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Pete,<br>
Sorry - time out. This was not intended as a functional RDF example -
I only intended for people to look at the web page so they could see
the specimen sheet and the metadata that shows up on the web page for
the purposes of understanding the questions I was posing. The RDF was
originally supposed to be put on <a class="moz-txt-link-abbreviated" href="http://www.cyberfloralouisiana.com">www.cyberfloralouisiana.com</a>, not
bioimages.vanderbilt.edu, but that never was implemented, so the URIs
in the RDF won't make sense at the actual current file location.
That's why the page has as a warning that it's for testing purposes
only. <br>
Steve<br>
<br>
Peter DeVries wrote:
<blockquote
cite="mid:AANLkTinPRPhALdRDMUAo+6tyONrNgaODSjcCNQDVZWc8@mail.gmail.com"
type="cite">Hi Steve,
<div><br>
</div>
<div>You need to fix this in two ways (independent of the vocab,
which I did not check)</div>
<div><br>
</div>
<div>1) It should show up correctly in URIburner.</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://linkeddata.uriburner.com/about/html/http/bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf">http://linkeddata.uriburner.com/about/html/http/bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf</a></div>
<div><br>
</div>
<div>2) In the description of the RDF itself (in your example it is
at the bottom), you need to make a foaf:topic link between that element
and each of the</div>
<div> entities that start with "rdf:about". This will allow you to
find the actual rdf page that describes these. To get the link back
from the entity to the</div>
<div> page add a "foaf:page" that points back to the RDF.</div>
<div><br>
</div>
<div>Remember that in the cloud or in your triple store entities like
<<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind</a>>
are not tied</div>
<div>to the RDF that contains statements about them, without some
link to and from the page </div>
<div><<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf">http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf</a>></div>
<div><br>
</div>
<div>* You could get the same result by using the
"dcterms:references" and its inverse "dcterms:ReferencedBy", but let me
run that past someone to see if</div>
<div> it is equally accepted.</div>
<div><br>
</div>
<div>Here is an abbreviated version of what this might look like:</div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"><rdf:Description
rdf:about="<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf">http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf</a>"></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <dcterms:description>RDF
formatted description of the preserved specimen <a
moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428">http://www.cyberfloralouisiana.com/specimens/lsu000/0428</a></dcterms:description></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <dcterms:modified>2010-09-25T06:35:58</dcterms:modified></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <xmp:MetadataDate>2010-09-25T06:35:58</xmp:MetadataDate></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265b">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265b</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231b">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231b</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231a">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231a</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265a">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265a</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428">http://www.cyberfloralouisiana.com/specimens/lsu000/0428</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#img">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#img</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#tn">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#tn</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#lq">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#lq</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:topic
rdf:resource="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#gq">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#gq</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"></rdf:Description></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"><rdf:Description
rdf:about="<a moz-do-not-send="true"
href="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind">http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind</a>"></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"> <foaf:page
rdf:resource="<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf">http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf</a>"/></span></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif"><span
class="Apple-style-span" style="font-size: x-small;"></rdf:Description></span></font></div>
<div><br>
</div>
<div>Following this pattern, your RDF will be browsable as in this
example:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://linkeddata.uriburner.com/about/html/http/lod.taxonconcept.org/rdf/area_example.rdf">http://linkeddata.uriburner.com/about/html/http/lod.taxonconcept.org/rdf/area_example.rdf</a><br>
</div>
<div><br>
</div>
<div>Note how you can click back and forth between the location and
the RDF that describes it.</div>
<div><br>
</div>
<div>- Pete</div>
<br>
<div class="gmail_quote">On Mon, Oct 18, 2010 at 11:49 AM, Steve
Baskauf <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
I've fallen behind on systematically perusing the list responses, but I
would like to focus in on a point that seems to be a consensus in the
responses that have shown up recently. The consensus seems to be that
documenting determinations (a.k.a. instances of dwc:Identification
class) that are applied to Individuals (or Occurrences if you don't
believe in Individuals) is the way to go. So in my usual graphical way
of thinking about this, I would draw a "relationship line" from the
determination to the Individual (or Occurrence) on one side and from
the determination to the species concept on the other. 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. 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. <br>
<br>
That all seems pretty clear. However, when I've started trying to do
this in real life, I immediately have questions. Take a look at<br>
<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf"
target="_blank">http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf</a>
which
should show up as a web page in your browser.<br>
<br>
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"?<br>
2. Do we draw a distinction between the initial identification and
subsequent annotations? I think the answer should be "no" and that's
why I refer to both generically as "determinations".<br>
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? Is this
just something we can't do for old annotations and just something that
we try to do from this point forward?<br>
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. One would be to correct an actual error in
identification. One would be to increase the precision of a previous
determination (e.g. an insect identified to family now is identified to
species). One would be to assert a difference in opinion as to the
correct way to group this individual with others (i.e. as in a
taxonomic revision). 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). Some of these four reasons may be
functionally equivalent, but how would you use Darwin Core to indicate
the reason why you applied the determination? Please don't say
"identificationRemarks"! From a machine-processing standpoint, this is
something we should know and there should be some kind of controlled
vocabulary to express it. For instance if an identification is
"deprecated" because it was in error (perhaps by the determiner
him/herself), one would like the incorrect determination to show up in
the historical metadata, but I wouldn't want it to be listed in a
website index. The same would hold true if an annotator was able to
pin the taxon down to a lower taxonomic level than the original
identifier. If someone goes to the trouble to connect an
Individual/Occurrence to several names under alternative concepts,
there should be a way the a machine would know this so that a software
user could select the concept they wanted to use and the name under
that concept would pop up.<br>
<br>
I don't really see any term under the current DwC that could be used to
do this last thing. Am I missing something? Do we need several terms
to explain the reason why we made the determination because the reasons
fall into different categories?<br>
<br>
The other comment that I'll throw out (since this is going out to the
bioblitz list as well as to tdwg-content) is that those of you who are
building apps to collect metadata in the field really need to separate
the process of entering (or acquiring) the collection metadata from the
determination process. In at least some apps, the user immediately has
to commit to a taxon as they enter the data at the time of collection.
It seems to me that it would be a very common situation (especially in
the case of "citizen science") that the collector/observer/photographer
would have no idea what the taxonomic identity was at the time of
collection. The process of determination (and the recording of the
various dwc:Identification class terms) is really a separate process
that should be able to happen at the time of collection OR later.<br>
<br>
Steve<br>
<br>
Peter DeVries wrote:
<blockquote type="cite">Hi Steve,
<div><br>
</div>
<div>I would hypothesize that for the vast majority of identified
records the process is something like this:</div>
<div><br>
</div>
<div>1) An individual uses some sort of key to determine what
species
(taxon concept) to assign to a given individual</div>
<div> * They may have created some sort of mental key in which
once
they recognize one individual mosquito they can then pretty quickly sort</div>
<div> a number of individuals into collections.</div>
<div><br>
</div>
<div>2) The actual name they assign to the specimen is usually
based
on what their key says the name is. Often this does not specify the
authorship.</div>
<div> Most of these human identifiers have not read the
original
species descriptions and for the species they are identifying.</div>
<div> So the specimen is actually tied to a concept that is
based
more on the "key" than the original description.</div>
<div> * An exception, would be where there is a key in the
original description and that was what what was used.</div>
<div><br>
</div>
<div>3) So in a sense, the process of modeling this as if the if
the
identifier actually asserted that the concept was the same as that
described by</div>
<div> the original description or a subsequent revision is
"fudging"</div>
<div><br>
</div>
<div>Side effects of this process include:</div>
<div><br>
</div>
<div>1) A new key for North American Mosquitoes comes out that
incorporates recent changes in nomenclature. The major change being the
elevation of</div>
<div> a subgenus to a genus. For most of the species described
the
"key concept" is unchanged.</div>
<div><br>
</div>
<div>Student identifier, Bob, in state X is using the latest key,
while student identifier, Joe, is state Z is using a slightly older
edition of the same key.</div>
<div><br>
</div>
<div>Bob identifies the species as <i>Ochlerotatus triseriatus</i>,
while Joe identifies what should be the same species as <i>Aedes
triseriatus</i>.</div>
<div><br>
</div>
<div>These show up in GBIF on two different maps, they show up in
the
EOL as two different pages.</div>
<div><br>
</div>
<div>Various TDWG'ers continue to argue that the original
description
and subsequent revisions were really important in determining what
these individuals</div>
<div>actually meant when they assigned a name to a specimen, and
that
this is how we should model it in excruciating detail.</div>
<div><br>
</div>
<div>I would argue this should be modeled as best as possible to
what
actually happens.</div>
<div><br>
</div>
<div>For example, how many of the species observed in the recent
BioBlitz were identified by referring to the original species
description or subsequent revisions?</div>
<div><br>
</div>
<div>In your diagram, I would suggest that you show that a taxon
concept may have many names associated with it. Since it is not clear
what the identifier intended by his or her choice of a name, it is
often difficult to determine what taxon concept they actually meant.</div>
<div><br>
</div>
<div>This is why I advocate a move to a more taxon concept based
identifier to link these data sets together because this allows the
intent of the identifier</div>
<div>is more accurately modeled. </div>
<div><br>
</div>
<div>This would be done in the form of:</div>
<div><br>
</div>
<div> "I assert that this specimen (of what I call <i>Aedes
triseriatus</i>) was observed here. I also assert that it is an
instance of the this species concept => URI"</div>
<div><br>
</div>
<div> Or I assert that this is an individual of the type
"Individual
of species concept X" = > URI</div>
<div><br>
</div>
<div> All of these are instances of the class "Individual"</div>
<div><br>
</div>
<div>So the resulting DarwinCore record would contain both the
name
and and an optional, but I think needed, asserted species concept.</div>
<div><br>
</div>
<div>The species concept is a subclass of taxon concept, but is
fundamentally different than the higher clades.</div>
<div><br>
</div>
<div>There are some guidelines as to what an entity needs to be
considered a species. </div>
<div><br>
</div>
<div>While their are no real guidelines as to what clades should
be
considered genera and what clades should be considered families etc.</div>
<div><br>
</div>
<div>Assigning properties at the level of genera or family is
also
problematic because it assumes that there will be inferencing and it
will require rechecking</div>
<div>that those properties are still valid if the species within
that
genera change.</div>
<div><br>
</div>
<div>So if there is some property that is common to all the
species
in the genus, make that a property of each of the individual species -
not a property</div>
<div>of the genus.</div>
<div><br>
</div>
<div>Respectfully,</div>
<div><br>
</div>
<div>- Pete</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On Fri, Oct 15, 2010 at 10:45 AM, Steve
Baskauf <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu" target="_blank">steve.baskauf@vanderbilt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">As
a background to this post, I want to reference a post by Bob called
"SubclassOrNot". I discovered this page on an early foray into the
TDWG website labyrinth and it has been very influential on my thinking
since then. The idea Bob discusses is central to what I'm writing
below so if you haven't read it you might want to do so first. You can
probably skip the "OWL Inference" section and still get the point which
is described in the first two sections of his post. The URL for the
page is <a moz-do-not-send="true"
href="http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot"
target="_blank">http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot</a>
.<br>
<br>
To preface what I'm going to say below, I want to put Darwin Core
Occurrences in the context of what Bob wrote. In my mind, one of the
hallmarks of the Darwin Core standard and one thing that makes it a
great improvement over previous versions is that the decision was made
to use what Bob called the "has a" approach rather than the "is a"
approach. In particular, the Darwin Core standard has a single class
called dwc:Occurrence rather than subclasses called "Specimen",
"Observation", and other possible things. The way that we
differentiate among different kinds of Occurrences is by using the DwC
types which are the controlled values for the term dwc:basisOfRecord.
Thus we say an Occurrence "has a" basisOfRecord=PreservedSpecimen
rather than saying it "is a" PreservedSpecimen. We say an Occurrence
"has a" basisOfRecord=HumanObservation rather than saying it "is
a"HumanObservation". This approach has greatly reduced the number of
different terms in the standard since we don't have to have separate
"ObservedBy" and "CollectedBy" terms, but rather can just have a single
"RecordedBy" term that applies to both specimens and observations. The
same thing applies to many other things, like eventDate rather than
DateCollected and DateObserved, locality rather than collectionLocality
and observationLocality, etc. With the ratification of Darwin Core,
this decision is now a fait acompli and not a subject of discussion or
something optional for users of the standard. It also seems to be
clear that as necessary new terms can be added to the DwC types which
would then be valid controlled values for basisOfRecord.<br>
<br>
Since the adoption of the DwC standard, the approach to Occurrences has
been what I would describe as "I know an Occurrence when I see one". I
consider this as a pretty sloppy practice and as I indicated in my post
last night, I think there is enough consensus about what an Occurrence
is that we can come up with a better definition than "an occurrence is
the category of information pertaining to evidence of an
occurrence...". Another part of what I would characterize as
sloppiness is the lack of a clear definition of what exactly
basisOfRecord means. When I wrote my attempt at summarizing consensus
last night, I dodged the question about what I called the "token".
This "thing" has been called various names. In the previous
discussion on the list, it was sometimes called "the evidence" of the
occurrence. In the past I have called it "a representation" - however,
I now think the term "token" is better because "representation" has a
different technical meaning in the context of content negotiation.
When we type an Occurrence by saying it has a
basisOfRecord=PreservedSpecimen, we are saying that this Occurrence has
as supporting evidence, or as a "token" if you prefer, all or part of
the dead remains of the organism (i.e. what I'm calling "the
Individual") that was being documented by the Occurrence. When we type
an Occurrence by saying it has a basisOfRecord=LivingSpecimen, we are
saying that this Occurrence has as a "token" the entire organism that
was being documented (or some vegetative part of the live organism that
was propagated). When we type an Occurrence by saying it has a
basisOfRecord=HumanObservation, we are saying that the Occurrence has
no supporting evidence other than the reputation of the observer to
accurately record the metadata about the Occurrence. In other words,
we "tag" a instance of a core class (to use Bob's words), Occurrence,
by telling a metadata consumer what kind of token we are using as
evidence of the Occurrence. <br>
A fundamental part of creating a clear definition of what an Occurrence
is, is to define exactly what we are including in the concept of
Occurrence. One possibility is to (1) say that the two boxes at the
right side of the diagram at <a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif"
target="_blank">http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif</a>
are fused and that both the Occurrence metadata and its associated
token are what we consider to be "the Occurrence". Another approach
(2) would be to say that the actual Occurrence as an entity is only the
metadata part and that the token is a separate thing. A third approach
is to say (3) that everything with the blue dotted lines is considered
a part of the Occurrence (i.e. the metadata, the token, the event, and
the locality). I don't think in an absolute sense, any one of these
approaches is "right". The problem is that these approaches are used
inconsistently, sometimes even by the same person, depending on the
basisOfRecord. Differences in ways of thinking about this issue is a
part of why people aren't understanding the way other people are
approaching the structuring of metadata. I have tried to consistently
take the approach (1) that the two boxes on the right are fused, i.e.
that the Occurrence metadata and the token should both be considered
part of the entity that we call "an Occurrence". I think this is why
Rich was confused in <a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001666.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001666.html</a>
when I said that it was "wrong" to assert that a scientific name is a
property of an Occurrence - obviously it is silly to say that the token
(photons on a film, sound patterns in a digital file) has a scientific
name. Yet that is exactly what people do routinely when the token is a
branch cut off a tree and glued to a piece of paper. They say that
they are "identifying a specimen". What I am asking (actually
demanding) is that the TDWG community get its act together and come to
some consistency on this. If we are going to take the approach (2),
then we need to take specimens off their pedestal and treat them like
we do any other token that we are using as evidence that an Occurrence
happened. If we are going to do what was suggested for the BioBlitz in
<a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001603.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001603.html</a>,
i.e. to call Occurrences "observations" and then link the tokens to
them by associatedMedia, ResourceRelationship, or some other means
(approach 2) then do it consistently for every kind of token, including
specimens, and don't single out media tokens for punishment. <br>
I have in a sense "thrown down the gauntlet" on this issue by proposing
that DigitalStillImage be added as a DwC type and as a controlled value
for basisOfRecord (<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=68"
target="_blank">http://code.google.com/p/darwincore/issues/detail?id=68</a>).
I know what some people are going to say in response to this proposal.
"Why do you need to have 'DigitalStillImage' as a value for
basisOfRecord when you can just say that the resource's
dcterms:type=StillImage?" The answer goes back to Bob's point. If we
are going to go the "has a" path (which we already have in DwC for
Occurrences) rather than subclassing everything, then we need to
provide an appropriate value for the "tag" for any type of resource
that a reasonable number of users will want to use as a token. I think
it is clear from this and other Bioblitzes, my work in Bioimages, the
whale tracking project, and many other examples, that there are plenty
of people who are already using DigitalStillImages as tokens and we all
need a controlled value to use for basisOfRecord. <br>
The other thing that we accomplish when we type an Occurrence by its
basisOfRecord is to tell a consumer what kind of metadata to expect to
get about the token in addition to the generic metadata that is
provided for all Occurrences. Thus for a LivingSpecimen we expect to
be told what zoo, botanical garden, bacterial collection, etc. contains
the specimen. For a PreservedSpecimen we expect to be told the
preparation type, the location of the repository, etc. For a
DigitalStillImage we expect to be told the file type, accessURL, etc.
Simply providing a value for dcterms:type=StillImage doesn't indicate
whether the image is a physical one (i.e. on film) or a digital one.
It is also unreasonable to expect a client to have to be checking two
different terms (basisOfRecord and dcterms:type) to find out what they
could learn from one (basisOfRecord). Of course it would be advisable
to provide a value for dcterms:type as well for clients outside the
biodiversity community who may not "understand" what basisOfRecord
means. <br>
I hate to keep bringing my posts back to the RDF issue, but thinking
about how one would write RDF forces clear thinking about how metadata
should be structured. If we intend to separate tokens as entities from
their associated Occurrence metadata, i.e. approach (2), then we open
up a whole other can of worms. To associate the occurrence resources
(i.e. the metadata) with the "different" resource (i.e. the token), we
will have probably have to be able to create URIs for the tokens and
separate RDF metadata blocks which will have to be rdfs:type'd. What
are we going to use for that rdfs:type - create another Darwin Core
class? I simply don't think that is a complicated road that we want to
travel. It would be far easier to just say that every Occurrence has a
one-to-one relationship with its token (which could be "the empty set"
for observations). This would not work for people who want to hang
multiple tokens on a single observation event, but I think that itself
is a bad idea because it makes it even harder to have "flat" occurrence
datasets. Just say that every time we collect a different token (or
make an observation that has no token), it is a new Occurrence record.
Realistically, a single collector can't actually take a picture of a
plant at the same time he or she collects it for a specimen anyway.
Those really should be considered two different events because they
happen at different times.<br>
<br>
OK, enough said. Consider this my defense of my proposal "issue 68" to
add DigitalStillImage. I would urge the powers that be to respond to
the issues that I've raised here before having any kind of "vote" (or
whatever is ultimately going to happen when there is an up or down
decision about the proposal).<br>
<br>
Steve<br>
<br>
Steve Baskauf wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">After
the flurry of emails recently, I had an opportunity to carefully<br>
read all the way through the threads again, followed by enforced "think<br>
time" during my long commute. I was actually pretty cheerful after that<br>
because I think that in essence, most of the conversation about what<br>
constitutes an Occurrence really boils down to the same thing. So I<br>
have sat down and tried to summarize what seems to me to be a consensus<br>
about Occurrences. To follow my points, please refer to the diagram at:<br>
<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif"
target="_blank">http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif</a><br>
<br>
Consensus on relationships<br>
1. The fundamental definition of an Occurrence involves evidence that a<br>
representative of a taxon occurred at a place and time.<br>
Note 1.A: For clarity, I have modified John's statement in his last<br>
email by replacing "taxon" with "representative of a taxon". I'm<br>
considering a taxon to be an abstract concept that is applied to<br>
individuals or groups of organisms.<br>
Note 1.B. This definition is far more useful than the official<br>
definition of the class Occurrence "The category of information<br>
pertaining to evidence of an occurrence..." which is essentially
circular.<br>
Note 1.C: This statement is extremely broad because the evidence could<br>
be of many sorts, the representative could range from a single<br>
individual to all organisms on the earth, the taxon could be anyone's<br>
definition at any taxonomic level, the place could range from a GPS<br>
point with uncertainty of less than 10 meters to the entire planet<br>
earth, and the time could range from a shutter click of less than one<br>
second to 3.4 billion years.<br>
2. The diagram is an attempt to summarize in pictorial form statements<br>
and relationships that have been described in the thread. The taxon<br>
representative is recorded as existing at a particular time and place<br>
(the arrow) and the result is an Occurrence record. That Occurrence<br>
record exists as metadata which may be associated with a token that can<br>
be used to voucher the fact that the taxon representative existed. That<br>
token may be the organism itself (or a living part of it as in a twig<br>
for grafting), all or part of the organism in preserved form, an<br>
electronic representation such as an image or sound recording, and other<br>
kinds of things like tissue or DNA samples. There may also be no token<br>
at all, in which case we call the Occurrence record an observation.<br>
Based on direct observation of the taxon representative, examination of<br>
one or more tokens, or both, some determiner asserts that a taxon<br>
concept applies to the taxon representative and as a result a scientific<br>
name can be used to "identify" the taxon representative. (There may be<br>
a lot of other complicated stuff above the Identification box, but that<br>
will have to be filled in by the taxonomists.)<br>
Note 2.A: I have mapped onto this diagram the letters that John used in<br>
his last email to refer to entities that are involved in an Occurrence<br>
(T, E, L, O, and G). I will beg the forgiveness of fossil people<br>
because I don't really know how the geological context fits in. I'm<br>
assuming that it is a way of asserting time and location on a much<br>
broader scale than we do for extant organisms.<br>
Note 2.B: I have put a dotted line around the part of the diagram that I<br>
think includes all the things that people might consider part of the<br>
Occurrence itself. I have left out "T" and the other parts related to<br>
identification because it seems to me that you can have an occurrence<br>
that you document which does not yet (and perhaps never will) have an<br>
identification. The Occurrence still asserts that a taxon<br>
representative existed at a time and place; we just don't yet know what<br>
the taxon is.<br>
3. The red lines indicate the relationships that connect the various<br>
entities (I'm going to go ahead and call them resources). Consistent<br>
with popular opinion, the Occurrence record is the center of the<br>
universe and most things are connected to it.<br>
Note 3.A: I am sticking to my guns and refuse to connect the<br>
Identification directly to the Occurrence. It is the taxon<br>
representative that is being identified, not the occurrence. One can<br>
assert another sort of relationship between the identification and the<br>
occurrence if one wants to say that one consulted the occurrence<br>
metadata and token in order to decide about the identification, but it<br>
is not correct to say that the Identification identifies either the<br>
Occurrence metadata or the token (as Rich pointed out).<br>
<br>
OK, so that's step one - defining what is related to what. If anyone<br>
disagrees with these relationships, please clarify or create your own<br>
diagram.<br>
<br>
Complicating circumstances/caveats<br>
1. It is noted and recognized that some users will not care to include<br>
all of these relationships in their models. In the interest of<br>
simplification or "flattening" the relationships, they may wish to<br>
collapse some parts of this diagram (e.g. incorporate time and location<br>
metadata within the Occurrence metadata rather than considering them<br>
separate resources, applying scientific names directly to the taxon<br>
representatives without defining a taxon concept or recording the<br>
determination metadata, connecting identifications directly to the<br>
occurrence, etc.). This doesn't mean that the relationships don't<br>
exist, it just means that some users don't care about them.<br>
2. It is recognized that different users will be interested in or able<br>
to specify the various resources to differing degrees of precision.<br>
Examples: A photographer might record times to the nearest second, a<br>
collector may only be interested in noting the date on which a specimen<br>
was collected. A location may be specified to the precision of a GPS<br>
reading or be defined as some geographic or political subdivision. The<br>
taxon representative may be an individual organism, a flock or clump, or<br>
some larger aggregation of taxon representatives.<br>
<br>
That's step two. If I've missed any complications, please point them
out.<br>
<br>
My opinions about the implications of this diagram<br>
1. The circle I've labeled as "taxon representative" is the resource<br>
type that I'm proposing to be represented by the class Individual. You<br>
will note that in both the definition of dwc:individualID ("An<br>
identifier for an individual or named group of individual organisms...")<br>
and the proposed class definition ("The category of information<br>
pertaining to an individual or named group of individual organisms<br>
represented in an Occurrence"), groups of individual organisms are<br>
included. Thus John's example of a fossil having myriad individuals, or<br>
Richard's examples of thousands of plankton, a large school of fish,<br>
herd of wildebeest, flock of<br>
birds, could all be categorized as "Individual" under this definition if<br>
there is a reasonable expectation that all of the individuals in the<br>
group are members of the same taxon. Perhaps there is a better name for<br>
this resource, but since dwc:individualID was already extant, I chose<br>
Individual as the class name for consistency with the pattern<br>
established with other classes and their associated xxxxID terms.<br>
2. Although in note 1.C. I have given the ranges of the various<br>
resources to their logical extreme (as was done previously in the<br>
thread), I think that as a practical matter we can adopt guidelines to<br>
set reasonable values for the "normal" ranges of the resources. One<br>
such guideline might be that we suggest a range that can accommodate<br>
about 95% of the user needs within the community (this came from Rich's<br>
comment about satisfying 95% of the user need with an establishmentMeans<br>
controlled vocuabulary). For example, it was suggested that the range<br>
for the location of an Occurrence could span the entire planet Earth.<br>
True enough, but virtually nobody would find such a span useful. 95% of<br>
users would probably find a range between a GPS reading with 10 meter<br>
precision and the extent of a county or province useful for recording<br>
the location of an Occurrence. I can suggest similar "useful" ranges:<br>
one second to one day for an event time (excluding fossils), one<br>
individual organism to the number of organisms that would fit within a<br>
50 meter radius for an "individual", and taxon identified to family for<br>
plants and maybe mammals, genus for birds, and order for insects. So<br>
framing the definition of an Occurrence in these terms it would be<br>
something like: "An occurrence involves evidence (consisting of a<br>
physical token, electronic record, or personal observation) that a<br>
representative (ranging from a single individual to the number that<br>
would fit on a football field) of a taxon (hopefully identified to some<br>
lower taxonomic level) occurred at a place (determined to a precision<br>
between that of a GPS reading and the size of a county/province) and<br>
time (spanning one second to one day)." A few people might object to<br>
this level of restrictiveness, but I would guess that it would make 95%<br>
of us happy.<br>
3. With the exception of the "missing" class Individual, every resource<br>
type on this diagram except for the "token" and Scientific name has a<br>
Darwin Core class. Every resource type on the diagram except for "token"<br>
has a dwc:xxxxID term that can be used to refer to a GUID for the<br>
resource. The implication of this is that any resource on this diagram<br>
except for the token and taxon representative (i.e. Individual) is ready<br>
to be represented in RDF by Darwin Core terms in the sense that the<br>
relationships (red lines) can be represented by the xxxxID terms and<br>
that the resources can be rdfs:type'd using Darwin Core classes.<br>
(Lacking a class for the scientific name doesn't seem like a big deal to<br>
me since the scientific name can be a string literal - but then I'm not<br>
a taxonomist.)<br>
4. OK, I've avoided it as long as I can, so I'm going to confess now to<br>
the RDF-phobes. The red lines and shapes are something pretty close to<br>
an RDF graph. What that means is that if the community can agree that<br>
this diagram correctly represents the relationships among the kinds of<br>
biodiversity resources that we care about, then the matter of providing<br>
guidelines on how to represent Darwin Core in RDF suddenly gets a lot<br>
simpler. Just convert the "picture" of the RDF graph into XML format<br>
and we have a template. Alright, that's an oversimplification, but I<br>
think it is essentially true because the most difficult part of<br>
achieving a consensus on RDF representations is to decide how we connect<br>
the resource types, not on the literals that we hang onto resources as<br>
properties.<br>
5. While I'm beating the RDF drum again, the importance of my opinion<br>
number 2 can be extended into the GUID adoption process. In my comments<br>
to Kevin about the Beginner's Guide to Persistent Identifiers, I think I<br>
commented on the question of how one decides whether a GUID needs to be<br>
assigned to something or not. I believe that the answer to that<br>
question boils down to this: we need a GUID for any resource that will<br>
be referenced by more than one other resource. Do we need to be able to<br>
assign a GUID to Taxon concepts? Yes, because it is likely that many<br>
identifications will want to reference a particular taxon concept. Do<br>
we need to be able to assign a GUID to an Event? Maybe or maybe not.<br>
If every occurrence has its own separate time recorded, then no GUID is<br>
needed because the time is just a part of every separate occurrence<br>
record. If the event is defined to be a time range that represents a<br>
collecting trip, then there may be many Occurrences that are associated<br>
with that trip and all of them could reference the GUID for that event<br>
rather than repeating the event information for every Occurrence. The<br>
point here is that every shape (class of resources) on this diagram at<br>
least has the POTENTIAL to be a node connecting multiple resources and<br>
therefore should have the capability of being assigned a GUID, having<br>
its own RDF record, and being appropriately typed (presumably by a DwC<br>
class). So this is a final technical argument for why we need to have<br>
the DwC class Individual. Whether or not people ultimately choose to<br>
assign GUIDs to particular resource types or not is their own choice,<br>
but they need to at least be ABLE to if they need that resource to serve<br>
as a node given the structure of their metadata.<br>
<br>
We need to clarify how the "token" thing fits in, but I'm stopping there<br>
for now. I would very much appreciate responses indicating that:<br>
<br>
A. you agree with the diagram and connections (and consider this<br>
definition and diagram a consensus)<br>
B. you disagree with the diagram (and articulate why)<br>
C. you provide an alternative diagram or explanation of the<br>
relationships among the classes related to Occurrences.<br>
<br>
Thanks for you patience with another tome.<br>
Steve<br>
<br>
--<br>
Steven J. Baskauf, Ph.D., Senior Lecturer<br>
Vanderbilt University Dept. of Biological Sciences<br>
<br>
postal mail address:<br>
VU Station B 351634<br>
Nashville, TN 37235-1634, U.S.A.<br>
<br>
delivery address:<br>
2125 Stevenson Center<br>
1161 21st Ave., S.<br>
Nashville, TN 37235<br>
<br>
office: 2128 Stevenson Center<br>
phone: (615) 343-4582, fax: (615) 343-6707<br>
<a moz-do-not-send="true"
href="http://bioimages.vanderbilt.edu" target="_blank">http://bioimages.vanderbilt.edu</a><br>
<br>
_______________________________________________<br>
tdwg-content mailing list<br>
<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><br>
<a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content"
target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
.<br>
<br>
<br>
</blockquote>
<br>
-- <br>
Steven J. Baskauf, Ph.D., Senior Lecturer<br>
Vanderbilt University Dept. of Biological Sciences<br>
<br>
postal mail address:<br>
VU Station B 351634<br>
Nashville, TN 37235-1634, U.S.A.<br>
<br>
delivery address:<br>
2125 Stevenson Center<br>
1161 21st Ave., S.<br>
Nashville, TN 37235<br>
<br>
office: 2128 Stevenson Center<br>
phone: (615) 343-4582, fax: (615) 343-6707<br>
<a moz-do-not-send="true" href="http://bioimages.vanderbilt.edu"
target="_blank">http://bioimages.vanderbilt.edu</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
----------------------------------------------------------------<br>
Pete DeVries<br>
Department of Entomology<br>
University of Wisconsin - Madison<br>
445 Russell Laboratories<br>
1630 Linden Drive<br>
Madison, WI 53706<br>
<a moz-do-not-send="true" href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept Knowledge Base</a> / <a
moz-do-not-send="true" href="http://lod.geospecies.org/"
target="_blank">GeoSpecies Knowledge Base</a><br>
<a moz-do-not-send="true" href="http://about.geospecies.org/"
target="_blank">About the GeoSpecies Knowledge Base</a><br>
------------------------------------------------------------<br>
</div>
</blockquote>
<br>
<pre 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 moz-do-not-send="true" href="http://bioimages.vanderbilt.edu"
target="_blank">http://bioimages.vanderbilt.edu</a>
</pre>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
----------------------------------------------------------------<br>
Pete DeVries<br>
Department of Entomology<br>
University of Wisconsin - Madison<br>
445 Russell Laboratories<br>
1630 Linden Drive<br>
Madison, WI 53706<br>
<a moz-do-not-send="true" href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept Knowledge Base</a> / <a
moz-do-not-send="true" href="http://lod.geospecies.org/"
target="_blank">GeoSpecies Knowledge Base</a><br>
<a moz-do-not-send="true" href="http://about.geospecies.org/"
target="_blank">About the GeoSpecies Knowledge Base</a><br>
------------------------------------------------------------<br>
</div>
</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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