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

[joel sachs]

Steve,

I agree with you that there is no consensus on what is a Darwin Core 
occurrence. In fact, the situation is worse than you describe, since you 
don't mention the "http://rs.tdwg.org/dwc/terms/type-vocabulary/" 
("dwctype:") namespace below. (I assume that by "dwc:", you mean 
"http://rs.tdwg.org/dwc/terms/".) As you know, part of the confusion 
about occurrences is that the term exists in two distinct Darwin Core 
namespaces.

In fact, I've been meaning to ask you something ... The DwC RDF guide 
(correctly, IMO) specifies that occurrences should be rdf:typed using the 
dwctype:Occurrence class [1]. But Darwin-SW uses the dwc:Occurrence class 
as the rdf:type of occurrence records. I also used dwc:Occurrence when 
representing bioblitz occurrence. So my question is: Were we both wrong, 
and should we remove our (incorrectly typed?) occurrence records from the 
web? Or are you saying that it's hard to say what's right and what's 
wrong, since the documentation and existing usage is inconsistent?

Best,
Joel.

1. https://docs.google.com/document/d/1OLyVFuveGX1a0Yt6Niok9FfGxkrghii-xlGYhwO8UqE/edit
Section 2.3.1.5


On Mon, 24 Jun 2013, Steve Baskauf wrote:

> 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
> 
> postal mail address:
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> 
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