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

[Jason Holmberg]

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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