[tdwg-content] practical details of recording a determination What is an Occurrence?
Steve Baskauf
steve.baskauf at vanderbilt.edu
Mon Oct 18 21:06:16 CEST 2010
Pete,
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 www.cyberfloralouisiana.com, 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.
Steve
Peter DeVries wrote:
> Hi Steve,
>
> You need to fix this in two ways (independent of the vocab, which I
> did not check)
>
> 1) It should show up correctly in URIburner.
>
> http://linkeddata.uriburner.com/about/html/http/bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf
>
> 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
> 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
> page add a "foaf:page" that points back to the RDF.
>
> Remember that in the cloud or in your triple store entities like
> <http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind> are not
> tied
> to the RDF that contains statements about them, without some link to
> and from the page
> <http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf>
>
> * 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
> it is equally accepted.
>
> Here is an abbreviated version of what this might look like:
>
> <rdf:Description
> rdf:about="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf">
> <dcterms:description>RDF formatted description of the preserved
> specimen
> http://www.cyberfloralouisiana.com/specimens/lsu000/0428</dcterms:description>
> <dcterms:modified>2010-09-25T06:35:58</dcterms:modified>
> <xmp:MetadataDate>2010-09-25T06:35:58</xmp:MetadataDate>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265b"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231b"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39231a"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#39265a"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#img"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#bq"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#tn"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#lq"/>
> <foaf:topic
> rdf:resource="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#gq"/>
> </rdf:Description>
>
> <rdf:Description
> rdf:about="http://www.cyberfloralouisiana.com/specimens/lsu000/0428#ind">
> <foaf:page
> rdf:resource="http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf"/>
> </rdf:Description>
>
> Following this pattern, your RDF will be browsable as in this example:
>
> http://linkeddata.uriburner.com/about/html/http/lod.taxonconcept.org/rdf/area_example.rdf
>
> Note how you can click back and forth between the location and the RDF
> that describes it.
>
> - Pete
>
> On Mon, Oct 18, 2010 at 11:49 AM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu <mailto:steve.baskauf at vanderbilt.edu>>
> wrote:
>
> 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.
>
> 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
> http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf which
> should show up as a web page in your browser.
>
> 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"?
> 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".
> 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?
> 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.
>
> 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?
>
> 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.
>
> Steve
>
> Peter DeVries wrote:
>> Hi Steve,
>>
>> I would hypothesize that for the vast majority of identified
>> records the process is something like this:
>>
>> 1) An individual uses some sort of key to determine what species
>> (taxon concept) to assign to a given individual
>> * They may have created some sort of mental key in which once
>> they recognize one individual mosquito they can then pretty
>> quickly sort
>> a number of individuals into collections.
>>
>> 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.
>> Most of these human identifiers have not read the original
>> species descriptions and for the species they are identifying.
>> So the specimen is actually tied to a concept that is based
>> more on the "key" than the original description.
>> * An exception, would be where there is a key in the original
>> description and that was what what was used.
>>
>> 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
>> the original description or a subsequent revision is "fudging"
>>
>> Side effects of this process include:
>>
>> 1) A new key for North American Mosquitoes comes out that
>> incorporates recent changes in nomenclature. The major change
>> being the elevation of
>> a subgenus to a genus. For most of the species described the
>> "key concept" is unchanged.
>>
>> 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.
>>
>> Bob identifies the species as /Ochlerotatus triseriatus/, while
>> Joe identifies what should be the same species as /Aedes
>> triseriatus/.
>>
>> These show up in GBIF on two different maps, they show up in the
>> EOL as two different pages.
>>
>> Various TDWG'ers continue to argue that the original description
>> and subsequent revisions were really important in determining
>> what these individuals
>> actually meant when they assigned a name to a specimen, and that
>> this is how we should model it in excruciating detail.
>>
>> I would argue this should be modeled as best as possible to what
>> actually happens.
>>
>> For example, how many of the species observed in the recent
>> BioBlitz were identified by referring to the original species
>> description or subsequent revisions?
>>
>> 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.
>>
>> 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
>> is more accurately modeled.
>>
>> This would be done in the form of:
>>
>> "I assert that this specimen (of what I call /Aedes
>> triseriatus/) was observed here. I also assert that it is an
>> instance of the this species concept => URI"
>>
>> Or I assert that this is an individual of the type "Individual
>> of species concept X" = > URI
>>
>> All of these are instances of the class "Individual"
>>
>> So the resulting DarwinCore record would contain both the name
>> and and an optional, but I think needed, asserted species concept.
>>
>> The species concept is a subclass of taxon concept, but is
>> fundamentally different than the higher clades.
>>
>> There are some guidelines as to what an entity needs to be
>> considered a species.
>>
>> While their are no real guidelines as to what clades should be
>> considered genera and what clades should be considered families etc.
>>
>> 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
>> that those properties are still valid if the species within that
>> genera change.
>>
>> 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
>> of the genus.
>>
>> Respectfully,
>>
>> - Pete
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Oct 15, 2010 at 10:45 AM, Steve Baskauf
>> <steve.baskauf at vanderbilt.edu
>> <mailto:steve.baskauf at vanderbilt.edu>> wrote:
>>
>> 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
>> http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot .
>>
>> 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.
>>
>> 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.
>> 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
>> http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif
>> 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
>> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001666.html
>> 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
>> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001603.html,
>> 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.
>> 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
>> (http://code.google.com/p/darwincore/issues/detail?id=68). 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.
>> 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.
>> 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.
>>
>> 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).
>>
>> Steve
>>
>> Steve Baskauf wrote:
>>
>> After the flurry of emails recently, I had an opportunity
>> to carefully
>> read all the way through the threads again, followed by
>> enforced "think
>> time" during my long commute. I was actually pretty
>> cheerful after that
>> because I think that in essence, most of the conversation
>> about what
>> constitutes an Occurrence really boils down to the same
>> thing. So I
>> have sat down and tried to summarize what seems to me to
>> be a consensus
>> about Occurrences. To follow my points, please refer to
>> the diagram at:
>> http://bioimages.vanderbilt.edu/pages/occurrence-diagram.gif
>>
>> Consensus on relationships
>> 1. The fundamental definition of an Occurrence involves
>> evidence that a
>> representative of a taxon occurred at a place and time.
>> Note 1.A: For clarity, I have modified John's statement
>> in his last
>> email by replacing "taxon" with "representative of a
>> taxon". I'm
>> considering a taxon to be an abstract concept that is
>> applied to
>> individuals or groups of organisms.
>> Note 1.B. This definition is far more useful than the
>> official
>> definition of the class Occurrence "The category of
>> information
>> pertaining to evidence of an occurrence..." which is
>> essentially circular.
>> Note 1.C: This statement is extremely broad because the
>> evidence could
>> be of many sorts, the representative could range from a
>> single
>> individual to all organisms on the earth, the taxon could
>> be anyone's
>> definition at any taxonomic level, the place could range
>> from a GPS
>> point with uncertainty of less than 10 meters to the
>> entire planet
>> earth, and the time could range from a shutter click of
>> less than one
>> second to 3.4 billion years.
>> 2. The diagram is an attempt to summarize in pictorial
>> form statements
>> and relationships that have been described in the thread.
>> The taxon
>> representative is recorded as existing at a particular
>> time and place
>> (the arrow) and the result is an Occurrence record. That
>> Occurrence
>> record exists as metadata which may be associated with a
>> token that can
>> be used to voucher the fact that the taxon representative
>> existed. That
>> token may be the organism itself (or a living part of it
>> as in a twig
>> for grafting), all or part of the organism in preserved
>> form, an
>> electronic representation such as an image or sound
>> recording, and other
>> kinds of things like tissue or DNA samples. There may
>> also be no token
>> at all, in which case we call the Occurrence record an
>> observation.
>> Based on direct observation of the taxon representative,
>> examination of
>> one or more tokens, or both, some determiner asserts that
>> a taxon
>> concept applies to the taxon representative and as a
>> result a scientific
>> name can be used to "identify" the taxon representative.
>> (There may be
>> a lot of other complicated stuff above the Identification
>> box, but that
>> will have to be filled in by the taxonomists.)
>> Note 2.A: I have mapped onto this diagram the letters
>> that John used in
>> his last email to refer to entities that are involved in
>> an Occurrence
>> (T, E, L, O, and G). I will beg the forgiveness of
>> fossil people
>> because I don't really know how the geological context
>> fits in. I'm
>> assuming that it is a way of asserting time and location
>> on a much
>> broader scale than we do for extant organisms.
>> Note 2.B: I have put a dotted line around the part of the
>> diagram that I
>> think includes all the things that people might consider
>> part of the
>> Occurrence itself. I have left out "T" and the other
>> parts related to
>> identification because it seems to me that you can have
>> an occurrence
>> that you document which does not yet (and perhaps never
>> will) have an
>> identification. The Occurrence still asserts that a taxon
>> representative existed at a time and place; we just don't
>> yet know what
>> the taxon is.
>> 3. The red lines indicate the relationships that connect
>> the various
>> entities (I'm going to go ahead and call them resources).
>> Consistent
>> with popular opinion, the Occurrence record is the center
>> of the
>> universe and most things are connected to it.
>> Note 3.A: I am sticking to my guns and refuse to connect the
>> Identification directly to the Occurrence. It is the taxon
>> representative that is being identified, not the
>> occurrence. One can
>> assert another sort of relationship between the
>> identification and the
>> occurrence if one wants to say that one consulted the
>> occurrence
>> metadata and token in order to decide about the
>> identification, but it
>> is not correct to say that the Identification identifies
>> either the
>> Occurrence metadata or the token (as Rich pointed out).
>>
>> OK, so that's step one - defining what is related to
>> what. If anyone
>> disagrees with these relationships, please clarify or
>> create your own
>> diagram.
>>
>> Complicating circumstances/caveats
>> 1. It is noted and recognized that some users will not
>> care to include
>> all of these relationships in their models. In the
>> interest of
>> simplification or "flattening" the relationships, they
>> may wish to
>> collapse some parts of this diagram (e.g. incorporate
>> time and location
>> metadata within the Occurrence metadata rather than
>> considering them
>> separate resources, applying scientific names directly to
>> the taxon
>> representatives without defining a taxon concept or
>> recording the
>> determination metadata, connecting identifications
>> directly to the
>> occurrence, etc.). This doesn't mean that the
>> relationships don't
>> exist, it just means that some users don't care about them.
>> 2. It is recognized that different users will be
>> interested in or able
>> to specify the various resources to differing degrees of
>> precision.
>> Examples: A photographer might record times to the
>> nearest second, a
>> collector may only be interested in noting the date on
>> which a specimen
>> was collected. A location may be specified to the
>> precision of a GPS
>> reading or be defined as some geographic or political
>> subdivision. The
>> taxon representative may be an individual organism, a
>> flock or clump, or
>> some larger aggregation of taxon representatives.
>>
>> That's step two. If I've missed any complications,
>> please point them out.
>>
>> My opinions about the implications of this diagram
>> 1. The circle I've labeled as "taxon representative" is
>> the resource
>> type that I'm proposing to be represented by the class
>> Individual. You
>> will note that in both the definition of dwc:individualID
>> ("An
>> identifier for an individual or named group of individual
>> organisms...")
>> and the proposed class definition ("The category of
>> information
>> pertaining to an individual or named group of individual
>> organisms
>> represented in an Occurrence"), groups of individual
>> organisms are
>> included. Thus John's example of a fossil having myriad
>> individuals, or
>> Richard's examples of thousands of plankton, a large
>> school of fish,
>> herd of wildebeest, flock of
>> birds, could all be categorized as "Individual" under
>> this definition if
>> there is a reasonable expectation that all of the
>> individuals in the
>> group are members of the same taxon. Perhaps there is a
>> better name for
>> this resource, but since dwc:individualID was already
>> extant, I chose
>> Individual as the class name for consistency with the pattern
>> established with other classes and their associated
>> xxxxID terms.
>> 2. Although in note 1.C. I have given the ranges of the
>> various
>> resources to their logical extreme (as was done
>> previously in the
>> thread), I think that as a practical matter we can adopt
>> guidelines to
>> set reasonable values for the "normal" ranges of the
>> resources. One
>> such guideline might be that we suggest a range that can
>> accommodate
>> about 95% of the user needs within the community (this
>> came from Rich's
>> comment about satisfying 95% of the user need with an
>> establishmentMeans
>> controlled vocuabulary). For example, it was suggested
>> that the range
>> for the location of an Occurrence could span the entire
>> planet Earth.
>> True enough, but virtually nobody would find such a span
>> useful. 95% of
>> users would probably find a range between a GPS reading
>> with 10 meter
>> precision and the extent of a county or province useful
>> for recording
>> the location of an Occurrence. I can suggest similar
>> "useful" ranges:
>> one second to one day for an event time (excluding
>> fossils), one
>> individual organism to the number of organisms that would
>> fit within a
>> 50 meter radius for an "individual", and taxon identified
>> to family for
>> plants and maybe mammals, genus for birds, and order for
>> insects. So
>> framing the definition of an Occurrence in these terms it
>> would be
>> something like: "An occurrence involves evidence
>> (consisting of a
>> physical token, electronic record, or personal
>> observation) that a
>> representative (ranging from a single individual to the
>> number that
>> would fit on a football field) of a taxon (hopefully
>> identified to some
>> lower taxonomic level) occurred at a place (determined to
>> a precision
>> between that of a GPS reading and the size of a
>> county/province) and
>> time (spanning one second to one day)." A few people
>> might object to
>> this level of restrictiveness, but I would guess that it
>> would make 95%
>> of us happy.
>> 3. With the exception of the "missing" class Individual,
>> every resource
>> type on this diagram except for the "token" and
>> Scientific name has a
>> Darwin Core class. Every resource type on the diagram
>> except for "token"
>> has a dwc:xxxxID term that can be used to refer to a GUID
>> for the
>> resource. The implication of this is that any resource
>> on this diagram
>> except for the token and taxon representative (i.e.
>> Individual) is ready
>> to be represented in RDF by Darwin Core terms in the
>> sense that the
>> relationships (red lines) can be represented by the
>> xxxxID terms and
>> that the resources can be rdfs:type'd using Darwin Core
>> classes.
>> (Lacking a class for the scientific name doesn't seem
>> like a big deal to
>> me since the scientific name can be a string literal -
>> but then I'm not
>> a taxonomist.)
>> 4. OK, I've avoided it as long as I can, so I'm going to
>> confess now to
>> the RDF-phobes. The red lines and shapes are something
>> pretty close to
>> an RDF graph. What that means is that if the community
>> can agree that
>> this diagram correctly represents the relationships among
>> the kinds of
>> biodiversity resources that we care about, then the
>> matter of providing
>> guidelines on how to represent Darwin Core in RDF
>> suddenly gets a lot
>> simpler. Just convert the "picture" of the RDF graph
>> into XML format
>> and we have a template. Alright, that's an
>> oversimplification, but I
>> think it is essentially true because the most difficult
>> part of
>> achieving a consensus on RDF representations is to decide
>> how we connect
>> the resource types, not on the literals that we hang onto
>> resources as
>> properties.
>> 5. While I'm beating the RDF drum again, the importance
>> of my opinion
>> number 2 can be extended into the GUID adoption process.
>> In my comments
>> to Kevin about the Beginner's Guide to Persistent
>> Identifiers, I think I
>> commented on the question of how one decides whether a
>> GUID needs to be
>> assigned to something or not. I believe that the answer
>> to that
>> question boils down to this: we need a GUID for any
>> resource that will
>> be referenced by more than one other resource. Do we
>> need to be able to
>> assign a GUID to Taxon concepts? Yes, because it is
>> likely that many
>> identifications will want to reference a particular taxon
>> concept. Do
>> we need to be able to assign a GUID to an Event? Maybe
>> or maybe not.
>> If every occurrence has its own separate time recorded,
>> then no GUID is
>> needed because the time is just a part of every separate
>> occurrence
>> record. If the event is defined to be a time range that
>> represents a
>> collecting trip, then there may be many Occurrences that
>> are associated
>> with that trip and all of them could reference the GUID
>> for that event
>> rather than repeating the event information for every
>> Occurrence. The
>> point here is that every shape (class of resources) on
>> this diagram at
>> least has the POTENTIAL to be a node connecting multiple
>> resources and
>> therefore should have the capability of being assigned a
>> GUID, having
>> its own RDF record, and being appropriately typed
>> (presumably by a DwC
>> class). So this is a final technical argument for why we
>> need to have
>> the DwC class Individual. Whether or not people
>> ultimately choose to
>> assign GUIDs to particular resource types or not is their
>> own choice,
>> but they need to at least be ABLE to if they need that
>> resource to serve
>> as a node given the structure of their metadata.
>>
>> We need to clarify how the "token" thing fits in, but I'm
>> stopping there
>> for now. I would very much appreciate responses
>> indicating that:
>>
>> A. you agree with the diagram and connections (and
>> consider this
>> definition and diagram a consensus)
>> B. you disagree with the diagram (and articulate why)
>> C. you provide an alternative diagram or explanation of the
>> relationships among the classes related to Occurrences.
>>
>> Thanks for you patience with another tome.
>> Steve
>>
>> --
>> 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
>> http://bioimages.vanderbilt.edu
>>
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> <mailto:tdwg-content at lists.tdwg.org>
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>> .
>>
>>
>>
>>
>> --
>> 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
>> http://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/>
>> ------------------------------------------------------------
>
> --
> 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
> http://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/>
> ------------------------------------------------------------
--
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
http://bioimages.vanderbilt.edu
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