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

Richard Pyle deepreef at bishopmuseum.org
Tue May 31 22:58:07 CEST 2011

I think you could require a minimum of at leats one identification for every
individual - even if that identification is simply "life".  I think in the
vast, vast majority of cases, you would have something more finely resolved
than "life" (e.g., at least a kingdom, probably usually at least a family,
and often a species).  So if "Individual" is defined as having at least some
taxonomic scope, then you wouldn't have any individuals without asserted
identifications.  It's just that you need to accommodate identifications at
ranks above species.


More later, after I digest your full message below (on another coffee break




From: Peter DeVries [mailto:pete.devries at gmail.com] 
Sent: Tuesday, May 31, 2011 10:39 AM
To: Richard Pyle
Cc: Nico Cellinese; tdwg-content at lists.tdwg.org; Paul Murray
Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]


Hi Rich,


The devil is in the expected use cases which I realized when I started to
create useful queries.


In theory, you could have the occurrence record marked up with only an
individual ID, no asserted identification.


Then in a separate file, map those ID's to species concepts.


Merge those in a knowledge base and you can run useful queries.


Look at this page: http://ocs.taxonconcept.org/ocs/index.html


or this


Think about how many people would find these usable if they had no species
or classification attached to them.


How would you know what to click on?


You also want to be able to make statements about how this individual
relates to other individuals and other species.


Populations and colonies relate in different ways.


You will find that records marked up with identifiers where one instance is
an individual organism and the next record is a colony will give you very
strange results.


For instance a colony at any given time has individuals of different sexes
and ages. An individual at any given time "usually" has one sex
classification and one age.


There will be cases where you have a fungus that spans three counties.
Different people will assume that observations of that same individual in
three counties are different.


If I thought what you are proposing would work I would use it for some
mosquito collections consisting of 10,000 individuals but treating that
record as the same kind of thing as a record of one mosquito will cause


I think it is best to create a separate but linked entity to represent
things liks a population or colony and keep those kinds of things
represented as different kinds of things.


There should be some way to relate a population of mosquitoes to both a
species concept and individuals that exist within that population.




- Pete


On Tue, May 31, 2011 at 3:02 PM, Richard Pyle <deepreef at bishopmuseum.org>

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


An occurrence that has been asserted to be an occurrence of that species


Which is documented by this page


Relationships between these entities can be browsed via the Knowledge Base


22444a-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


dual> <bioimages:individualHasStevesSpeciesConcept>


* 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




- Pete

On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese at flmnh.ufl.edu>

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 <http://www.taxonconcept.org/>   &  GeoSpecies
<http://about.geospecies.org/>  Knowledge Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>   Project

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 Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>   Project

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