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

Peter DeVries pete.devries at gmail.com
Thu Oct 14 21:09:15 CEST 2010


I think that it might be useful to point out that there are actually two
different "kinds" of DarwinCore at least as I see it

1) The first is the current more XML-ish version that people use for their
records,  A format largely intended to consumed by GBIF.
This is a representation that allows users to map the Excel or RDMB tables
to a standard set of fields.
This appears to pretty close to workable. Two areas where I am not sure
about are:

    Does this form need an "Individual" class as you propose?
    Should this form allow the use of the geo vocabulary?

In this version, something like TaxonConceptID is probably fine because the
consuming application will know to look at the contents of that field,
determine if it is an LSID or a URI and handle it appropriately. Generic
semantic web tools will not be able to handle these but if this is
understood ahead of time, it is not a problem. These are not made for
generic tools but for specific tools and use cases.

So what I propose is we address the issues of the current XMLish DarwinCore
so that it handles some of the issues you mention.

I think Markus would probably have some valuable insight into how this can
be done in a way that will work with GBIF.

This should result in a clear form 1 version of the Darwin core fairly

This allows the submission process to continue without confusion while the
issues of the other version get worked out.

For most users, form 1 is all they will need to understand.

2) The second version is a more fully semantacized version which I think
will require a lot more discussion. This version should be understandable
by the generic semantic web tools and should ideally also work well in the
LOD cloud. But it will take some time for us to agree how this should
be done and even longer for the general community to get familiar with it.
For most users, form 1 is all they will need to understand.

Once we have actually figured out a more semantic version that makes sense,
GBIF can process and express the submitted data in this version.
(I am over simplifying here but I will be more specific below)

This process might take a while and I think a number of groups will probably
want to stick to submitting their data in DWC form 1.

I think the issue that you and I have run into are where we are trying to
use form 1 as if it was more like form 2 and running into problems.

Some of these issues are relatively easy to solve, others are very tricky
and are only visible when you try to run specific kinds of SPARQL queries on
the knowledge base.

Others are even more complicated. For instance, I see that there might be a
need for several forms of "species concepts".

Those that I have created have specific use cases in mind. A lot of the use
cases that Steve's describes overlap with my use cases.

Most of my concepts are structured to provide basic informatin and a map to
other potentially related information sources.

What I eventually intend them to be serve as a form of "key element" that
that allows different people to repeatably map the same
specimens to the same concepts.

I think these will eventually useful as concepts for DWC form 1 because they
basically represent a  "key element"

As currently proposed, do they cover some of the issues and relationships
handled by Rich Pyle's TNC's?

No they don't.

(We do think that we can make some interesting and useful interlinkages
between the TNC's and the TXN's)

There are probably other groups with use cases for species concepts which
may necessitate different underlying assumptions.

So, for just the aspects relating to species concepts, there still needs to
be a lot more discussion.

As to the related things like occurrences, and individuals, it is clear to
me there are a lot of similarities and overlap.

The differences seem to mainly involve the specifics of the RDF

There are other aspects where the meaning or mental constructs are different
for what - may at first - seem similar. For instance, I would see the
specimens derived from one individual plant but now existing as two separate
plant in a different locations as a separate individuals. In the same way
as I see identical twins as different individuals.

So we have a slightly different conceptualization of what an "individual"

To solve this we will need to have some sort of meeting or videoconference
between those groups that have a pretty good understanding of RDF.
This will allow us to hash these issues out. Here we could explain our
different conceptualizations and use cases and see if we can come up with
some common standards that will allow people to do what they need to do
while following a common standard.

This will need some sort of whiteboard enabled discussion, sample data sets,
and example SPARQL queries.

We should also have use cases in the form of SPARQL queries, that allow the
resulting knowledge bases to be successfully queried in the ways that people
need, and return the kinds of results they expect.

It appears to me that the more semanticized version of the DarwinCore will
require RDF that differentiated between:

1) entries that are literals,
2) entries that a LOD compatible URI's
3) entries that are LSID's dereferencable via a proxy.

There are a number basic issues involving RDF, which the members will need
to have a common understanding about.

Does the entire TDWG community have to understand these nuances?

No, but the group working on a more semantic version will need to.

When we think we have something workable, I would suggest that we have
others in the semantic web and LOD community look at it to see if we missed

If this all goes well, we will have an example data set, and documentation
that explains how it works and why specific things are done the way they

This then goes to GBIF (if they want it) where they can work out exposing
their current records in this new format.

My guess is that this might take a few passes to get right - simply because
that is the nature of the beast.

GBIF will have to come up with some A.I type error and interpretation system
to process data. (Which is a pretty cool problem in itself)

They seem to already have a lot of this in place.

The initial example set and a GBIF set can be included in some of the
gigantic billion triple challenge and inferencing studies that are going on.

I suspect that these studies will expose some issues and insights that we
would have never been able to see ourselves.

These studies will also feed back on the process standards process, where we
can figure out how to deal with the strange edge-cases they expose.

In the end, we should have a well-vetted format, that is also well

So what I propose is that do the following to work out a future more
semantic version of the DarwinCore:

We break this into a smaller group to work on pulling together the similar
semantic representations, come with a list of use cases and a test set.

The discussion of this new version should probably be moved to one of the
separate lists (as, I think, Markus suggested).

This will avoid confusion between issues in the current DarwinCore and those
issues relating to some more fully "semantic" future representation.

While this potential standard gets worked out groups can use form one of the
DarwinCore to submit their records.

As I said previously, I think this might be the only version they really
need to be familiar with.

Does this plan seem to make sense to everyone?


- Pete

On Thu, Oct 14, 2010 at 10:43 AM, Steve Baskauf <
steve.baskauf at vanderbilt.edu> wrote:

>  Thanks for the various replies.  I'm going to try to respond to several of
> them in this one.  I realize that these lengthy replies may overwhelm some
> readers.  However, I will beg your collective indulgence because I've got a
> proposal on the table for adding Individual as a Darwin Core class.  It
> appears that the submission process is moving forward and you can consider
> this as the "pleading of my case" for why that addition is desirable (and in
> my opinion) necessary.
> One point which I think has permeated the Darwin Core discussions since
> I've started following them is that DwC is designed to facilitate many
> uses.  Although somebody might use Occurrence records to make dots on a
> distribution map, somebody else might be using the same records to track the
> movement of the individual organism as it swims around the sea.  Somebody
> else may just be using the location and time metadata to demonstrate that
> the photo that they took places the organism in a reasonable location for
> the species they assert they have photographed.  Another person may be using
> the location and time metadata to indicate that two species co-occurred at
> the same location at the same time.  Darwin Core will be functioning well
> when it allows occurrence records to do any of these things or possibly all
> of these things at the same time.  The case that I'll try to make here is
> that Darwin Core mostly allows these things, but lack of an Individual class
> is making it difficult to do some of them.  I will illustrate with a couple
> examples.
> The first one is the problem of tracking an individual over time.  As Rich
> correctly points out, the "new" Darwin Core standard has the term
> dwc:individualID which is designed to facilitate exactly this kind of
> thing.  In a previous thread when we discussed the appropriate use of the
> xxxxID terms, I believe that there was a consensus that using them as
> "idrefs" (I can't remember the technical database term for this, I mean when
> an item in a record points to the identifier of another record) was
> appropriate.  In a flat "table-based" database system, you would just have a
> table of records (i.e. rows) for some kind of "thing" with a column heading
> of  "xxxxID".  You would place the identifier for the related other thing in
> that column.  In the case of dwc:individualID, the rows would be occurrence
> records and the entry in the individualID column would be the identifier for
> the individual.  In RDF, you would make statements asserting the
> relationship between the thing and the other thing.  For example, if you
> wanted to say that a dwc:Identification asserted that something was a
> particular dwc:Taxon, you could make the statement in RDF that
> [identification] dwc:taxonID [taxon], where [identification] and [taxon] are
> instances of those two classes that have been assigned some kind of
> (hopefully gobally unique) identifiers.  In the case of asserting that a
> number of occurrence records track the same individual over time, in RDF, I
> would for each occurrence make the statement [occurrence] dwc:individualID
> [individual].  That's great and I can (and do) do that with Darwin Core as
> it exists.  The problem that I face is that in RDF any time that one makes a
> statement about a resource (I'm switching to that term because "thing" is to
> vague) using an identifier for it (in the form of a URI), the identifier
> must dereference (resolve? sorry Bob!) to produce metadata about the
> resource.  So when I assign a URI to an individual organism a semantic
> client should be able to retrieve information about the individual.  One of
> the fundamental pieces of information that a client should (according to the
> TDWG GUID applicability statement) be given about a resource is what type of
> thing the resource is.  This is called the "rdfs:type" of the resource.  The
> TDWG Applicability statement (recommendation 11) says that resources
> identified by a GUID "should be typed using the TDWG ontology or other
> well-known vocabularies".  I hate to be cynical about this, but I don't have
> confidence that the TDWG ontology will be ready to use in my lifetime.  The
> only "well-known" vocabulary that I know of that will work for this purpose
> at the moment is Darwin Core and the Darwin Core classes are just right for
> typing all of the kinds of resources I want to talk about (occurrences,
> taxon, identifications, etc.) EXCEPT for Individuals.  I think that
> dwc:individualID is the only one of the xxxxID terms that refers to a type
> of thing that doesn't have a class defined for it, hence my request to add
> Individual as a class.  At the TDWG meeting, somebody (Roger maybe?)
> commented that there isn't anything that would stop me from creating my own
> URI for an Individual class.  That is absolutely true and I already did that
> (http://bioimages.vanderbilt.edu/rdf/terms#Individual), but that doesn't
> make my term "well known".  I want Individual to be a class in Darwin Core
> so that people other than me know what it means.  There is no way that I can
> currently follow the "rules" for GUIDs and RDF on this, and anybody in the
> future who uses dwc:individualID in RDF is going to face this same problem
> (i.e. anyone who wants to track individuals over time).
> In the case of putting "dots on a map" to show the distribution of a
> species, the case is simple if the occurrences are specimens where the whole
> dead organism is collected.  It is not so simple with other types of
> occurrences.  Let me illustrate with an example.  There is currently
> precisely one known individual of Crataegus harbisonii in nature.  I have
> given this individual the URI
> http://bioimages.vanderbilt.edu/ind-baskauf/70905 .  I have approximately
> 62 images of that individual at
> http://bioimages.vanderbilt.edu/ind-baskauf/70905.htm and
> http://www.cas.vanderbilt.edu/bioimages/species/crha2.htm .  Each one of
> these images represents an occurrence in that I pressed the shutter on my
> camera at different times for each one.  Ron Lance has collected tissue from
> this tree for grafting purposes and now has an occurrence with
> basisOfRecord="LivingSpecimen" in his arboretum in North Carolina.  Andrea
> Bishop of the Tennessee Dept of Environment and Conservation has seeds
> collected from the tree - I'd call the collection of those seeds an
> occurrence record.  I'm pretty sure that there are one or more specimens
> from this tree in herbaria (although I'm not sure where).  So my question to
> Marcus and others at GBIF is: how many dots will you put on your map for
> this tree?  65 (one for each occurrence) or 1 (one for each individual)?  I
> think the answer should be one, but it isn't clear to me how a data
> aggregator is going to achieve the goal of having one dot per individual if
> the basic unit "dot creation" is an occurrence rather than an individual.
> At the present moment, this question seems like a moot point because most
> records in big databases like GBIF are based on one specimen (or
> observation) per record of an individual, but that won't necessarily be the
> case in the future if people take multiple live organism images, perhaps
> also at the same time they collect a physical specimen.  I anticipate that
> one response to this question will be to call each imaging bout one
> "observation" having a number of dwc:associatedMedia references.   That
> collapses the number of occurrence records considerably, but not down to
> one.  I took images of that tree on at least three separate instances over
> the course of a year and Ron collected his graft tissue years before that.
> There is simply no way to reduce the number of occurrences for this tree to
> one, nor should we want to.  A possible use of multiple occurrence records
> (i.e. my first point above) of this sort might be to establish how long
> individuals of Crataegus harbisonii live and each occurrence record (whether
> separated by years or by the seconds between shutter clicks) is a part of
> the record that we should be able to (and want to) preserve.  Another use
> would be to track a non-sessile organism (e.g. a whale) in both time and
> space.  In that case, the record on a map for an individual would be some
> kind of curve rather than a dot.  But in any case, recognizing the existence
> of an entity that I'm calling an Individual facilitates these broader uses
> of occurrence data and it's really hard for me to see how that is going to
> happen if we ONLY have occurrences as separate entities.  Response Markus?
> How does GBIF deal with whale tracks or multiple banded bird observations
> for a single bird?
> The third compelling reason for recognizing the existence of Individuals as
> a resource type is that it is the best way to maintain the linkage between
> multiple occurrences of the same individual and identifications.  (In the
> oversimplified examples I gave earlier, I applied a scientific name directly
> to an individual.  In actual practice, I relate individuals to
> identifications and then relate the identifications to taxa.)  Again, to
> illustrate with a real-life example, when Bruce Kirchoff was developing his
> Woody Plants of the Southeastern US learning software, he asked a taxonomist
> to go through the images of mine that he was using for the project to verify
> that they were identified correctly.  My old website just threw together all
> images of a particular species onto one page without regard to the
> individuals from which they originated (e.g.
> http://www.cas.vanderbilt.edu/bioimages/species/sarar3.htm and
> http://www.cas.vanderbilt.edu/bioimages/species/soam3.htm).  It turns out
> that I had carelessly misidentified a vegetative Sambucus racemosa ssp.
> racemosa individual as Sorbus americana.  The taxonomist asked me which of
> the various bark, twig, leaf, etc. images were from the same plant and the
> only way I could find out was through the laborious process of looking for
> images with similar time/date values and my hand written field notes.  It
> was a nightmare finding all of the particular image records that needed to
> have their identifications fixed and then correcting them.  On my new
> website (e.g. http://bioimages.vanderbilt.edu/metadata.htm, then click on
> Quercus chrysolepis), the images are connected to the individual from which
> they originated.  If I discover by looking at a particularly informative
> image that I have misidentified the individual, I only need to add an
> updated determination (i.e. identification) to that individual's record and
> automatically all images from that individual are displayed with the correct
> name and are placed on the correct species page.  Now imagine a situation
> that is larger and even more complicated than this (think a Bioblitz).
> Herbarium curators and live plant photographers are working together to
> document the flora of an area.  Multiple images and multiple specimens may
> be collected from the same individual.  The images may go one place and the
> specimens may go to several herbaria (if "duplicates" are distributed).
> It's possible that people might come back to the same individual later to
> photograph or collect fruit having initially seen flowers.  Suppose on down
> the line a taxonomist looks at one of the specimen duplicates and realizes
> that the initial identification was wrong (or maybe just wants to assert an
> alternative opinion about the identity).  If the record is based on that
> individual, then all that is required is for the annotating taxonomist to
> add a determination (i.e. dwc:Identification) to the Individual's record and
> poof! all images and duplicate specimens have that opinion associated with
> them.  In contrast, if all of these separate occurrence records are not tied
> together via the Individual, and if each individual occurrence record has
> its own determination, nobody is possibly going to ever track down and
> correct every one.  Granted, the scenario that I've suggested is contingent
> on the existence of a large scale database that can connect metadata across
> institutions, but exactly that kind of thing is what projects like the US
> Virtual Herbarium and our Live Plants Imaging group are trying to create.
> Let's enable this by making it possible within Darwin Core to have a record
> structure that is Individual-based.
> I recognize that many "specimen-based" organizations aren't really going to
> care one whit about this.  That's fine.  In their databases and personal XML
> schemas they can ignore Individuals as it is their prerogative.  But when we
> build RDF templates, I believe strongly that for the benefit of those of us
> who care about the broader applications of occurrences those templates
> should use individuals to connect (one or more) occurrences and (one or
> more) identifications.  For those with a technical bent, you can see how I
> have done this for an herbarium specimen by looking at the page source RDF
> of the example
> http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0429.rdf .  For those
> of a non-technical bent, just look at the webpage that shows up when you
> click on the link.  It looks just like any other web page for a specimen and
> you don't even have to know that the underlying RDF supports using
> Individuals as a grouping mechanism.
> In summary, I think we need Individual as a DwC class to enable
> understandable rdfs:typing of records of individuals and to create a context
> in which instances of individuals can be placed (i.e. people would assign
> and use identifiers for individuals when they document occurrences).  These
> instances (and their assigned URI GUIDSs) would allow for "connecting"
> identifications and occurrences in a more meaningful way.  I am not
> suggesting that the occurrence be dethroned as the center of biodiversity
> records.  Assuming that the xxxxID terms end up being moved out of the
> various classes and into the record-level terms area as was suggested
> recently, I think that there are really only about two terms that should be
> put into a new Individual class: the other new term I have proposed
> (individualRemarks) and establishmentMeans (but that is the topic of another
> email).  It may seem odd to suggest a adding a class that has very few terms
> in it, but if you follow my reasoning above you will hopefully understand
> why I have done so.
> I hope that the discussion (and criticism!) will continue.  Again, I'm
> interested in hearing alternatives.
> Steve
> Richard Pyle wrote:
>  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.orghttp://hbs.bishopmuseum.org/staff/pylerichard.html
> .
> --
> 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) 343-6707http://bioimages.vanderbilt.edu

Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies
Knowledge Base <http://lod.geospecies.org/>
About the GeoSpecies Knowledge Base <http://about.geospecies.org/>
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