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New Term - materialSampleType #345
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Where I get stuck on |
@dshorthouse : Excellent points! (as always!) And I think you really get to the heart of what I've struggled with both for
Yes, I've been down that road as well. If I pluck a leg off a beetle, I'd be inclined to brand the leg as a "part", and retain the rest of the beast as "whole". But if I split it right down the middle, I'd probably call them both "parts". However, this is a bit beside the point, because technically no So the point is, there will always be subjectivity in deciding how to split those hairs (no pun intended), when deciding among the options for either What is the lesser of evils? Dealing with subjectivity at the edge-cases, or having no idea whether a particular
Probably... but I'll leave that for someone else to propose. |
The term |
@tucotuco I like your idea for a task group to specify a MaterialSample extension! Regarding MaterialSampleType, note that this is also being discussed in the MIDS (see tdwg/mids#14) and CD task group, and related to work going on in iSamples and DiSSCo. Ideally the results should be aligned. I am currently writing a proposal to describe the 'what is it' terms for MIDS. |
I'm assuming this means that there is no room in the model for an individually curated object that no longer has a physical manifestation, right? Is there a mechanism to strike a digital record from the index when its physical counterpart has evaporated? |
I don't see that no longer having a physical manifestation obviates keeping
a record of it and the uses derived from it when it still existed. In fact,
we have the means to capture its state with dwc:disposition.
…On Thu, Apr 29, 2021 at 11:55 AM David Shorthouse ***@***.***> wrote:
a specimen is an individually curated object, at least that is how we
defined in DiSSCo after community consultation
I'm assuming this means that there is no room in the model for an
individually curated object that no longer has a physical manifestation,
right? Is there a mechanism to strike a digital record from the index when
its physical counterpart has evaporated?
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Yes, that is one reason why we have the concept of a digital specimen, which will keep existing if the physical specimen no longer exists. In a catalog of physical specimens the record might be deleted, but the digital specimen record will be maintained and further curated. |
@tucotuco @wouteraddink Fair enough. What I'm mindful of in this instance is the potential for a philosophical schism or a functional disconnect between the physical items cared for by collections/museums and their virtual, digital representations that may lead fundamentally different lives. |
Yes! I think that is exactly the right way to proceed.
I've subscribed to the MIDS discussions, and they always end up in my Outlook calendar, but they usually happen in the middle of the night or very early morning Hawaii time. This, itself, is not a problem for me, except that by pure coincidence, each one so far has been on a morning that I needed to stay up late, and therefore could not drag myself out of bed to attend. I see the next one is May 6 at 3:30am Hawaii time, so I'll make a special effort to get to bed early the night before, if this topic is likely to be on the discussion agenda.
This is exactly my working definition for On a related question (to all): Do you consider "Specimen" to be synonymous with
The digital record is the proxy for the physical thing (or in the case of Events, Occurrences, Taxa, etc., the abstract idea). They lead fundamentally different lives from the moment they are born. The trick is for the digital proxies to accurately capture the information concerning the physical/abstract "thing" that we care about, as completely and accurately as possible. The significance of the "end of life" of a physical or abstract thing is not that the data records should be deleted, or even that the data records cannot change. The only real significance is that the physical/abstract thing can no longer yield new derivatives, or in many/most cases, participate in any new relationships, after the end of life. For example, I would define the lifespan of an One exception to the inability to "participate in any new relationships" thing is with respect to |
Try as I might, I can not get my head around a "Specimen" not being a
MaterialSample.
…On Thu, Apr 29, 2021 at 2:50 PM Richard L. Pyle ***@***.***> wrote:
@tucotuco <https://github.com/tucotuco> :
my recommendation is to charter a Task Group within the Observations &
Specimens Interest Group for the specification of a MaterialSample
extension, including the development of the needed terms and vocabularies
as a package.
Yes! I think that is exactly the right way to proceed.
@wouteraddink <https://github.com/wouteraddink> :
Regarding MaterialSampleType, note that this is also being discussed in
the MIDS (see tdwg/mids#14 <tdwg/mids#14>) and
CD task group, and related to work going on in iSamples and DiSSCo.
I've subscribed to the MIDS discussions, and they always end up in my
Outlook calendar, but they usually happen in the middle of the night or
very early morning Hawaii time. This, itself, is not a problem for me,
except that by pure coincidence, each one so far has been on a morning that
I needed to stay up late, and therefore could not drag myself out of bed to
attend. I see the next one is May 6 at 3:30am Hawaii time, so I'll make a
special effort to get to bed early the night before, if this topic is
likely to be on the discussion agenda.
a specimen is an individually curated object
This is exactly my working definition for MaterialSample, so perhaps I've
been subconsciously joining the MIDS discussions in spirit?
On a related question (to all): Do you consider "Specimen" to be
synonymous with MaterialSample? If not, what does the Venn diagram look
like for these two concepts?
Yes, that is one reason why we have the concept of a digital specimen,
which will keep existing if the physical specimen no longer exists. In a
catalog of physical specimens the record might be deleted, but the digital
specimen record will be maintained and further curated.
What I'm mindful of in this instance is the potential for a philosophical
schism or a functional disconnect between the physical items cared for by
collections/museums and their virtual, digital representations that may
lead fundamentally different lives.
The digital record is the proxy for the physical thing (or in the case of
Events, Occurrences, Taxa, etc., the abstract idea). They lead
fundamentally different lives from the moment they are born. The trick is
for the digital proxies to accurately capture the information concerning
the physical/abstract "thing" that we care about, as completely and
accurately as possible.
The significance of the "end of life" of a physical or abstract thing is
not that the data records should be deleted, or even that the data records
cannot change. The only real significance is that the physical/abstract
thing can no longer yield new derivatives, or in many/most cases,
participate in any new relationships, after the end of life.
For example, I would define the lifespan of an Event as the period of
time between the Event StartTime and the Event EndTime. Related Occurrences
can only exist if they occur within that range of time. Similarly, an
Organism lifespan begins at fertilization (or division for single-cell
organisms) and ends either when it ceases to be alive, or perhaps when all
the molecules have dissociated (disintegration). Between those two points
in time, the Organism may participate in multiple Occurrences, and be the
source of multiple MaterialSample instances. The lifespan of a
MaterialSample begins whenever the curation process begins for biological
material (When someone picks the dead bird off the road? When the dead bird
arrives at a Museum?), and ends when the all the molecules have dissociated
(or perhaps when it ceases to be curated). Within that timeframe, there may
be multiple derivative MaterialSample instances extracted from it.
One exception to the inability to "participate in any new relationships"
thing is with respect to Identification instances. An Organism could
participate in new Identification instances into perpetuity, even after
the end of life for the Organism (and after the end of life for any of
its derived MaterialSample instances).
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@deepreef you may contact alex and elspeth, they are probabably willing to see if they can accomodate your timezone if you want to participate in the mids meetings |
@deepreef i think a specimen is a kind of materialsample, a subset perhaps as there is a subtle difference between a specimen and a sample. Not in what they are but in how they are treated:a specimen acts as representation of a class (organism or type of geological material) and the aim is therefore to preserve it, while a sample is an example, and usually destroyed after doing some measurements or data extraction. |
I don't remember from the original discussion of creating the MaterialSample class that there was any expectation that it be destroyed. It could be destroyed, but didn't have to be. I'm with @tucotuco, I don't see how a twig clipped from a tree to be glued to an herbarium sheet is fundamentally different from a twig clipped from a tree for some other purpose. They are both the same material, they are a sample from an organism, and they could have the same metadata. The only difference to me is in our heads. |
Yes that is what I was saying, perhaps i was not clear, there is no difference in what they are, we just treat them differently/for a different purpose |
Same here, but the other part of the question is: are there any instances of
I guess my question is: Is there value in maintaining the two terms ("specimen" and "MaterialSample") with distinct (if overlapping) definitions in our biodiversity informatics discussions? Or, for purposes of defining the various biodiversity standards, can we use the two terms interchangeably? I agree that each word invokes different presumptions (e.g., destined for destruction or preservation), but for the purposes of modelling the data we care about, I think they are two words that mean the same thing.
Thanks, but the time zone thing isn't a problem, except when I have late-night obligations the previous day (which is rare, but coincidentally coincided with the last several MIDS gatherings). I willfully accept that one of the costs of living in the middle of the Pacific is that I often get the short end of the stick for international meeting scheduling. That's PERFECTLY fine with me, and a price that I'm more than happy to pay. |
From the term name |
A specimen is a materialSample (so in a venn diagram it falls into that), but I think a materialSample is not always a specimen, e.g. if it is not a curated object. A specimen should always have a storage location (past or present). I think for the model that does not matter, they are the same 'thing' but a specimen is required to have some specific associated data regarding curation and storage location. I think a livingSpecimen also falls completely into materialSample, it is different from an Organism in that it is a curated object. But it can change back to an Organism when it escapes into the wild and is no longer a curated object. |
I've stayed quiet on the issue of While I agree that terms like With respect to these "pseudo classes", I'm also a little fuzzy on how best to characterize the situation where a person first sees an organism in-situ, then photographs it using a digital camera, then collects it an preserves the specimen. Does the "PreservedSpecimen" supersede the "HumanObservation"? What does the photograph represent? A "MachineObservation"? Or is it only a "MachineObservation" if no organism identifiable to Homo sapiens participated in the Event? What if the photograph was taken by an autonomous robot that was also present at the Event? (Don't laugh -- we are actively working on this with non-trivial funding). To me, what is interesting/important to us are:
I would like to see our information structures oriented around tracking these things. I'm just not sure how including the "pseudo classes" among the options for |
This conversation has become relevant to #302 and would also benefit from related discussions in tdwg/dwc-qa#134. |
The proposed definition and vocabulary correspond nicely to the SpecimenType we're workign on in iSamples. See the Decision tree for the vocabulary on GitHub. We're taking a broader cross domain view of the kinds of physical samples that are in scope, and not included information objects (which are linked to samples as related resources). for the examples given in the proposed definition: The concepts in the iSamples SpecimenType are generally higher level that those in the examples; the more domain-specific specimen types would be in vocabularies with a narrower scope, as subtypes. |
This issue has been superseded by #454 |
New term
Proposed attributes of the new term:
lot
,whole specimen
,specimen part
,tissue sample
,multiple fossils
,serial thin sections
,microfossil
,water sample
,soil sample
,microbial sample
,nest
Discussion around changes to MaterialSample on DwC (#314) and GBIF issue #37. This new term has direct relevance to
dwc:preparations
. Some additional discussion is required to determine what values are more appropriate to represent aspreparations
, and what values are more appropriate to represent asmaterialSampleType
.The text was updated successfully, but these errors were encountered: