> people will take the time to read.  So I will draw it to a close and 
> post a separate email on the topic of competency questions for John's 
> proposed class "CollectionObject" which I believe address Rich's 
> desire to track "real-world" objects (samples, re-samples, etc.).

Rather than respond separately to the other post, I've just made this single
response with the new subject heading, because I think we're narrowing down
the scope of the debate in such a way that we should now focus on the
difference between the two proposed new classes
("Individual"/"BiologicalEntity", and "Evidence"/"CollectionObject").

For a while, I thought I saw the difference as being the "Evidence" was more
like an instance of "Documentation" (e.g., an image, a label on a preserved
specimen, etc.); rather than the flesh-and-bones organism itself.  But with
your suggestion that this class may serve the function(s) of my desires for
the "Individual" class, the waters have been muddied a bit in my own mind.

I guess if there are to be two separate classes, then I would favor a more
generalized "Organism" class to serve the functions of what Steve has
described for both the "CollectionObject" and "BiologicalEntity" classes,
but then define a separate "Documentation" class that serves as the basis of
"proof" for an Occurrence.

On a semi-related topic, I don't think it's appropriate to create a DwC
class simply to establish a Many-to-Many relationship between instances of
other classes.  That function (in my mind) is already elegantly fulfilled by
the existing dwc:ResourceRelationship class (another major discussion that
will need to take place on this list).  While it's true that certain DwC
classes do serve a M:M function (e.g., Occurrence), I think that classes
should represent "things" that are unambiguously different, with very
specific sets of properties.

On a final, somewhat encouraging note, I *really* like the diagram
represented in the link that Cam sent earlier:

http://code.google.com/p/darwin-sw/

During one of our non-diving days in South Africa, Rob Whitton and I spent
some time thinking about the BiSciCol project (BCC'd on this post), and we
studied this diagram and both agreed it represents an *excellent* foundation
to both this discussion on proposed new DwC classes, and the BiSciCol
project in particular.

Aloha,
Rich