[tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]

[Steve Baskauf]

Comments inline

Paul Murray wrote:
...
> How about:
> An Occurrence is the /reification/ of an individual's involvement in 
> (entaglement with? presence at? relationship to?) an event. It reifies 
> an "Event involvesIndividual Individual" fact.
>
> The need for this construct is that we often need to say a number of 
> additional things about an individual's involvement with (presence at) 
> an event beyond simply assertin that there is some relationship. We 
> need to say what tokens that individual left, what role that 
> individual had (Predator? Prey? Parasite?), perhaps temporal or other 
> limits of that particular individual at the event. Occurrence is the 
> object to which these facts may be attached. An individual might 
> meaningfully have more than one occurrence at an event - particularly 
> in cases where events are part-of larger events, or where an 
> individual somehow has multiple roles (hyenas chased away from their 
> kill by a lion - or is it the other way around?).
>
> To put it another way: "reification" = "tuple" = "association table" = 
> "pulling a property out into an object". More or less.
>
Yes and I would add "=RDF graph node" to your list above.  It is a 
relationship made into something onto which we can slap an identifier 
and link other resources via object properties.  I would add that its 
nature is similar to that of dwc:Event (which you could say is a 
reification of an Occurrence's relationship to a Location and time) and 
a dwc:Identification (which you could say is a reification of the 
relationship between an "Individual" and the Taxon that somebody asserts 
that it represents).  None of these things (Occurrence, Event, or 
Identification) have a physical existence.  They exist because we need 
them to connect instances of other classes of resources.  We give them 
names that have something to do with the nature of the connection, but 
they really are just connections (or nodes if you wish).

Peter DeVries wrote:
 > Wouldn't the individual be asserted to be an instance of a species 
"concept"
Defining an Individual this way assumes that one knows what taxon the 
Individual represents.  What about the Individual I've assigned the GUID 
http://bioimages.vanderbilt.edu/ind-baskauf/70858 ?  I don't really have 
any idea what it is.  That really shouldn't prevent me from assigning it 
a GUID and an rdf:type.  I suppose that you could do what Rich suggested 
which was to require at least one dwc:Identification at a level as high 
as "Life" but I would prefer to say that an Individual could have 0 to 
many dwc:Identifications, with "many" being the number of Taxa that 
people wish to assert that it represents.  That number is never fixed 
because somebody could always come along later and assert that it was 
something else, or even assert that it is the same taxon that somebody 
else previously had asserted. 

Richard Pyle wrote:
 >
 > I think the hardest part will be to define the allowable scope of 
"Individual".  In my mind, it should at least span from single organism 
to multiple organisms up to
 >colony and population; and can be circumscribed by any taxon concept 
(including "Life").  I have been re-thinking whether "part" should be 
treated as a separate
 > individual.  I used to think yes, but lately I've been thinking no.

I think that the answer to this question is related to the original 
definition of Paul's that started this thread (i.e. reification of 
relationships to create identifiable/linkable entities).  Back in 
October when you and I were butting heads on this topic, I think that 
the mistake was to try to demand that an Individual represent both a 
physical individual organism and the "reification" (my new favorite 
word) of an conceptual entity that connects an Identification to an 
Occurrence (a so-called TaxonomicallyHomogeneousUnit) [see Kevin 
Richard's comment at 
http://lists.tdwg.org/pipermail/tdwg-content/2010-November/001956.html 
which first made this distinction clearly].  In some cases, it is easy 
to define a resource as being both things (e.g. discrete organisms) but 
in others it's not (colonial organisms, clones, herds, tissue cultures, 
etc.).  After thinking about this for a long time I felt that the best 
thing to do was to cleanly separate the physical thing (a.k.a. a 
"token") from the conceptual thing (the reified entity onto which we can 
hang Identifications and Occurrence records).  If one wishes or if it is 
convenient, one could describe a particular resource as both the token 
and the conceptual thing (e.g. in the case of a discrete organism) but 
if it is more convenient one can identify the conceptual entity as a 
separate thing and identify any number of related tokens associated with 
this entity.  These related tokens could span the range from individual 
cells to tissues to discrete organisms to herds to populations and the 
relationships among them could be described using dcterms:hasPart or 
other appropriate object properties.  This was the approach we decided 
to take with darwin-sw (see 
http://code.google.com/p/darwin-sw/wiki/ClassIndividual 
http://code.google.com/p/darwin-sw/wiki/TokenIssues and 
http://code.google.com/p/darwin-sw/wiki/ClassToken for a more detailed 
description of the approach with diagrams and references).  This 
approach can handle these situations:
Richard Pyle wrote:
 > Most people think of a coral head as an "individual", but it's really 
a colony of polyps.  Ants are usually curated as individual organisms, 
but can also be useful to collapse to colonies. 
Nico Cellinese wrote:
 > I also agreed that an individual doesn't have to be whole, so in my 
opinion "parts" can also be considered 'the individual in question'. 
Similarly, I also agree that up to populations we can still talk about 
individuals.  However, it is important to be able to link "parts" to the 
whole individuals if needed, e.g. is_part_of.

Separate the abstract TaxonomicallyHomogeneousUnit from the physical 
tokens and this issue goes away:
Richard Pyle wrote:
 > That is my old thinking.  My new thinking is that you abstract up to an
 > whole organism when you have a part (e.g., tissue sample), when 
representing
 > an Occurrence; just as you would abstract down to "Indidividual", 
when you
 > what to represent Taxon-at-Event for an Occurrence.

In darwin-sw we did not attempt to define a real ontology of tokens that 
are physical parts or conglomerations of organisms 
(cells/tissues/discrete 
organisms/herds/populations/colonies/clones/etc.), but that would be a 
good thing to do.  It could be done in isolation from the definition of 
the "reified" TaxonomicallyHomogeneousUnit. 

Steve

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

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