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

Peter DeVries pete.devries at gmail.com
Tue Jun 7 00:47:21 CEST 2011

There are too many ideas here for me to digest at once, but I have some

One of the problems with my examples is that I have to make a separate code
base to fully support each "thing" I try to include

In my occurrence examples I simply stub out an "individual", it would have
been better to have these exist as a separate table.

One data set might make statements about a specific individual and coin
their own URI for that individual, that is later observed and recorded in a
different data set.

Since it is difficult to determine ahead of time what other studies might
have data about that same individual, it would be easiest to create the
following triple after verifying that it is true.

IndividualDataSetA owl:sameAs IndividualDataSetB

Also I have no examples for unknown or partially identified taxa.

My thinking is that this is still a kind of species concept but one that is
unspecified. I don't think it would be good to mark it up as only an
instance of a genus.

So something like <SpeciesConceptUnspecifiedInsect_Culex>

This would indicate that the individual has been identified as some Insect
in the genus Culex,

This can be interpreted as as asserting that the individual is an instance
of some species concept within the Insect genus Culex.

The way to deal with observations of multi-individual groups might be
handled with "something like" the following:

A swarm of bees

This has different allowed properties than an individual.

For instance it could have a count for each sex.


#Swarm could be a subproperty of #MultipleIndividualGroup

This is somewhat like a #Population, but I can think of instances where the
#Population and #MultipleIndividualGroup are different things.

- Pete

On Mon, Jun 6, 2011 at 5:09 PM, Steve Baskauf
<steve.baskauf at vanderbilt.edu>wrote:

>  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.htmlwhich 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
> postal mail address:
> VU Station B 351634
> Nashville, TN  37235-1634,  U.S.A.
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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 <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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