[tdwg-content] Please unsubscribe me

Yuri Roskov y.roskov at reading.ac.uk
Wed Oct 27 13:23:51 CEST 2010

Dear Moderator,

Could you please unsubscribe me from all TDWG mailing lists? Unfortunately, without my will I am flooded with TDWG emails since 8th October. Most of subjects are very interesting, but I have my job to do.

Yours, Yuri 

Dr. Yury Roskov
Catalogue of Life Executive Editor
School of Biological Sciences
The Harborne Building
The University of Reading
Reading, RG6 6AS, UK
Tel. +44 (0) 118 378 6466
Fax +44 (0) 118 378 8160
E-mail: y.roskov at reading.ac.uk
www.sp2000.org, www.catalogueoflife.org
EC projects: www.4d4life.eu, www.i4life.eu 

  ----- Original Message ----- 
  From: Steve Baskauf 
  Cc: tdwg-content at lists.tdwg.org 
  Sent: Wednesday, October 27, 2010 11:42 AM
  Subject: Re: [tdwg-content] Treatise on Occurrence, tokens, and basisOfRecord

  Please note that in various examples, I have incorrectly placed rdf:type in the namespace rdfs: (http://www.w3.org/2000/01/rdf-schema#) rather than rdf: (http://www.w3.org/1999/02/22-rdf-syntax-ns#).  Thanks to Bob for pointing out this serious error.  

  Also, the ACS model information is very cool.  I wish I'd seen it a long time ago.  I especially like the giant relationship chart.  Thanks Stan and Rich.

  Steve Baskauf wrote: 
    Thanks for taking the time to read the whole thing.  Based on the first series of comments you made, it seems as though we are in agreement on most points.  I think that what I wrote was (as I had anticipated) somewhat less clear due to my use (or failure to use) some appropriate terms to describe what I was talking about.  For example, when I said "atomized" I probably should have said something like "fine-grained" and correct use of the term "normalized" would have helped.  Some other comments inline:

    Richard Pyle wrote:

I believe that historically the assumed token model has been
the one which most people have had in mind.
Actually, I've always envisioned it as you have in your token-explicit
version (and have said as much at various meetings to discuss DwC, going
back to 1.0).  In fact, I remember discussing this exact issue with Stan
Blum long before DwC existed (he was the first to suggest to me the term
"evidence" in this context -- which I think is functionally equivalent to
your "token"). However, I've conceeded that this level of normalization
would probably be too much for the intended purpose of the DwC terms.  But
I'll keep an open mind on that.

  Before the new DwC standard, we had specimens and we had
observations.  In order to avoid redundancies in terms for
those two types of "things", a combined "thing" called
"Occurrence" was created.  An Occurrence that was an
observation didn't have a token and an Occurrence that
was a specimen had a physical or living specimen as its
My rationalization of it in the early days (pre-DwC) was that *everything*
was effectively an observation, and beyond that, the only question was a
matter of evidence.  In my earliest models, I categorized "evidence" into
"Specimen", "Image", "Literature Report", and "Unvouchered Observation" (I
was using the word "voucher" in the general sense, as in the verb "to vouch"
-- not in the more specific sense for our community, which implies "Specimen
preserved in Museum").  My read on the history of DwC is that it was
initially established as a means to aggregate and/or share Specimen data
amongst Museums (hence its Specimen-centric nature).  Later, the
Specimen/Observation dichotomy was introduced to allow DwC content to allow
more sophisticated and complete representations of the occurrence of
organisms in place and time, because there was muchmore information than
what existed as specimens in Museums.  In my mind, the "Observation" side
was effectively a collapsing of my "Image", "Literature Report" and
"Unvouchered Observation" -- which I was OK with in the context of the time.
Because at the time, the vast majority of content available in computer
databases came from museum specimen databases, and from observational
databases (largely in the bird realm).
  Well, I'm not surprised that the ideas that I'm trying to put down in words and diagrams predate my entry into this arena a year and a half ago.  What is a bit frustrating to me is that ideas like these aren't laid out in an easy-to-understand fashion and placed in easy-to-find places.  I have spent much of that last year and a half trying to understand how the whole TDWG/DwC universe is supposed to fit together.  I think that the idea of having the Google Code site where there are explanations and examples for the various DwC terms is the kind of thing we need.  Unfortunately, most of the terms do not yet have entries there.  Perhaps I'm just impatient.  If it turns out that any of the summaries that I've written here accurately reflect any kind of consensus, then maybe someone could "clean them up" (i.e. use correct technical terms after giving definitions of what they mean) and paste them somewhere where people can find them.  That would prevent another person 10 years from now re-articulating the same ideas a third time.  I'm particularly thinking of the summary diagram http://bioimages.vanderbilt.edu/pages/token-explicit.gif along with an explanation of how people use the more normalized and more flattened versions of it.  We already do have quite lucid examples in the Simple Darwin Core (flattened) and Darwin Core XML guide (normalized), but some sort of overview of the big picture might be helpful.  If an RDF guide ever gets off the ground, that would be another example of how the relationships assumed in DwC are expressed in a very explicit way.  

So...I see the current iteration of DwC as another step in the evolution of
moving from "sharing and aggregating specimen data among museums" to
"documenting biodiversity in nature".  It's not all the way into the fully
normalized representation of biodiversity data, but it's far enough that it
is a nice compromise between practical and effective for the majority of the
user constituency. In my mind, the next logical step in this evolutionary
trajectory would be to recognize "Individual" as a class (which DwC is
apready primed for, via individualID).
  I think I understand the message that you are trying to convey above and in your later comments about creating new versions of DwC (or new evolutionary states of DwC) that don't break the previous ones.  I think that is one reason why the process of examining and clearly articulating the community consensus on what Darwin Core terms and classes "mean" and how they are connected to each other is so important before we embark on implementing GUIDs and RDF.  Pete has suggested that we may need a second version of DwC in order to make it work in the Linked Open Data world and he's probably right.  I'm not sure that the existing vocabulary has all of the terms we need to do that.  However, if we are going to "evolve" Darwin Core so that it will work in the LOD world, I hope that we do it in such a way that we maintain the same "meaning" of things as Darwin Core 1.0 .  I think that is the way to maintain the kind of "stability" that you described below.  

Unlike specimens where the token's metadata terms are placed in the
Occurrence class, I guess in the case of an image one is supposed
to use associatedMedia to link the so-called MachineObservation to
the image record.  If DNA were extracted, one would link the
sequence to the Occurrence using associatedSequences (although
it's not clear to me what the basisOfRecord for that would be -
"TookATissueSample"?).  But what does one do for other kinds of
tokens, like seeds or tissue samples - create terms like
associatedSeed and associatedTissueSample?
In my mind, things like seeds, tissue samples, and DNA sequences are simply
different kinds of specimens (just like dried skeletons vs. botanical
pressed sheets vs. whole organisms in jars of alcohol vs. prepared skins,
etc.)  They may have certain properties specific to each subclass of
specimen, but fundamentally I think it's fair to treat them as specimens.
DNA sequences are a bit different, of course, because they are not the
"stuff" of an organism, but rather an indirect representation of the
"stuff".  In my mind, that difference justifies associatedSequences, where
we don't have associatedSeeds, associatedTeeth, associatedSkins,
associatedSkeletons, etc.
  Your point is well taken in that we don't need a proliferation of types of associated tokens.  We need as many different token "types" as we have coherent sets of metadata terms.  One of the points of typing resources is to let potential users know what kinds of metadata properties (terms) they can reasonably expect to receive about that resource.  If one will receive the same set of properties about two kinds of resources (e.g. skins and skeletons), there is no reason to type them differently.  The point that I was trying to get at (eventually) was that it was inconsistent to say that images need to be referenced as associatedMedia and sequences needed to be referenced as associatedSequences, and yet not say that specimens needed to be referenced as "associatedSpecimens".  I actually think that based on Roger's explanation of "to subclass or not" (http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot), it makes more sense to talk about using a generic "hasToken" or "tokenID" along with "tagging" the token using rdfs:type (as I suggested toward the end of my "treatise") rather than a bunch of associatedXXXX terms.  

  If we accept the explicit token model, then as a biodiversity
informatics resource type "observation" will have to disappear
into a puff of nothingness
Not necessarily.  See my comment earlier about patterns on neurons in a
human brain that constitute a memory.  Just as a digital image rendered on a
hard disk requires certain machinery to convert into photons that strike our
retinas (i.e., a computer and monitor), so too does a memory require such
machinery (e.g., the brain itself, transmission of sound waves via vocal
chords, soud ways striking ear drums, etc.)  This may sound weird, but I'm
being serious: a human memory is, fundamentally, every bit as much of a
"token" as a specimen or a digital image.  It's just considerably less
accessible and well-resolved.
  I guess I'm thinking about this in terms of a token being something to which we can assign an identifier and retrieve a representation (a la representational state transfer).  Although I don't deny the existence of memory patterns in neurons that are associated with a HumanObservation, there isn't any way that we can receive a representation of that memory directly.  If the person draws a sketch of what he/she remembers, then we have a media item that we can convert into a digital form and transmit through the Internet (a token).  If the person types up notes, then we have a text document  (a token that can also be delivered as a digital file or scan of typewritten page).  On the other hand, if the person simply records the values of recordedBy, eventDate, and Location terms, then we have only Occurrence metadata (no token).  If someone claims "basisOfRecord=HumanObservation" and has no token of any kind, then what is there that is deliverable other than the basic Occurrence metadata?  That's why I'm claiming that basisOfRecord=HumanObservation simply corresponds to an Occurrence record with no token.

  Realistically, I can't see this kind of separation ever happening,
given the amount of trouble it's been just to get a few people
to admit that Individuals exist.
I don't think the issue was ever in convincing people that Individuals exist
-- that much, I think, was clear to everyone (as proof: see
dwc:individualID).  The issue was always more about where the current DwC
should lie on the scale of highly flattened (e.g., DwC 1.0) to highly
normalized (e.g., ABCD and CDM).  It's necessarily a compromise between
modelling the information "as it really is", vs. modelling the information
in a way that's both accessible to the majority to content providers, and
useful to the majority of contnent consumers.  I think we both understand
what the trade-offs are in either direction. The question is, what is the
"sweet spot" for the majority of our community at this time in history?

I would venture that at the time DwC 1.0 was developed, that hit the sweet
spot reasonably well.  As more content holders develop inclreasingly
sophisticated DBMS for their content, and as the user community delves into
increasingly sophisticated analyses of the data, the "sweet spot" will shift
from the flattened end of the scale to the normalized end of the scale. And,
I would hope, DwC wll evolve accordingly.

  It is just too hard to get motion to happen in the TDWG community.
People make the same complaint about another organization that I'm involved
with (ICZN).  But here's the thing: as in the case of nomenclature,
stability in itself can be a very important thing.  If DwC changed every six
months, then by the time people developed software apps to work with it,
those apps would already be obsolete.  If someone writes code that consumes
DwC content as expressed in the current version of DwC, then that code may
break if people start providing content with class:individual and
class:token content.  If our community is going to move forward
successfully, I think standards like DwC need to evolve in a punctuated way,
rather than a gradualist way (same goes for the Codes of nomenclature). That
is, a bit of inertia in the system is probably a good thing.

  OK, I've now gone on for eight pages of text explaining the
rationale behind the question.  So I'll return to the basic
question: is the consensus for modeling the relationship
between an Occurrence and associated token(s) the assumed
token model:


      or the explicit token model:


Here's how I would answer:  When modelling my own databases, tracking my own
content, I would *definitely* (and indeed already have, for a long time now)
go with the token-expicit.

But when deciding on a community data exchange standard (i.e., DwC),
compromise between flat and normalized is still a necesssity, and as such,
the answer in terms of modifying DwC needs to take into account the form of
the bulk of the existing content, the needs of the bulk of the existing
users/consumers, and the virtues of stability of Standards in a world where
software app development time stretches for months or years.

Maybe the answer to this is to treat different versions of DwC as
concurrent, rather than serial.  That is, as long as the next most
sophisticated version can easily be "collapsed" to all previous versions
(aka, backward compatibility), then maybe we just need a clear mechanism for
consuming applications to indicate desired DwC version. That way, apps
developed to work with v2.1 can indicate to a provider that is capable of
produding v3.6 content, that they want it in v2.1 format.  Assuming we
maintain backward compatibility (i.e., the more-normalized version can be
easily collapsed to the more flattened version), then is should be a very
simple matter for the content provider to stream the same content in v2.1
  Yes, I agree about this concept.  I think that what I'm really advocating for is that we agree on what the most normalized model is that will connect all of the existing Darwin Core classes and terms.  In that sense, when I'm asking for Individual to be accepted as a class, I'm not arguing for a "new" thing, I'm arguing for a clarification of what we mean when we use the existing term dwc:individualID.  When I'm asking for terms to facilitate a logically consistent way to connect Occurrences with their tokens, I'm also not really asking for an expansion of Darwin Core, I'm asking for a more consistent model than "subclassing" by using associatedMedia and associatedSequences but not using "associatedSpecimens".  I think that this is important because if we don't agree on these things, we are going to have a royal mess on our hands if we try to start trying to develop an RDF guide for Darwin Core.  As an eternal optimist, I think that describing a fully normalized model that can be translated into RDF can be achieved with only a few minor additions to the existing terms as opposed to requiring a complete new version.  If we really need to completely rewrite Darwin Core for RDF I don't have any delusions that it will be accomplished before I retire.  

But now I'm dabbling in areas that are WAY outside my scope of expertise...

Anyway...I would reiterate that I, for one, appreciate that you took the
time to write all this down (took me over 3 hours to read & respond -- so
obviously I care! -- of course, I'm waiting for a taxi to go to the airport,
so really not much else for me to do right now).  If I didn't reply to parts
of your message, it was either because I agreed with you and had nothing to
elaborate or expound upon, or I didn't really understand (e.g., all the rdf
  Again, thanks for taking the time to read and comment.


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

postal mail address:
VU Station B 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 343-6707

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

postal mail address:
VU Station B 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 343-6707


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