I have quoted below part of an email which has been sitting in my inbox for a month.  It been stuck there because there was a statement in it that (in my mind) needed clarification.  In John Deck's email, he says "...since an Occurrence represents an organism at a place and time...".  What I am wondering is whether there is actually a consensus that an Organism represents an organism at a place and time.

Caveat: I use "individual organism" here in a general way that probably includes more than individual organisms.  But that is a different issue, so let's not rehash that in this thread.

The history of the discussion of the meaning of Occurrence is extensive.  You can find my attempt to summarize it at: http://code.google.com/p/darwin-sw/wiki/ClassOccurrence so I won't repeat that here.  In a nutshell, it seems to me that people have used dwc:Occurrence in three general ways:

- to indicate that we know from aggregate records that a taxon occurs or ever occurred, in a particular geographic area (the "checklist" meaning of Occurrence)
- as a broad term that includes both preserved specimens and observations (the "superclass" meaning of Occurrence)
- as a join between Events and individual organisms [database description]/as a node connecting Event instances to instances of individual organisms [RDF description]/as a tuple of (individual organism,Event) with properties to connect it to the individual organism and Event [computer science description] (the "node" meaning of Occurrence). 

It has been noted that the "checklist" meaning of Occurrence is related to Occurrence as a primary unit of data gathering ("superclass" and "node" meanings; see history reference for details) but the "checklist" meaning is probably the least likely to be considered a consensus view, so I'm going to ignore it for the moment.  The "node" meaning of occurrence corresponds to what is described by John Deck (quoting Markus Döring) in his email below.  It is also the view taken by Darwin-SW and is reflected in Rich Pyle's emails (related since Darwin-SW was influenced by Rich Pyle's emails!).  However, although it isn't explicitly stated as such, the Darwin Core standard as it currently stands really reflects the "superclass" meaning.  I was involved in a conversation with John Wieczorek a few months ago which was on the topic of "fixing" dwc:Occurrence (i.e. getting rid of the ambiguity surrounding it).  In that conversation, I confirmed with John W. that as things stand currently, Darwin Core effectively considers dwc:Occurrence to be a superclass of PreservedSpecimen and Observation.  So to me it does not seem that there actually is a consensus about what dwc:Occurrence means.  Is an Occurrence the *thing* that documents the presence of an organism at a place and time ("superclass" meaning), or is the Occurrence an *abstract resource* connecting organisms to place/time with the thing itself as documentation for the abstract resource ("node" meaning)?

In order to "fix" Occurrence by clarifying its meaning, it seems to me that there are two courses of action:

1. Declare clearly that Occurrence is a superclass of PreservedSpecimen and Observation and create a new term for the more abstract "organism at a place and time".
2. Declare clearly that Occurrence is an organism at a place and time and that it is NOT a superclass of PreservedSpecimen and Observation. 

The second course of action would be the easiest from the standpoint of making a change to the standard.  However, it might be the worst from an implementation standpoint because of the thousands (millions?) of specimen records that are typed as Occurrence. 

If we can clarify these two uses of Occurrence, then the terms currently listed in DwC under the dwc:Occurrence class could be separated among the two "kinds" of Occurrence.  Terms related to the recording of the presence of an organism at a time and place (dwc:recordedBy, dwc:behavior, etc.) would be separated from terms related to the specimens themselves (dwc:preparations, dwc:disposition, etc.).  This may not seem like a big deal for flat specimen records, but it would be very helpful from the standpoint of advancing the use of DwC in RDF to clarify the types of resources that these terms can serve as properties of. 

I would be interested in hearing some discussion about concrete steps that could be taken to "fix" Occurrence.  The "best" solution would probably be to create a robust consensus ontology that includes Occurrence.  However, that is not likely to happen on the timescale of a year or less.  Given that this issue has dragged on for at least two years already, in the interest of moving forward it would be good to take some kind of decisive action in the near term. 

Steve

-------- Original Message --------
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
Date: Wed, 29 May 2013 16:00:35 +0200
From: John Deck <jdeck@berkeley.edu>
To: Richard Pyle <deepreef@bishopmuseum.org>
CC: Markus Döring <m.doering@mac.com>, Steve Baskauf <steve.baskauf@vanderbilt.edu>, TDWG Content Mailing List <tdwg-content@lists.tdwg.org>, Robert Whitton <whittonr@gmail.com>, "Ramona Walls" <rlwalls2008@gmail.com>
References:

Since the original proposal was from a group of folks, we decided to put our heads together to construct a general response to the various issues and ideas expressed on this thread.


John Deck for Rob Guralnick, Ramona Walls, and John Wieczorek


...

How is MaterialSample different from Individual?  The intent of individualID is fairly clear:  since an Occurrence represents an organism at a place and time (per Markus’ email), the individualID term allows us to assign an instance identifier for a particular organism that can be present in multiple events. MaterialSampleID, on the other hand, is intended to allow users to say that the basis of an occurence is a material entity (i.e. matter) that has been sampled according to some particular method. Whether or not

...

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Vanderbilt University Dept. of Biological Sciences

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