[tdwg-content] New Darwin Core terms proposed relating to material samples
Markus Döring
m.doering at mac.com
Fri May 31 07:55:56 CEST 2013
The id value is actually very useful and the only trustworthy way of grouping records, e.g. all occurrences of the same whale.
Markus
Am 31.05.2013 um 07:41 schrieb Jason Holmberg <holmbergius at gmail.com>:
> >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
>>
>>
>>
>>
>>
>>
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