[tdwg-content] New Darwin Core terms proposed relating to material samples

[Jason Holmberg]

>will never be all things to all people; but at least it is enough things
to enough people that it represents an important “flag pole”
>around which our community has (more or less) successfully rallied.

Too true! DWC allows me (as a programmer and info. architect) to move
beyond laborious and endless discussions of data definitions for a new
project and rather point over at DWC and say "Let's use this standard as a
starting point. It has a rich history behind iy, so let's build on it's
wisdom and move the project ahead faster."

Jason Holmberg
ECOCEAN Whale Shark Photo-identification Library
http://www.whaleshark.org

Please consider adopting a shark to support our mission:
http://www.whaleshark.org/adoptashark.jsp


On Fri, May 31, 2013 at 1:41 AM, Jason Holmberg <holmbergius at gmail.com>wrote:

> >The “ID” value itself is never useful data/metadata – it is just a way
> to reference a data record that (presumably) contains properties that can
> >be expressed as data/metadata for the object represented by the “ID”
> value.
>
> Too true! I have been in so many conversations wherein complex ID schemes
> for wildlife population members have been generated, and my response has
> always been "The ID does not matter so long as it is unique."
>
>
> Jason Holmberg
> ECOCEAN Whale Shark Photo-identification Library
> http://www.whaleshark.org
>
> Please consider adopting a shark to support our mission:
> http://www.whaleshark.org/adoptashark.jsp
>
>
> On Fri, May 31, 2013 at 12:24 AM, Richard Pyle <deepreef at bishopmuseum.org>wrote:
>
>> Thanks Ramona;****
>>
>> ** **
>>
>> Actually, the basic elements of our data mode precede DwC by quite a
>> bit.  What we’ve tried to do, however, is mold the data model to be more
>> compatible with DwC, to make the task of mapping for data export & exchange
>> that much easier.  Of course, DwC is not (and is not intend to be) a data
>> model in any sense of the word; however, it’s impossible to avoid
>> representing core elements of a bona-fide data model within DwC.  This is
>> especially true when it comes to each of the “ID” terms (and
>> doubly-especially true when the “ID” terms correlate to class terms).  The
>> existence of an “ID” term implies that some class of object exists to which
>> an “ID” value is applied.  The “ID” value itself is never useful
>> data/metadata – it is just a way to reference a data record that
>> (presumably) contains properties that can be expressed as data/metadata for
>> the object represented by the “ID” value.****
>>
>> ** **
>>
>> This was all well-understood when the original DwC was being drafted; but
>> as it evolved into its current iteration (with the addition of all the “ID”
>> terms), it has been drawn ever more (in some ways subtly, and in some ways
>> not-so-subtly) in the direction of a data model.****
>>
>> ** **
>>
>> Of course, what we all (desperately!) need is a robust ontology that fits
>> our world.  The task is not easy in part because our data domain is not so
>> easily modeled, in part because different sections of our broader community
>> have different priorities, and in part because there is always a delicate
>> balance between developing a model or ontology that is practical and useful
>> for the data providers and consumers, with one that is robust and detailed
>> and flexible, to allow asking questions of the data that were never even
>> considered at the time the model/ontology were conceived.  The parallel
>> experience in database modeling is normalization (as Paul Kirk likes to
>> say: “Normalize until it hurts; then de-normalize until it works”).****
>>
>> ** **
>>
>> The original DwC was completely flat.  The current DwC moved into the
>> direction of more complex structures by clustering terms into classes and
>> sprinkling with “ID” terms.  It even tip-toed into RDF-space with
>> dwc:ResourceRelationship.  I think that’s definitely an improvement, but it
>> still must strike a delicate balance between the needs by some to represent
>> a robust data model, and the needs by others to have a simple/practical
>> mechanism to exchange biodiversity data in a standard form.  It will never
>> be all things to all people; but at least it is enough things to enough
>> people that it represents an important “flag pole” around which our
>> community has (more or less) successfully rallied.****
>>
>> ** **
>>
>> Hmmmm…. Now I’ve forgotten what my point was.  I guess I was just in a
>> ramblin’ mood. Well….sorry about the bandwidth!****
>>
>> ** **
>>
>> Aloha,****
>>
>> Rich****
>>
>> ** **
>>
>> *From:* Ramona Walls [mailto:rlwalls2008 at gmail.com]
>> *Sent:* Thursday, May 30, 2013 6:05 PM
>> *To:* Richard Pyle
>> *Cc:* Jason Holmberg; TDWG Content Mailing List; John Deck; Robert
>> Whitton
>>
>> *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to
>> material samples****
>>
>> ** **
>>
>> Jason,
>>
>> Thanks for sharing how you have been using the Darwin Core terms. I am
>> intrigued by the data structure you have developed. It is quite interesting
>> how both you and Rich have adapted the DwC to fit your specific needs.
>> While I am often troubled by the vagueness of DwC, I guess in some ways it
>> is that vagueness allows it to be used in many different applications. Of
>> course, I don't think vagueness is necessary for wide application, or a
>> good thing for data exchange, but it does seem to be working for a lot of
>> different purposes.****
>>
>> Ramona****
>>
>> ** **
>>
>> On Thu, May 30, 2013 at 3:07 PM, Richard Pyle <deepreef at bishopmuseum.org>
>> wrote:****
>>
>> Hi Jason,****
>>
>>  ****
>>
>> Many thanks for this input.  If I understand you correctly, then you are
>> using “Encounter” as equivalent to what we have been using “Occurrence”
>> for.  That is, by our definition, an “Occurrence” is the instance
>> representing an intersection between an Event (i.e., where, when, who,
>> etc.) and what we have been calling an “Individual” (i.e., what); and the
>> properties we attach to the Occurrence are the “how” bits (including things
>> like size, etc.).****
>>
>>  ****
>>
>> In my mind, the essence of an “Individual” is the collective physical
>> material of the individual.  If I see a fish on a reef, its “Occurrence” on
>> that reef and at that time exists (and is worth documenting) regardless of
>> whether I took an image of it (what we would call “Evidence”), or whether I
>> took a tissue sample from it, or whether I collected and killed the whole
>> damn thing.  To me, the “essence” of the individual – or its occurrence at
>> an event – is unaffected by what I end up doing to it.  By extension,
>> following a hierarchical model of “individual”, a sub-sample
>> (materialSample) extracted from it is just another instance of
>> “Individual”.  This is why I generally think of “materialSample” (if it
>> were represented as a class – which it is currently not propsed for DWC) as
>> a subclass of a broader concept (e.g., “material”, but what I have naively
>> been referring to as “Individual”).****
>>
>>  ****
>>
>> That part of our model has proven to be very stable and effective for
>> representing the information as we want it.****
>>
>>  ****
>>
>> Where it gets complicated is instances of taxonomically heterogeneous
>> objects treated as a single “individual” – which (in my mind) includes such
>> things as soil samples.****
>>
>>  ****
>>
>> In that contect, I see (and agree) with John and others that really it’s
>> a separate axis of classification from what I have called “Individual”.**
>> **
>>
>>  ****
>>
>> I don’t expect that to make a lot of sense (I barely understand it
>> myself).****
>>
>>  ****
>>
>> Aloha,****
>>
>> Rich****
>>
>>  ****
>>
>> *From:* Jason Holmberg [mailto:holmbergius at gmail.com]
>> *Sent:* Thursday, May 30, 2013 11:28 AM
>> *To:* Richard Pyle
>> *Cc:* Ramona Walls; TDWG Content Mailing List; John Deck; Robert Whitton*
>> ***
>>
>>
>> *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to
>> material samples****
>>
>>  ****
>>
>> Hi everyone.****
>>
>>  ****
>>
>> List lurker here. DWC has been a great inspiration in my work, so I hope
>> I can contribute some small amount of insight on the "individual" and
>> "material sample" threads. I have no grand thoughts on the subject, but I
>> can tell you how the DWC has inspired my own information architecture for
>> open source mark-recapture software:****
>>
>>  ****
>>
>> http://www.ecoceanusa.org/shepherd/doku.php?id=manual:2.0.x:1_overview***
>> *
>>
>>  ****
>>
>> I felt the very clear need for a distinct Individual Class and to
>> separate that from the concept of a sample taken from nature. When
>> reviewing DWC, I interpreted Occurrence.individualCount to be somewhat
>> contradictory to Occurrence.individualID, so I created a
>> one-individual-at-a-point-in-time class called Encounter that reuses quite
>> a bit of DWC.Occurrence. Occurrence I then broadened to include the
>> potential for multiple marked individuals.****
>>
>>  ****
>>
>> I neither present this as "right" nor "good" (though they have worked
>> very well for us). I just present it as a practical example from
>> mark-recapture in which we have tried to adhere to DWC in order to expose
>> data to GBIF, iOBIS, etc. The concepts of "material sample" and
>> "individual" are very important to us, and this is how we have defined them.
>> ****
>>
>>  ****
>>
>>  ****
>>
>> Cheers,
>> ****
>>
>> Jason Holmberg
>> ECOCEAN Whale Shark Photo-identification Library
>> http://www.whaleshark.org
>>
>> Please consider adopting a shark to support our mission:
>> http://www.whaleshark.org/adoptashark.jsp****
>>
>>  ****
>>
>> On Wed, May 29, 2013 at 4:13 PM, Richard Pyle <deepreef at bishopmuseum.org>
>> wrote:****
>>
>> Hi Ramona,****
>>
>>  ****
>>
>> Yes, I agree, and thanks.  I’ve always felt that there has been a trend
>> towards trying to push too much “ontology” (or other semantic meaning) onto
>> DWC terms and classes, when DWC was fundamentally intended to represent an
>> mechanism for data exchange; not a mechanism to describe the ontological
>> landscape of biodiversity data.  The only reason I brought this up now
>> (and, I think, why we discussed it in 2010), is that the term
>> “individualID” in DWC sort of hinted that something like “Individual” was
>> the “forgotten class” for DWC.  I sincerely hope that BCO and DSW gain more
>> traction (and, ideally, harmony between them) than earlier attempts at
>> developing ontologies in this space have met – and clearly that is the
>> right path forward.****
>>
>>  ****
>>
>> My main concern for this thread (and the reason I engaged in it), was to:
>> ****
>>
>> 1)      Find out the status of the discussions that began in 2010; and***
>> *
>>
>> 2)      Clarify where the current materialSample proposal overlaps, or
>> does not overlap, with that earlier effort.****
>>
>>  ****
>>
>> Steve has very adequately answered the first question, and you, John, and
>> others have answered the second, and I’m happy with both sets of answers.
>> ****
>>
>>  ****
>>
>> I’m sorry for the voluminous exchange, but I felt the discussion was both
>> important, and very helpful (certainly to me).****
>>
>>  ****
>>
>> Aloha,****
>>
>> Rich****
>>
>>  ****
>>
>> *From:* Ramona Walls [mailto:rlwalls2008 at gmail.com]
>> *Sent:* Wednesday, May 29, 2013 1:03 PM
>> *To:* Richard Pyle
>> *Cc:* John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing
>> List; Robert Whitton****
>>
>>
>> *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to
>> material samples****
>>
>>  ****
>>
>> Hi Rich,
>>
>> Sorry I didn't mention this sooner, but your emails were also helpful to
>> me in describing an important and generalizable use case.
>>
>> I don't know whether or not the TDWG community is ready to deal with the
>> level of abstraction we are talking about, but my assessment is that
>> whether or not they are ready, the Darwin Core is not constructed to deal
>> with it. That is why (among other reasons) we started work on the BCO, and
>> perhaps one reason why Steve and others developed DSW. ****
>>
>> Our goal with the material sample proposal was not to overhaul DwC, but
>> to work within the DwC framework to make it more compatible with other
>> standards such as MIxS. That is why we tried to keep our proposal fairly
>> narrowly focused.****
>>
>> Ramona****
>>
>>  ****
>>
>> On Wed, May 29, 2013 at 3:21 PM, Richard Pyle <deepreef at bishopmuseum.org>
>> wrote:****
>>
>> Thanks, Ramona – this is an **extremely** helpful email! It helps clear
>> things up a lot in my mind.****
>>
>>  ****
>>
>> Just to be clear, what I am looking for is the notion of a defined
>> physical object (what I think you mean by “material entity”), and I
>> explicitly mean the material entity itself.  Yes, there is information
>> (properties) that relate to that material entity, but to me that is a
>> separate issue.  What I would like to see clearly defined is the class
>> representing the material (physical) entity – which seems to me to be a
>> superclass of what materialSample is intended to represent.****
>>
>>  ****
>>
>> Perhaps our (TDWG/DWC) community is not yet ready to deal with this level
>> of abstraction (unfortunately, I absolutely have to, because “Occurrence”
>> is simply way too overloaded a class for me to use independently of what I
>> have been calling “individual” and what I have been calling “Evidence”).
>> In that case, I guess the best thing to do is accept materialSample as a
>> basisOfRecord for Occurrence and move on.  But this is more or less the
>> same thing that happened the last time we engaged in this conversation (2
>> years or so ago), and I was hoping this conversation about materialSample
>> could leverage progress on the larger issue.****
>>
>>  ****
>>
>> As I’ve said before, the last thing I want to do is confuse or otherwise
>> slow down the process of incorporating the term “materialSample” into DWC.
>> It’s just that I saw enough overlap with that “other” issue, that I was
>> hoping we could find a reasonable pathway forward on both.****
>>
>>  ****
>>
>> Thanks again for the very helpful comments.****
>>
>>  ****
>>
>> Aloha,****
>>
>> Rich****
>>
>>  ****
>>
>> *From:* Ramona Walls [mailto:rlwalls2008 at gmail.com]
>> *Sent:* Wednesday, May 29, 2013 9:14 AM
>> *To:* Richard Pyle
>> *Cc:* John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing
>> List; Robert Whitton****
>>
>>
>> *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to
>> material samples****
>>
>>  ****
>>
>> Rich,****
>>
>> I now understand more fully what you are asking for ( a clear definition
>> goes a long way!). A material sample, as we discussed it at the Kansas and
>> Oxford workshops, does indeed need to be physically removed from its
>> environment. This is also the case with the OBI term material sample,
>> which, as a subclass of OBI:specimen is the output of some collecting
>> process. It is true that concept of material sample could be defined to
>> include sampling in an observational sense, but that is not how it is
>> defined at this point. Based on this, material sample is NOT the term you
>> are looking for or defined as :****
>>
>> "The category of information pertaining to the physical basis of a
>> sampling, subsampling, or observational event. In biological collections,
>> the [SuperclassTerm] is typically a defined group of organisms, a single
>> whole organism, or a part of a whole organism that is collected or
>> otherwise documented in nature, and either preserved, destructively
>> processed, or documented through some form of Evidence (such as images or
>> reported visual observations)."****
>>
>>  ****
>>
>> What you have defined is a category of information (whatever that may be)
>> that pertains to some material entity. Not the material entity itself, but
>> information about that entity. The "SuperclassTerm" you refer to in the
>> definition sounds an awful lot like a material entity from the Basic Formal
>> Ontology, which is used for defining material sample in OBI and the
>> Bio-collections Ontology.****
>>
>> Ramona****
>>
>>  ****
>>
>> On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef at bishopmuseum.org>
>> wrote:****
>>
>> Many thanks, John.  This is extremely helpful!****
>>
>>  ****
>>
>> First of all, in the context of a distinct term for basisOfRecord, I see
>> absolutely no problem with adding the term “MaterialSample”. I fully
>> support your proposal (although if this is simply a basisOfRecord term to
>> be used alongside Occurrence, PreservedSpecimen, LivingSpecimen,
>> FossilSpecimen, HumanObservation, MachineObservation; does it need a
>> defined “ID” term? Do all the others have defined “ID” terms?). ****
>>
>>  ****
>>
>> However, I’m excited by this conversation because I think we are very
>> close to solving a bigger problem (which was the focus of the 2010
>> discussion on this list around “IndividualOrganism”).****
>>
>>  ****
>>
>> This bigger problem involves the need for a defined “concept” (I’m
>> hesitating to say “class”), and an associated “ID”, in dwc that refers to
>> the physical/material basis of an Occurrence.  We don’t yet have a term for
>> this concept in dwc (“IndividualID” hinted at the need for one, but that
>> term was not well-defined, and the term itself seems to cause confusion).
>> As Steve Baskauf and I have both been advocating for the establishment of
>> new class in dwc for exactly this purpose, I just want to make sure that
>> we’re on the same page about what each concept is.  The more I understand
>> about what you need for “materalSample”, the more convinced I am that both
>> of our needs can be met with the same concept.****
>>
>>  ****
>>
>> I am perfectly happy to adopt the term “MaterialSample”, but I guess it
>> all boils down to this: In order for something to be a “MaterialSample”,
>> must it necessarily be removed from nature?   ****
>>
>>  ****
>>
>> If the answer is “No”, then I think we can merge the two concepts into
>> one.****
>>
>>  ****
>>
>> If the answer is “Yes”, then I think “materialSample” is best
>> characterized as a subclass of what Steve and I have been pushing for
>> (setting aside, for the moment, the additional complexity of taxonomically
>> homogeneous vs. heterogeneous).****
>>
>>  ****
>>
>> In the latter case, I would define the superclass (whatever term is used
>> for it), along the lines of:****
>>
>>  ****
>>
>> "The category of information pertaining to the physical basis of a
>> sampling, subsampling, or observational event. In biological collections,
>> the [SuperclassTerm] is typically a defined group of organisms, a single
>> whole organism, or a part of a whole organism that is collected or
>> otherwise documented in nature, and either preserved, destructively
>> processed, or documented through some form of Evidence (such as images or
>> reported visual observations)."****
>>
>>  ****
>>
>> Aloha,****
>>
>> Rich****
>>
>>  ****
>>
>>  ****
>>
>> *From:* jdeck88 at gmail.com [mailto:jdeck88 at gmail.com] *On Behalf Of *John
>> Deck
>> *Sent:* Wednesday, May 29, 2013 4:01 AM
>> *To:* Richard Pyle
>> *Cc:* Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert
>> Whitton; Ramona Walls****
>>
>>
>> *Subject:* Re: [tdwg-content] New Darwin Core terms proposed relating to
>> material samples****
>>
>>  ****
>>
>> Since the original proposal was from a group of folks, we decided to put
>> our heads together to construct a general response to the various issues
>> and ideas expressed on this thread. ****
>>
>>  ****
>>
>> John Deck for Rob Guralnick, Ramona Walls, and John Wieczorek****
>>
>>  ****
>>
>> In the text of the  issue submitted for MaterialSample (
>> https://code.google.com/p/darwincore/issues/detail?id=167) we noted
>> cases where the current basisOfRecord terms pertaining to the Occurrence
>> class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen,
>> HumanObservation, MachineObservation) do not adequately cover certain
>> cases, including: environmental sample (for metagenomic analysis),
>> transcriptomes (measuring genes but not taxa), and destructive samples
>> (e.g. tissues destructively sampled in order to generate genomic DNA).  The
>> term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747)
>> is broad enough to be utilized across various cases that fulfill our
>> criteria while still maintaining a consistent, clear and human
>> understandable meaning.  For our purposes, we can think of “Material
>> Sample” as any type of matter that we can use in order derive further
>> evidence needed for identifications, and taxa, whether it is taxonomically
>> homogenous, heterogenous, a single individual, sets of individuals, or
>> populations. ****
>>
>>  ****
>>
>> How is MaterialSample different from Individual?  The intent of
>> individualID is fairly clear:  since an Occurrence represents an organism
>> at a place and time (per Markus’ email), the individualID term allows us to
>> assign an instance identifier for a particular organism that can be present
>> in multiple events. MaterialSampleID, on the other hand, is intended to
>> allow users to say that the basis of an occurence is a material entity
>> (i.e. matter) that has been sampled according to some particular method.
>> Whether or not this material entity is an individual (sensu individualID in
>> DwC) is an independent axis of classification. As was already pointed out,
>> there is no restriction on specifying that an occurence is associated with
>> more than one type, so any occurrence can have both an individualID and a
>> materialSampleID.****
>>
>>  ****
>>
>> We maintain our position on the proposal for MaterialSample as a value
>> for the basisOfRecord, with an associated materialSampleID to identify
>> instances of them. Per Steve’s initial comments, we have already withdrawn
>> the proposal for a MaterialSample class distinct from that in the Darwin
>> Core type vocabulary, which should make it easier to evaluate the
>> implications of what we’re discussing.  ****
>>
>>  ****
>>
>> ************************
>>
>>  ****
>>
>> NOTES, MaterialSample from OBI:****
>>
>>
>> OBI has fairly broad definitions of samples & specimens that are meant to
>> be utilized across many different scientific activities.  Material Sample
>> is defined as a “*material entity that has the material sample role*”,
>> while a material sample role is defined as “ *a specimen role borne by a
>> material entity that is the output of a material sampling process*”, and
>> a material sampling process is “*a specimen gathering process with the
>> objective to obtain a specimen that is representative of the input material
>> entity*”.  ****
>>
>>  ****
>>
>>  ****
>>
>>  ****
>>
>>  ****
>>
>> On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef at bishopmuseum.org>
>> wrote:****
>>
>> Hi Markus,
>>
>> Great question!  Particularly because this is exactly the sort of use case
>> we designed our model around.****
>>
>>
>> > if you take a tissue sample of the same tree every year, would the
>> identifier
>> > in individualID be the same for all of them or be different? WIth the
>> current
>> > dwc:individualID definition it would be the same for all samples. If I
>> > understand you correct each sample would have its own "individual"
>> > identifier in your proposal? It can't see how you can collapse these two
>> things
>> > into one definition.****
>>
>> No, that is not how we would handle it.
>>
>> In our model, there would be one IndividualID to represent the tree,
>> spanning the time period beginning (more or less) when the seed was
>> germinated, until the time at which the entire physical structure of the
>> tree was disintegrated.  It is an individual tree.
>>
>> There would be multiple Occurrence instances, for each time that someone
>> observed or sampled or otherwise wished to document some condition of that
>> tree. All of these Occurrence instances would refer to the same
>> individualID
>> value (i.e., the "tree").  In the example above, this means there would
>> be a
>> different Occurrence instance for each year that a sample is taken --
>> because in each case, an assertion that the full tree existed at a certain
>> time and place can be made (I understand that trees tend not to move
>> around
>> very much, so the Location for each event associated with each Occurrence
>> would, in this case, remain the same; but the other Event properties --
>> such
>> as eventID, samplingProtocol, samplingEffort, eventDate, eventTime,
>> startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate,
>> habitat,
>> fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly
>> for
>> each sampling Occurrence instance).
>>
>> Suppose that the tree is visited every month, but only sampled once per
>> year.  In that case, there would be an Occurrence record for every monthly
>> visit.  In other words, an Occurrence instance exists regardless of
>> whether
>> a physical sample was made or not.  Any in-situ images made of the tree
>> would likewise be associated with the specific Occurrence instance, and
>> each
>> image would represent a separate instance of "Evidence".
>>
>> Now, let's focus on the annual samplings.  Every time a new sample is
>> taken
>> from the tree, at least one new instance of Individual (with a unique
>> individualID value) is created to represent the sample.  This sample
>> (individual instance) may be a "gathering" (set of multiple individual
>> specimens gathered at the same time), or it may be a single specimen, or
>> it
>> may be simply a tissue sample intended for destructive analysis.  In any
>> case, it's a new individual instance derived from the "parent" individual
>> instance representing the whole tree.  In our implementation, "Individual"
>> can be hierarchical, such that a whole-organism tree can be sub-sampled
>> with
>> many "child" instances of "gatherings" (say, one gathering each year), and
>> each gathering may have multiple child "specimen" individuals (e.g.
>> individual botanical sheets created from the multiple items of a single
>> gathering), and each specimen may have further "child" subsamples
>> extracted
>> for DNA analysis (or whatever), and the hierarchy can continue on down to
>> whatever derivatives that people feel a need to keep track of (e.g.,
>> aliquot).
>>
>> The point is, all Individual instances are well-defined physical objects
>> (or
>> well-defined sets of physical objects), and they can be arranged in a
>> n-tiered hierarchy.
>>
>> Moreover, each Individual that can be characterized as a "sample" (what we
>> refer to as a "CollectionObject") may also have a property value for
>> "CollectionOccurrenceID" -- which refers to the specific Occurrence
>> instance
>> at which the sample was obtained.
>>
>> So, for example, if the tree is visited on May 27, 2013 and a specimen
>> (sample) is taken, then:
>> 1) An Event instance is generated to represent the event where the tree
>> was
>> visited;
>> 2) An Occurrence instance is generated, which refers to the new EventID,
>> and
>> the existing IndividualID for the whole tree, and includes whatever other
>> Occurrence properties are relevant for the tree at the time of this
>> Occurrence
>> 3) An Individual instance is generated for the specimen, which has a
>> property value for parentIndividualID that refers to the individualID for
>> the whole tree, and a property value for collectionOccurrenceID that
>> refers
>> the Occurrence instance where the specimen was collected.
>>
>> So, to summarize the answer to your question:
>> - There are multiple Occurrence instances that refer to the same
>> Individual
>> instance representing the whole tree (and, hence can be collapsed to the
>> same IndividualID value).
>> - Any Individual can have derivatives that are themselves unique
>> Individual
>> instances.
>> - Individuals are arranged hierarchically, and certain properties can be
>> inherited up or down the hierarchy, depending on the properties and their
>> associated logical constraints.
>>
>> At some point, I will assemble a set of other specific use cases, and how
>> we
>> manage them through our use of the "Individual" instance (although I will
>> probably not use the word "Individual", as this seems to cause too much
>> confusion in these discussions).
>>
>> Aloha,
>> Rich****
>>
>>
>>
>> ****
>>
>>  ****
>>
>> --
>> John Deck
>> (541) 321-0689****
>>
>>  ****
>>
>>  ****
>>
>>
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content****
>>
>>  ****
>>
>> ** **
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20130531/77ec6e5f/attachment.html