Boundary between dwc:Organism and dwc:MaterialSample #22
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what is the thing/class taking part in an Event ... in and Occurrence. How do we model environment or ecosystem or nature types or geology? (which are not appropriately modeled as Organism). Would these only be properties of a Location? Or is there room for a new class for these things (in Darwin Core? from before they became MaterialSamples?). In my mind, we sample MaterialSamples (which also can become accessioned collection specimens) from such things. E.g. water samples, minerals, geological samples, etc. for other purposes than recording any living things. In my mind, we thus already have many MaterialSamples (accessioned specimens) at the museum in Oslo that is not derived from any Organism. |
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The key property of a Sample - material- or otherwise - is the intention that it be representative of something larger. |
Where in this timeline can |
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but that calls into question the scope of the definition of
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Maybe it is easier, after all, if the Organism ceases to be an Organism when it dies??? |
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@Jegelewicz , where you consider dwc:MaterialSample a verb, i.e. "The key property of a Sample - material- or otherwise - is the intention that it be representative of something larger. This is particularly obvious from the verb form 'to sample'", I treat MaterialSample a noun. I have used it as the primary or original sample (termed originalSample in my CMS) obtained from a locality during an event. As a verb the term infers a derivative sample (termed that in my CMS). The derivative sample includes fossils and other processed subsamples used to document the physical and chemical properties of the original sample. The term "sample" used as a noun is common in paleo and other earth sciences. In my mind, original samples are more related to an eDNA sample where you collect a water sample from a stream and process for derivatives represented by the DNA of organisms upstream of that event, or a trawler net sample where you hope to obtain organisms at a set depth in a body of water. You are never quite sure of what you will get, but you already have some facts of the event and maybe the anticipation of results. I always want the ability to trace those samples back to the original event, and that has been how I have used MaterialSample, the what of the where, who, and when. |
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First, many thanks to @Jegelewicz for forking this off into a separate, dedicated issue. Now I can feel much less self-conscious pontificating endlessly on this issue while trying to maintain its relevance to I also want to thank you for this comment on the other issue:
As I assume is self-evident from my numerous posts on this, I wholeheartedly agree! I'm only mostly joking when I refer to "keeps me up at night" and "not getting any sleep tonight"; but in fact thinking about this stuff actually does keep me awake when I should be sleeping, and literally works its way into my dreams, and it turns out last night literally was a very restless night for me because of this. First of all, I think both The same is fundamentally true for To summarize this first point, I think it's helpful to acknowledge that the principles we wrestle with on defining the boundary between To avoid a single massive multi-chapter dissertation post, I'll leave this as it is on that first point, and start a second post for the next point. |
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OK, now the second point, which I think is the more important one, and the larger reason for why I'm not well rested this morning. To me, the main thing that distinguishes an instance of The reason I think of an The point here is that any properties of an By contrast, I think instances of |
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Chapter 3. Another important distinction between an instance of This has important implications for how instances of these two classes relate to other DwC classes. For example, it makes much more sense that During the discussions about establishing the For practical/implementation purposes, this implies that every I'll address this in more detail in the next chapter. |
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Chapter 4. Inheritance If it's true that In our original data model (described a few chapters ago), we structured "Individual" (superclass of Organism) as a hierarchical entity. That is, one of the properties of an The point is: instances of That, then raises a couple of questions related to parent/child relationships among First, is it always obvious which is the "parent" and which is the "child"? Sometimes it is obvious. For example, if I have a dead fish and take a fin clip that I plop into a vial for later DNA analysis, then preserve the rest of the fish in formalin to serve as a voucher, it's pretty obvious that the voucher is the "parent" and the tissue sample is the "child". But what if I have a dead bird, and then through various curatorial steps separate that dead bird into a skin/feathers, a jar of meat and entrails in alcohol, and a dried skeleton? Which is the parent and which is/are the child(ren)? Or, maybe the whole/intact dead bird was its own Second: If we agree that Third: Is inheritance bidirectional? In other words, if we do have inheritance across the parent-child link connecting two MaterialSample instances (e.g., a voucher and a tissue sample), then does that inheritance always (or sometimes) flow in both directions? For example, if a DNA sequence is linked to the tissue sample from which it came, does the parent voucher "inherit" that DNA sequence? Sometimes, yes -- but sometimes no. For example, if the "parent" Many of these problems may become more evident in the next chapter... |
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Chapter 5. The Fossil Conundrum. Thanks to posts by @RogerBurkhalter, I've been wrestling with the fossil example quite a bit. I already outlined two distinct events associated with a fossil that we want to track and represent through DwC:
I gather that most fossilologists are focused primarily on the second (fair enough -- although I still maintain that the first is also important, and Some cataclysmic event hundreds of millions of years ago causes the deaths of thousands of marine critters. The bodies of these critters sink to the silty bottom and are covered in sediment. The physical matter of the organism at the time of their deaths disappears completely over time, and is replaced by other molecules that were not present within the organisms when they were alive. Hundreds of millions of years later, the mineralized impressions of these long-dead critters is exposed to the surface, and a chunk of rock is removed from the Earth and taken to a Museum, where it is curated by various means. The rock contains impressions of numerous long-dead critters from multiple different taxa, but the rock itself is maintained intact at the Museum, and assigned a single catalog number. There are a bunch of interesting things we could get out of this use case in teasing apart the subtleties of Maybe this is obvious to everyone except me, but from my perspective, I think I can now get more restful sleep going forward. And it means that I am now leaning heavily to these sorts of timeline representations:
By "Disintegrated" I mean essentially complete molecular dissolution -- to the point where no physical manifestation of the organism exists either in nature or in a collection. The implication of this is that the lifespan of an Of course, there are other implications of this as well, such as: "Is an |
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OK, I have at least two more chapters in my head; one about the LivingSpecimen thing, and another representing a summary/conclusion articulating the key differences between |
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One more thing, just to add the derivative
For example, Of course, the |
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@deepreef so much to unpack - I'll probably miss or misinterpret something...but here goes. I too dream about this stuff and clearly wake up at all hours of the night to contemplate it. My ramblings are not as educated (given the reponses to them!) but I hope they do prod people to think about what those in the world who are not (and never will be) Darwin Core experts may be thinking.
In an ideal world, I think your proposal for the "whole" sample divided into multiple children is appropriate, and we have definitely discussed this in Arctos. But that might be too large of an administrative burden, so perhaps the idea can be that the condition of the original MaterialSample (the whole fish) is changed by the sampling event, so that you still have only two samples. The parent (now fin-less fish) and the child (the fin clip). There is no reason the relationship couldn't go the other way! For the bird - I do think the destructive sampling leads to the loss of the original MaterialSample - I am sure some amount of information from the whole dead bird was left on the prep table or went into the trash. For the case of destructive preparation (which seems to be more than "sampling a sample") I think it would be worth it to know that there once was a whole bird and when and how it was transformed into skin/meat/bones and even who completed the transformation.
I don't know about these being equal. One is due to the life process of the "organism" and the other is not. The same goes for decay. I worry about creating a definition for organism (as we use it as part of dwc:Organism) that seems to differ significantly from what is apparently understood as a living thing. Why does the organism have to continue existing in order for evidence of it (MaterialSample) to continue existing? Let's take scat. I find some and record that I found it on my front porch at 9Am today. If I can identify it as coyote, then I know the coyote was actually on my porch at some time between the last time I was there (when there was no scat) and when I found it. So, I can record an occurrence, but the TIME portion of it will be vague. In my opinion, finding a fossil is exactly the same situation, only both the PLACE and TIME are vague because the T-Rex did not occur in the exact place I found it's mineralized bones and the date could be any time from whenever T-Rex roamed the Earth until they no longer did so (or maybe more precise if I can date something). The act of finding it is something other than occurrence to me, in the same way finding something dead on the road is different than collection of a live critter, which would also have a vague PLACE and TIME for an occurrence (Did it die right here? When exactly did it die?). If we are going to use a definition of "organism" for the term used in the definition of dwc:Organism that doesn't include "alive", "living" or something like that, we definitely need to make that more explicit. Actually, I think we need that clarity no matter what. |
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Many thanks, @Jegelewicz
I agree. I was just representing two extremes (dead bird split into three roughly equivalent parts, vs. fish/fin clip asymmetry). The continuum between these two extremes is complete, and I doubt we'd find an objective point where we could distinguish a case of "A was split into B & C" from "B was extracted from A". That's what I was getting at with my "Perhaps it's handled on a case-by-case basis, ..." option (which I think is the one that best balances ideal with practical).
Yeah, that was making me queasy as well. But I still wanted to throw it out there as one interpretation. These kinds of data become a LOT more simple/manageable within the existing definitions if we just allow a fossil to represent an instance of
Yeah, I see that (and good example!) But as to "Why does the organism have to continue existing in order for evidence of it (MaterialSample) to continue existing?", the answer is "it doesn't", But if it does, the practical informatics side of this becomes a lot easier (for reasons alluded to above). A lot of this boils down to Angels dancing on the head of a pin stuff, so we shouldn't get too bogged down. But my general preference (as the dude who has to design the databases and the user interfaces to those databases) is to broaden the scope of existing informatics constructs (like
Agreed -- but we also care about where and when the fossil itself was found, and that's what @RogerBurkhalter says he records as the "Occurrence". Strictly speaking, it can only be a Suppose you left your coyote scat on the porch for decades, and then eventually someone collected it and preserved it to serve as evidence the coyote was there once. Don't we want to track both the Occurrence of the live coyote on your porch, and the event where the scat was collected? Or do we need some way besides
100% agreed. And with respect to the other post by @baskaufs : we don't want to change the definition of |
I think that is my point. We do want to track both and they are different kinds of things. Even in my scenario, there are two events. The dwc:Occurrrence (when the coyote was actually on my porch) and the collection of evidence (when I picked up the scat). The difference between these events can be quite small and maybe make no real difference or as in your coyote scenario where I don't mind the scat on my porch for decades, it can be significant and the evidence can be significantly altered in the time that passes between occurrence and collection of evidence (like those T-Rex fossils). It's a bit of a continuum, like the fish/fin clip or dead bird/skin/skeleton/meat continuum, but at some point the difference seems significant enough to make note of? |
Agree - we want to clarify the meaning of "organism" in the definition of |
I also think that we want to record events involving material things that fall well outside of any broadening of the dwc:Organism class, such as e.g. the soil- and the water sample (and the scat). If the rationale for broadening dwc:Organism is to expand the use cases for dwc:Occurrence, I believe this might anyway not be fully resolved by such an approach? -- Besides current actual dwc:Occurrence implementations already sort of describe the "occurrence" of MaterialSamples if we take the basisOfRecord (sensu type of the subject thing) literary. No need to broaden dwc:Organism - when the "rdfs:domain" of dwc:Occurrence is already broad enough 😜 -- If dwc:Organism is broadened so far as to include almost any biotic "Evidence" (or even any "Evidence" of something that once was biotic), might the resulting "new" dwc:Occurrence instances maybe risk to break some fundamentals in some of the current use cases for "primary biodiversity data"??? Might a new "Evidence" class be a better route to explore? |
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OK, so it seems are quandary boils down to this:
Some of the options that have been thrown on the table include:
I think each one of these has pluses and minuses, and at this point I don't have a strong preference (although I'm not exactly sure how an Evidence class really solves it). Great... it's bedtime here in Hawaii. Another restless night of semi-sleep awaits. |
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closing for focus on MaterialSample and properties |
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The main fuzzy part (in terms of both idealized conceptualization and practical implementation) is this business of the boundary between
dwc:Organismanddwc:MaterialSample, and the respective lifespans of each. Depending on how we lock in those boundaries and lifespans, and whether and to what extent they overlap in space and time, we may (or may not) have another question of how to manage instances of "An existence of a MaterialSample (sensu however we end up defining it) at a particular place at a particular time."Originally posted by @deepreef in #21 (comment)
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