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

Richard Pyle deepreef at bishopmuseum.org
Wed Jun 1 01:54:16 CEST 2011

>  So you're saying that it would be dangerous to frame an occurrence as a taxon 
> concept at a place/time and should be an Individual at a place/time instead 
> (with which I would agree), 


> but then you go on to say that the scope of Individual should be wide enough 
> to accommodate anything that can be circumscribed as a taxon concept. 

Not quite.  See the long discussions of this topic on this list last fall.  Obviously, "Population" is simply one step along the continuum between "Individual organism" and "taxon" -- so in that sense, I can only say "not quite", rather than "no".  But when you frame it that way, there is no fundamental difference (conceptually) between an individual organism and a taxon -- they are just different extremes of the same continuum.  Indeed, an "Individual Organism" is not even at the extreme -- it's closer to the middle (when you consider how many "individual organisms" are comprised of multitudes of individual cells, each of which is comprised of multiple organelles, etc.)

So, if we are going to make a distinction between "Individual" and "taxon", then it is necessarily an arbitrary distinction.  I think that we, in the biodiversity informatics world, see value in distinguishing between "Individual" and "Taxon Concept", because each tends to have different properties, and it's also much more intuitive for us to model it that way.  All I'm saying is that, in my opinion, the arbitrary line between "Individual" and "Taxon Concept" is better drawn somewhere in the realm of "population", rather than what I think a lot of people would define as "individual organism".  My reasons for having this opinion are documented in part in the earlier thread (and I have no time to go into it now).  But I'll be happy to elaborate later.

> Does that mean that you view a taxon concept and something that can 
> be circumscribed aa a taxon concept as two very different things? 


> In ontological terms, the set of things (a class) that can be sufficiently 
> circumscribed with a taxon concept (a class) and the taxon concept 
> would seem semantically the same to me. 

To me as well.

> I think it's important here to distinguish between instances of (individuals 
> that are a members of) the taxon concept class (but never comprise 
> of all members of the class), and the taxon concept itself as a class. 
> But perhaps that is what you had in mind anyway?

No, but I don't think it's as simple as you make it seem.  It is at face-value, but not when you really dissect it.  For example, to what taxon concept does the thing typing this email message belong?  Presumably, Homo sapiens L. sec. L.  But >90% of the cells encapsulated within the boundaries (skin) of that thing are non-human.  Sure, the majority of the *mass* is represented by human cells, but by that logic, the majority of the mass is non-living H2O.  We abstract the sack of matter within the boundaries of my skin as an "individual organism", because it's intuitive and convenient to do so.  But there are other kinds of organisms for with it is much less intuitive or obvious where "individual organism" ends and "small set of individual organisms" begins  -- even if the "small set" is implied to refer to the organisms sharing the same genome (i.e., excluding the endo parasites alluded to previously).

So, if there are pragmatic reasons why the scope of "Individual" should extend beyond "single organism" (and I think there are several), then we need to know where the scope of "Individual" ends, and "Taxon Concept" begins.

If I had to come up with a more ontologically-friendly(?) distinction, I guess I would say that the scope of "Individual" should be limited to cases where the instances can (effectively) be enumerated; whereas "Taxon Concept" would encompass instances both enumerated and implied.



Sent with a tap.

On May 31, 2011, at 4:02 PM, Richard Pyle <deepreef at bishopmuseum.org> wrote:
I’m glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc.  I’m on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a “species” (or any taxon concept) at a place/time.  I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time).  However, I think these should all be framed as “Individual-at-Event”, even if “Individual” is nothing more than a GUID to which Taxon identifications can be linked.
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.
From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Peter DeVries
Sent: Tuesday, May 31, 2011 9:24 AM
To: Nico Cellinese
Cc: tdwg-content at lists.tdwg.org List; Paul Murray
Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
Hi Nico, 
Wouldn't the individual be asserted to be an instance of a species "concept"
For instance:
The species concept http://lod.taxonconcept.org/ses/ICmLC#Species
An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual
An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurrence
Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html
Relationships between these entities can be browsed via the Knowledge Base view.
< http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9%23Occurrence >
bit.ly http://bit.ly/jgRUxv
* Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base.
Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or
with a different predicate. Note the hypothetical links below don't work.
The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual
<http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species>
* We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept.
  For instance those that are linked to a specific name or classification hierarchy.
- Pete
On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese at flmnh.ufl.edu> wrote:
I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made.  What I don't seem to be able to digest is the notion that same individual will later be equaled  by some to a species. That assertion is hard to swallow.
On May 31, 2011, at 3:44 AM, Paul Murray wrote:
> An Occurrence is a combination of an Individual and an Event.
> An Occurrence is a coupling of an Individual and an Event.
> An Occurrence is a pairing of an Individual and an Event.
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.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept  &  GeoSpecies Knowledge Bases
A Semantic Web, Linked Open Data  Project
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