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