[tdwg-content] "Wrong" RDF, was Re: What I learned at the TechnoBioBlitz

[Richard Pyle]

> In many cases, a specimen is created by killing an organism and gluing it
to a 
> piece of paper (if it's a plant) or putting it in a jar (if it's an
animal).  
> It is natural to ask the question "what kind of species is the specimen?".

> We can look at the specimen and make a statement like [specimen] 
> dwc:scientificName "Drosophila melanogaster" and it pretty much makes
sense.  
> However, in the new Darwin Core standard, we have a broader category of 
> "things" (a.k.a. resources) that we call Occurrences which include
specimens 
> but which also includes observations and probably all kinds of things like

> images, DNA samples, and a whole lot of other things.  If we try to apply 
> the same kind of statement to other kinds of Occurrences besides specimens

> we immediately run into problems.  If we say that [digital image] 
> dwc:scientificName "Drosophila melanogaster" we are making a nonsensical 
> statement.  The digital image can have properties like its photographer, 
> its format, its pixel dimensions, etc. but the image itself does not have
a 
> scientific name.  The scientific name is a property of the thing that was 
> photographed.  It makes even less sense if we are talking about
observations.  
> An observation is a situation where somebody observes an organism.  
> The observation can have properties like the observer, the location, etc. 
> However, if we say [observation] dwc:scientificName "Drosophila
melanogaster"
> we are saying that that act of observing has a scientific name. 
> That is an incorrect statement.  So the general statement [Occurrence] 
> dwc:scientificName "Drosophila melanogaster" does not make sense when 
> applied to all possible types of Occurrences.  Rather, the organism 
> that we are observing is the thing that has a scientific name.  

OK, I admit that I have not been following this list as closely as I should
have -- especially during the latter half of 2009.  But I have to
ask....seriously....is this the level of misunderstanding that still exists
in our community?

Perhaps I'm the idiot here, but it has *always* been my understanding that
the "thing" (I hesitate to use the word "basis") of an Occurrence instance
is *always* the organism (or set of organisms, or impression of an organism
in the case of fossils).  If the organisms were captured and preserved in a
Museum, then we call it a specimen.  If the organisms were only witnessed
and not captured, we call it an observation.  Everything else (including the
physical specimen) is just layers of evidence to support the existence and
taxonomic identification of the organism within the Occurrence.  When
photons reflected off the outer surface of an organism find their way
through a lense and onto some mechanism for recording said photos (either a
human retina and neurons in the brain, or sheet of celluloid, or digital
image sensor and memory stick), it's still the organism that the photons
reflected off of, which represents the "thing" of the Occurrence to which
metadata apply. Same goes for vocalizations transmitted through pressure
waves in the air onto some recording device (ear/brain, or microphone/tape).

So while it's certainly true that a media object such as a 35mm slide or
digital image file does not itself have a scientificName (then again, some
of my old Kodachromes have enough mold on them that they might....), said
media objects are *not* the Occurrence itself -- they merely represent
evidence of the occurrence.  Even a specimen in a jar is not the Occurrence
itself.  The Occurrence occurred when the specimen was captured (e.g., 400
feet deep on a coral reef).  A specimen in a jar on a shelf in a Museum is
no longer the "Occurrence"; it is the evidence of the Occurrence.

When I assign a GUID to an Occurrence record that lacks a voucher (i.e., an
"Observation"), I'm certainly not trying to identify the act of observation;
I'm identifying the organism that was observed, at the time and place that
it was observed.

For what it's worth, if I only have a still or video image of an organism
(e.g., http://www.youtube.com/watch?v=GVTd11q3Ppc; taken by Rob Whitton, who
some of you met at TDWG this year), and didn't collect the specimen, I
create an Observation record, and link the image to it as associatedMedia.
I would never assign a taxon name to the video clip -- only to the "content
item" of the video that represents an organism, serving as the basis of an
Occurrence record.
	
> The specimen is an occurrence of the individual organism.  
> The image is an occurrence of the individual organism.  
> The observation is an occurrence of the individual organism.  

I would say in all three cases that the presence of an organism at a place
and time was the Occurrence.  Specimens, images, and reported observations
are merely the evidence that the occurrence existed (and to varying degrees,
can also allow for subsequent interpretations of taxonomic identification).

> These statements may seem odd because we are used to 
> thinking of an Occurrence being an occurrence of the 
> "species" but it's not really.  

I completely agree.  The occurrence was the organism at a place and time.
The "species" is merely the taxon concept that someone identified the
organism as belonging to.  The scientificName is merely the label that
someone applied to the taxon concept.  In other words, the scientificName is
really a property of the Taxon Concept, and the Taxon Concept is the subject
of an identification event, and the identification event was applied to the
organism, which itself represents the basis of an Occurrence.  But very few
people go to the trouble of creating that full chain of relationships, so as
a short-hand, the scientificName is often treated as a direct property of
the occurrence (collected or observed organism).  I think this short-hand is
perfectly fine in the context of DwC, but only as long as people understand
the implied chain of linked entities.  If we start to forget what's really
going on, then we run into trouble. 

Which, I guess, was the whole point of Steve's post.

What concerns me, though, is that we're not (yet?) already beyond this.

> This point becomes more clear if we look at a situation where several 
> types of occurrence records are collected from the same individual.  
> Let's say that we capture a bird, photograph it, collect a feather from
it, 
> collect a DNA sample and band it and let it go.  Later somebody sees the 
> band and reports that as an observation.  
> How do we connect all of these things?  

Two Occurences:  The first one when it was captured, photographed, and
relieved of a feather. The second when it was observed at a later date.

> Do we create an identifier for the specimen (the feather) 
> and then say that the image and the DNA sample came from it?  

We create an identifier for the first Occurrence, capture the
specimen-relevant metadata of the preserved feather, and track the DNA
sample via associatedSequences.

> That would be wrong.  We could take an image of the feather, 
> but that would be a different thing from an image of the bird.  

It's certainly different from an image of the whole Bird, but that doesn't
preclude us from including both bird and feather images among
associatedMedia for the first Occurrence.

> We didn't get the DNA sample from the feather, we got it 
> via a blood sample from the bird.  

I don't see that as a problem, because the feather is only the evidence of
the bird at the place and time (i.e., the first Occurrence). Thus, the
sequence can still be included as part of the associatedSequences for the
first Occurrence.

> The band observation is not an observation of the feather, 
> or the image or the DNA sample.  It's an observation of 
> the bird which was never any kind of specimen living or dead.  
> The bird is an individual organism and that's what we need to call it.  

Agreed -- it forms the basis for the second Occurrence record (later date).
The two Occurrence records can be cross referenced, either via a shared
individualID, or via associatedOccurrences.

> Right now we don't have anything in Darwin Core that can 
> be used to rdfs:type the bird, which is why I proposed Individual 
> as a Darwin Core class.  

As someone else alluded to earlier in this thread, there are near-infinite
ways that we can slice & cluster biodiversity data. I think there are some
cases where "individual" makes a lot of sense as a class (banded birds,
managed organisms in zoos and curated gardens, whale and shark observation
datasets, plant monitoring projects, etc.). But I think the notion of
"Occurrence" makes more sense at this point in biodiversity informatics
history, because the vast majority of datasets can be organized in this way
realtively painlessly, and because the majority of questions being asked of
these data revolve around presence of organisms identified to taxon concepts
occurring at place and time.
	
> I could say these things more clearly in RDF, but since 
> because many members of the audience of this message 
> aren't familiar with RDF/XML they would probably zone 
> out and the point would be lost.  

Myself among them.  Thank you for presenting it in the less-efficient
English Prose form.

> The point is that we need to have identifiable classes of "resources" 
> (the technical name for "things" like physical artifacts, concepts, 
> and electronic representations) for all of the things that that we
> need to describe and inter-relate in the Darwin Core world.  
> Right now, we are missing one of the important pieces that we need, 
> which is a class for the Individual.  If we are satisfied with creating 
> an RDF model that only works for specimens and one-time observations, 
> then we probably don't need Individual as a Darwin Core class.  On the 
> other hand, if TDWG and GBIF are really serious about creating a 
> system (Darwin Core and RDF based on it) that can handle other types 
> of Occurrences like multiple images of live organisms, observations 
> of the same organism over time, and multiple types of Occurrences 
> collected from the same organism, then this capability should be built 
> into the system from the start.  When I got back from the TDWG meeting, 
> I was all excited about trying to use Darwin Core Archives with my 
> live plant image collection.  However, it quickly became evident 
> that it could not work because Occurrences were at the center of the 
> diagram rather than Individuals.  So unless something changes, we 
> are already embarking on the process of locking out these other 
> Occurrence types.

Well...I certainly agree with you that we need *clear* documentation on what
these classes are intended to represent.  I had *thought* it was clear that
an Occurrence was as I have outlined above.  But like I said, I'm perfectly
willing to accept that I'm the idiot in this case, and am completely out of
phase with the rest of the community.

As to whether or not we need to define a class for Individual, I'm not so
sure that's entirely necessary.  I guess DwC is already primed for it
(http://rs.tdwg.org/dwc/terms/index.htm#individualID) -- but I'm not sure
what properties would apply to such a class that are not already covered in
DwC.  Pronbably the next intieration of DwC would move some of the
properties of the Occurrence class (catalogNumber, individualCount,
preparations, disposition, associatedSequences, previousIdentifications)
over to the Individual Class, at which point the Occurrence becomes the
intersection of an Individual and an Event.

But let me ask: how would you scope "Individual"? (see my previous rants on
this list in recent days)  Would it be restricted to a particular individual
organism? Or, would it be extended to include specified groups of organisms
(as dwc:individualID already does)? What about populations?  Taxon Concepts?

> I hate to sound like a broken record (do we have those any more?),
> but read my paper on this subject.  

I've had gotten through the first few pages, and intend to finish soon.  But
it's much more fun to write emails about this stuff..... :-)

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
Associate Zoologist in Ichthyology
Dive Safety Officer
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html