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Rich,<br>
Thanks for the great summary diagram and even more amazing that it was
made under mushed brain conditions. Hopefully you've gotten sleep
since then. Unfortunately, when I tried to
look at it I had some problems with line breaks. I've tried to
recreate your diagram at<br>
<a class="moz-txt-link-freetext"
href="http://bioimages.vanderbilt.edu/pages/rich1.gif">http://bioimages.vanderbilt.edu/pages/rich-diagram1.gif</a><br>
Please correct me if I didn't get it right. My arrow-drawing utility
put the arrow heads on the other end of the lines, but I think the
arrows still maintain the "many to one" relationships you were trying
to represent. I also replaced eventTime with eventDate since the
latter is a broader term that also can include the time.<br>
<br>
In principle, I agree with this diagram to the left of taxonNameUsage
completely. (I still need clarification about a few things on the
right end.) My main
reason for using determination as a term rather than identification is
because it is not ambiguous to refer to the person doing the
identifying as the determiner, whereas referring to that person as the
"identifier" creates confusion between that person and the identifying
string for resources (as in "persistent identifier"). So if we agree
that determination, annotation, and identification all mean the same
thing (namely an instance of the dwc:Identification class), I'm happy
to just use the term "identification". For the person doing it, I
guess dwc:identifiedBy would be the best term although it's a bit
awkward in regular speech so I may slip and still say "determiner". <br>
<br>
Although I agree in principle that there can be many occurrences at an
Event and many events at a Location, I think there are two practical
reasons why it may be better to assign separate eventDate and Location
metadata to each Occurrence. The first is that it makes the database
structure simpler. As Markus has already noted, we really would prefer
for the database to be as "flat" as possible. When I look at the terms
listed in the DwC term page (<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/index.htm">http://rs.tdwg.org/dwc/terms/index.htm</a>)
under Event, the most important one that I see which everyone should be
providing is eventDate. The rest I would pretty much consider optional
and as a shortcut Rich's diagram could be collapsed to make them direct
properties of the Occurrence. The second reason involves the practical
matter of defining a Location. I will note that my thinking about this
has been deeply influenced by a previous discussion on the topic from
2008-2009 summarized at
<a class="moz-txt-link-freetext" href="http://www.sernec.org/files/summary-of-discussion.pdf">http://www.sernec.org/files/summary-of-discussion.pdf</a> on p.78-84. I
don't think most people will want to wade through all of that text, so
I'll just sum it up here. Somebody (I think it might have been Debbie
Paul at Morphbank) suggested to me that we really have an intrinsically
globally unique identifier for Location. It's the combination of
dwc:decimalLatitude and dwc:decimalLongitude along with
dwc:coordinateUncertaintyInMeters to establish precision and
dwc:geodeticDatum to establish the reference system. (If we like
geo:lat and geo:long, then the reference system is implied and we are
down to three terms to unambiguously define a Location and its
uncertainty. For the benefits of humans, a Locality description is
probably also beneficial. Also, elevation and depth might be provided,
although at least in theory elevation could be calculated with a
sufficiently good digital elevation model). I will grant that we don't
have this information for a lot of old records, but based on the
massive efforts to geolocate specimens, I would say it's pretty clear
that this is what we would like to have if we could get it. I
certainly hope that there aren't any serious collectors, observers, and
live organism photographers who aren't by this point trying to record
this information as they establish new Occurrence records. If you look
at all of the Location terms on the dwc list, most of the other terms
are either concessions to the fact that we don't have what we want
(e.g. the "verbatum" terms), things we could generate using a computer
program if we were clever (like stateProvince, county, etc. - I know at
least Mike Giddens has succeeded in doing this), ways of indicating how
we got lat and long from old records (e.g. georefererenceSources), or
methods to define larger scale Locations that aren't points (e.g.
footprintWKT). I think it is safe to say that in the future (if not
now already), many or most Events associated with Occurrences will have
an associated button click (on a GPS receiver, camera phone, or GPS
enabled camera) that will automatically generate dwc:eventDate,
dwc:decimalLatitude, dwc:decimalLongitude (with geodeticDatum=WGS84)
and maybe coordinateUncertaintyInMeters. Thus designing a system that
requires that these time/space snapshots be grouped together into
artificial "Locations" is really counterproductive when those data are
now generated and can be associated with Occurrences automatically. I
don't know if Greg Riccardi of Morphbank is following this thread or
not. If so he may want to comment on this issue based on practical
experience at Morphbank. When the Morphbank system was set up, it
required the creation of a separate Location record which was assigned
a unique Morphbank identifier. Specimens were then linked to this
Location. What ended up happening was that each Specimen having GPS
metadata ended up being assigned to its own separate Location even if
it was 20 meters from another specimen. In effect, each Occurrence
record ended up having its own decimalLatitude/decimalLongitude record
anyway. So the system ended up being more complicated than necessary.<br>
<br>
As I said, I agree in principle with the left side of Rich's diagram.
Taking the practical considerations I just mentioned into account, I
would simplify the diagram as<br>
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/pages/rich-diagram2.gif">http://bioimages.vanderbilt.edu/pages/rich-diagram2.gif</a><br>
Superficially, it looks more complicated, but I've gotten rid of
several "one to many" relationships and enthroned Occurrence at its
accustomed place in the center of the universe (or at least the center
of the left side of the diagram). I don't have any philosophical
objections to people structuring their data according to Rich's
original diagram and the existing Darwin Core terms certainly make it
possible to do so (well except for the Individual thing). However, I
submit that many people will find it simpler (and easier to use tools
like Darwin Core Archives) if they use the flatter structure that I
have in the revised diagram.<br>
<br>
I will save my questions about the right side of Rich's diagram for
later.<br>
Steve<br>
<br>
Richard Pyle wrote:
<blockquote cite="mid:1D6EF22F847C423E8B1BE1E889142838@RLPLaptop"
type="cite">
<pre wrap="">All,
I'm in Stockholm, and right now it's 10am in Hawaii, and I've effectively
been awake since 7pm Hawaii time -- so my brain is a bit mush. But I'll take
a chance and comment anyway.
</pre>
<blockquote type="cite">
<pre wrap="">I will leave up to the taxonomy people the
different things would be connected to the
species concept and how all of their lines
would be connected.
</pre>
</blockquote>
<pre wrap=""><!---->
In my mind the "fully-normalised" (sensu Döring) relationship graph is
something like this (notation is [One]--<[Many]; [One]--[One]) (Be sure to
view as a fixed-width font, like Courier):
[identifiedBy]
|
[Location]--<[Event]--<[Occurrence]>--[Individual]--<[Identification]--[Taxo
nNameUsage]>--[nameAccordingTo]
| |
|
[eventTime] [dateIdentified]
[scientificName]
I'm following what I *think* Steve defined for [Individual], which is that
it can be either a single individual organism or a defined set of organisms
(e.g., up to at least a population).
So, an Occurrence is the intersection of an Individual and an Event. An
Event is a Location+Time[+other metadata]. Each Event may have multiple
Occurrences (i.e., one for each distinct Individual at the same
Location+Time). Also, an Individual may have multiple Occurrences (one for
each Event at which the same Individual was documented).
An Individual may have multiple Identifcations. I make no distinction
between "Identification" and "Determination" (nor do I make a distinction
between the first identification and subsequent identifications). I
slightly prefer "Identification", because "Determination" seems to imply
that there is a correct answer, whereas "Identification" (to me, anyway),
implies an opinion. Steve, I didn't quite follow how you were
distinguishing these two terms -- so if you have a clear reason for
distinguishing them, I'd like to understand it better.
A single Identification should, in my mind, always join a single individual
with a single "TaxonNameUsage" instance. I'm not 100% sure how
TaxonNameUsage maps in DwC. I *think* it's an instance of a dwc:Taxon, as
most of the core attributes of a TNU (acceptedNameUsage[ID],
parentNameUsage[ID], originalNameUsage[ID], scientificName, taxonRank) are
represented as terms in the Taxon Class. But I'm a little fuzzy on whether
a "taxonID" maps directly to a TNUID, or if a TNUID more correcly maps to
taxonConceptID.
</pre>
<blockquote type="cite">
<pre wrap="">The determination would have any of the properties that are
terms listed in the dwc:Identification class (identifiedBy,
dateIdentified, identificationReferences, identification Remarks,
identificationQualifier, and typeStatus). Some properties like
dateIdentified and identificationReferences would be string
literals and others (especially identifiedBy) should probably
be GUIDs but could be literals if they had to be.
</pre>
</blockquote>
<pre wrap=""><!---->
I agree with what Steve wrote above. However, I'm uncomfortable with
Markus' suggestion of treating dwc:nameAccordingTo as a property of an
Indentification -- even as a shortcut. I think this is a bit dangerous. If
there is no TaxonID instance (aka "TaxonNameUsage" in my diagram above)
available to link the Identification to, then I would suggest using
identificationReferences as the shortcut. But that would still force you to
attached scientificName directly to the Identification instance, which I
think is also unwise. I'd rather the Best Practice be to "manufacture" a
place-holder dwc:Taxon instance (if a proper one doesn't already exist in
the content source), and apply the scientificName property to that Taxon
instance, rather than directly to an Identification. I know it's often
short-hand to attach the scientificName directly to the Occurrence instance;
but I actually feel less uneasy about that, because it is much more
obviously a shortcut. But if you're going to the trouble to provide an
instantiated "Identification", then you ought to anchor it to a Taxon
instance (manufactured or real).
But, I guess as Greg said in his post, it may not really matter, as in the
long run, we'll probably be able to make inferences about the proper
Individual<-->TaxonConcept mapping, even when it's not explicitly
documented.
</pre>
<blockquote type="cite">
<pre wrap="">1. The original label identifies the species as Juncus
diffusissimus. However, there is no indicator as to who
originally identified it or when. My assumption is that
it was the collector (Glen N. Montz) but I don't really
know that. Do I assume that, or list the original
determiner as "unknown"?
</pre>
</blockquote>
<pre wrap=""><!---->
I would make no assumptions about who was the identifiedBy person. Instead,
in these cases I handle these cases by either going with "Unspecified", or,
in some cases (when I have confidence), something like "Bishop Museum Staff
Member". Often I can deduce the identifier with some degree of confidence,
but usually I don't have the time to do this. The dateIdentified can either
not be provided, or set as some range (e.g., at the very worst, on or after
the eventDate/eventTime, and before today).
This is why I think that identification tags ("annotations" sensu Baskauf)
can be "documentation sources for TNUs.
In the web example given by Steve, we have an idetification as follows:
Juncus diffusissimus Buckl.
Determined by: L. Urbatsch
Determination date: 2009
Completely independantly of the specimen itself, we can infer from the tag
that:
- Sometime between 1 Jan 2009 and 31 Dec 2009, L. Urbatsch regarded the
genus "Juncus" as valid.
- Sometime between 1 Jan 2009 and 31 Dec 2009, L. Urbatsch regarded the
species epithet "diffusissimus" [of Buckl.] as a valid species, placed
within the genus "Juncus".
Thus, we have at least two implied TNUs from this identification, which was
documented on a piece of paper that happens to be fixed to LSU-BR 39823.
The Identification instance would link the Individual (manifest as a
specimen, in this case) to the TNU of "[Juncus] diffusissimus Buckl. sec L.
Urbatsch 2009". The nameAccordingTo would be "L. Urbatsch 2009". This may
seem redundant to have "L. Urbatsch 2009" in both the nameAccordingTo
attribute of thr Taxon instance, and in the identifiedBy & dateIdentified
attributes of the Identification instance -- but the fact remains they are
fundamentally different pieces of information. One establishes an instance
of an (implied) taxon concept, and the other establishes the placement of
LSU-BR 39823 within that taxon concept circumscription.
Eventually, a third party may be able to deduce (perhaps through a suite of
other, external information) a RelationshipAssertion that maps the TNU
"[Juncus] diffusissimus Buckl. sec L. Urbatsch 2009" to some other, perhaps
published and well-defined taxon concept (of the same or different name).
Also, if there are 100 specimens in the collection that L. Urbatsch
identified as "Juncus diffusissimus Buckl." in 2009, then anchoring all 100
Identification instances to the one TNU, allows all of those specimens to
inherit the mapping of the one "[Juncus] diffusissimus Buckl. sec L.
Urbatsch 2009" TNU instance to some other better-defined taxon concept.
I know this is a lot of stuff to keep in one's head at the same time -- but
as cumbersome as it seems, I am conviced it can be packacged into a
relatively straightforward and intuitive user UI, and modelling it this way
improves the utility of the data (maybe dramatically) in the long run.
</pre>
<blockquote type="cite">
<pre wrap="">2. Do we draw a distinction between the initial identification and
</pre>
</blockquote>
<pre wrap=""><!---->subsequent annotations?
</pre>
<blockquote type="cite">
<pre wrap="">I think the answer should be "no" and that's why I refer to both
</pre>
</blockquote>
<pre wrap=""><!---->generically as "determinations".
I agree.
</pre>
<blockquote type="cite">
<pre wrap="">3. There is really no indication given on the annotation
labels as to many of the things that we would like to know,
such as the concept they had in mind, any source they used (if any),
or the reason why they did the annotation. So how does one
connect the name that they applied to the determination when
there is no indication of the concept?
</pre>
</blockquote>
<pre wrap=""><!---->
As I said in an earlier post, the single most important way to reduce
taxonomic ambiguity is to try to capture (or confidently deduce) the source
(=mapping to taxon concept). But if it can't be done, then it can't be done
-- so I'm inclined to establish a "place-holder" dwc:Taxon instance, with no
nameAccordingTo, and no other metadata besides the scientificName.
</pre>
<blockquote type="cite">
<pre wrap="">Is this just something we can't do for old annotations
and just something that we try to do from this point forward?
</pre>
</blockquote>
<pre wrap=""><!---->
Probably.
</pre>
<blockquote type="cite">
<pre wrap="">4. The last question is one that I really want to some
opinions about. It seems to me that there are a number
of reasons why one would apply a determination.
</pre>
</blockquote>
<pre wrap=""><!---->
Hmmm....I don't think this is really useful information. I don't
undersatand how you would use this information ina machine-processing sort
of way. An Identification is an Identification. In some cases, the
Identifier may not even be aware of the previous identification, and so we
can necessarily infer there was a particular "reason". And even if there is
a reason, how doe we use that information? What if there is more than one
reason (i.e., if we are restricted to a controlled vocabulary)?
As far as I'm concerned, the Identifications should stand as they are. If
needed people can annotate the Identification instances; but I don't see the
value in machine-processing these things.
Also:
</pre>
<blockquote type="cite">
<pre wrap="">Finally, a single determiner might apply
several determinations to one individual and indicate
in each determination the concept intended (i.e. if
you subscribe to Cronquist, you'd call it X; if you
like Radford's book, you'd call it Y; if you like
Weakley's treatment, you'd call it Z).
</pre>
</blockquote>
<pre wrap=""><!---->
YIKES! I don't like the idea of loading all that information on an
Identification instance. If the person wants to make this sort of
assertion, then they should establish the appropriate relationshipAssertion
instances among the various taxonConcepts cited.
Damn. Now my head is really tired. And so is the rest of me....
Aloha, and g'night..
Rich
.
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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