[tdwg-content] Consensus on what constitutes an Occurrence? (was Re: New Darwin Core terms proposed relating to material samples)

[Steve Baskauf]

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 at berkeley.edu>
To: 	Richard Pyle <deepreef at bishopmuseum.org>
CC: 	Markus Döring <m.doering at mac.com>, Steve Baskauf 
<steve.baskauf at vanderbilt.edu>, TDWG Content Mailing List 
<tdwg-content at lists.tdwg.org>, Robert Whitton <whittonr at gmail.com>, 
"Ramona Walls" <rlwalls2008 at 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

...

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

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