Boundary between dwc:Organism and dwc:MaterialSample

[Jegelewicz]

The main fuzzy part (in terms of both idealized conceptualization and practical implementation) is this business of the boundary between dwc:Organism and dwc: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)

[Jegelewicz]

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.

@dagendresen in #21 (comment)

[Jegelewicz]

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'. If you don't want to consider the act that created it, or the intention to represent something, then 'sample' is just a fancy name for 'thing'.

@dr-shorthair in #21 (comment)

[Jegelewicz]

1. At what point does it stop being an instance of dwc:Organism (if ever), and therefore no longer eligible to participate in new/future dwc:Events, and by extension, no longer eligible to participate in new/future dwc:Occurrence instances? (This assumes that dwc:Occurrence=[dwc:Organism+dwc:Event] -- which I guess is still open to debate).

2. At what point did it start being an instance of dwc:MaterialSample? My gut tells me this happened when a human took control of its disposition (in this case, when it was captured from the reef).

3. How do we characterize the participation of instances of dwc:MaterialSample directly in instances of dwc:Event (e.g., DNA sequencing of a tissue sample, loaning of a specimen, etc.) in the absence of an instance of dwc:Organism, if we agree that dwc:Occurrence=[dwc:Organism+dwc:Event] and if we agree that, at some point, the dwc:Organism ceased to be.

dwc:Event instances through Time -->
Sperm meets egg    Captured    Dies    Preserved    Subsampled    Analyzed    Disintegrated
<------------- dwc:Organism ---------?->
                                    <-?---------------------- dwc:MaterialSample-------------------?->

Where in this timeline can dwc:Occurrence instances exist? How do we represent intersections of dwc:MaterialSample and dwc:Event when we can't comfortably reference an instance of dwc:Organism (right side of the timeline)? Should those dwc:MaterialSample+dwc:Event instances be represented as dwc:Occurrence instances? If not, then what are they? Some other sort of properties/history of the dwc:MaterialSample instances (not necessarily framed as dwc:Event instances)?

@deepreef in #21 (comment)

[Jegelewicz]

but that calls into question the scope of the definition of Organism. Obviously it would mean that neither death nor disarticulation nor disintegration (mineralization) represents the termination of an instance of dwc:Organism, so maybe my timelines would look more like these:

dwc:Event instances through Time -->
Sperm meets egg    Captured    Dies    Preserved    Subsampled    Analyzed    Disintegrated
<------------------------------------------ dwc:Organism ---------------------------------------...
                                    <-?------------------------ dwc:MaterialSample------------------------...

dwc:Event instances through Time -->
Sperm meets egg    Dies                    Fossilized                    Collected
<------------------------------------ dwc:Organism ------------------------------------...
                                       <----- non-organism thing----->
                                                                                             <- dwc:MaterialSample-...

@deepreef in #21 (comment)

[Jegelewicz]

Maybe it is easier, after all, if the Organism ceases to be an Organism when it dies???

@dagendresen in #21 (comment)

[RogerBurkhalter]

@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.

[deepreef]

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 catalogNumber... :-)

I also want to thank you for this comment on the other issue:

So I think a clarification is needed, because until we can disentangle dwc:Organism from dwc:MaterialSample, I don't think we can move on.

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 Organism and MaterialSample, as defined in DwC, are conceptually subclasses of broader ideas that transcend biology. This is more obvious for MaterialSample, where we've already discussed abiotic "things" (geology samples, cultural artifacts, etc.) in this context. We in DwC-land are focused on those instances of MaterialSample associated with biodiversity, but we acknowledge the same principles apply to abiotic stuff.

The same is fundamentally true for Organism. When this class was first proposed for DwC, one of the big points of discussion was whether to use the term "Organism" or the term "Individual". A significant basis for the proposed new class was to allow proper instantiation of what was then a DwC term organized in the Occurrence class called individualID. The purpose of this now-deprecated (or, rather, rebranded to organismID and re-organized into a new class) term was to serve to link together multiple Occurrence instances that apply to the same individual organism (e.g., a tagged wolf, or a particular whale, or a particular bird) that was repeatedly recorded across multiple place/time Events. At the time, I was a strong proponent of the new class. Also at the same time, we were developing a data model that would unify our Museum's natural sciences collections with our cultural collections. For this and other reasons, in our implementation we retained "Individual" as a superclass (seemed more professional-sounding than "thing"), of which "Organism" represented a subclass (i.e., "biological thing").

To summarize this first point, I think it's helpful to acknowledge that the principles we wrestle with on defining the boundary between Organism and MaterialSample apply equally to non-biological things. But because this is TDWG, and DwC, we can focus our discussion going forward on use-cases more relevant to our biological focus. We just should keep in mind the more general use cases as we hammer this stuff out.

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.

[deepreef]

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 Organism from an instance of MaterialSample (both for biological and non-biological use-cases), is that the former represents an abstract concept, and the latter represents a physical object.

The reason I think of an Organism as an abstract concept is that its existence goes beyond the atoms and molecules that form it at any given moment. Few (if any) of the atoms and molecules contained in a sperm and an egg at time of fertilization (or even birth) remain as part of the physical body at the time of death. Indeed, a quick Google search yielded this factoid: "98 percent of the atoms in the [human] body are replaced yearly". One of the use-cases I point to for tracking a specific individual organism over time is this video, which documents the same fish at the same location at two different times 10 months apart. Clearly, the collection of physical material comprising that individual organism at the second Event is substantively (if not almost entirely) different from the physical material comprising it at the first Event. This is why I think fundamentally an Occurrence is correctly defined as an Organism at an event. The linked video represents evidence of two distinct Occurrence instances in which the same Organism participated; but there is no logical way you could say that the same MaterialSample participated in both Occurrence instances.

The point here is that any properties of an Organism that were true at the moment of its conception (e.g., sperm fertilizing an egg) should also be true at the moment of its death -- even though the physical/material makeup of the Organism changed dramatically over the course of its lifespan.

By contrast, I think instances of MaterialSample are -- at least in part -- defined by their physical makeup. Although they certainly do change over time (no preservation method is perfect), the nature of that change is not as dramatic or fundamental as the material change that happens between the time a sperm meets an egg and the time the resultant organism dies. I can defend this further, but to save time and space I'll proceed with the assumption that this is a non-controversial assertion. Again, the point is that properties of a MaterialSample instance should apply to the physical matter itself, rather than some abstract notion of an entity that fundamentally changes over time.

[deepreef]

Chapter 3.

Another important distinction between an instance of Organism and an instance of MaterialSample is that the former is, by definition, constrained to a single taxon; whereas the latter may represent many different taxa (e.g., soil or water sample); or even no taxa at all (abiotic MaterialSample instance).

This has important implications for how instances of these two classes relate to other DwC classes. For example, it makes much more sense that dwc:Identification instances should apply to Organism instances, because the identification applies to the entirety of the organism. The same would break down if taxonomic identifications were applied directly to instances of MaterialSample.

During the discussions about establishing the Organism class, some of the key talking points related to cases where a single physical object tracked and curated in a Museum collection might have multiple taxonomic identifications associated with it. Water and soil samples are obvious examples, and many fossil specimens are also in this situation. Another example would be a hermit crab in a molluscan shell, which has an anemone attached to it. The conclusion was that a single instance of MaterialSample should inherit taxonomic identifications through instances of dwc:Organism (one per taxon) associated with the MaterialSample. It also underscores the many-to-many nature of the relationship between Organism and MaterialSample (i.e., a single Organism might be represented by multiple MaterialSample instances, and a single MaterialSample might represent multiple Organisms).

For practical/implementation purposes, this implies that every MaterialSample instance involving biological objects requires the existence of at least one associated Organism instance for each taxon represented by the MaterialSample. This is necessary not only for associating taxonomic identifications to the MaterialSample, but also in associating MaterialSample instances with Occurrences. In both cases, at least one Organism instance is needed to bridge a MaterialSample with either a Taxon or an Occurrence.

I'll address this in more detail in the next chapter.

[deepreef]

Chapter 4. Inheritance

If it's true that MaterialSample instances can only be linked to Taxon and Occurrence instances through at least one Organism instance, this creates some situations that are both counterintuitive and cumbersome. But before I get into that, I should step back and outline another fundamental difference between Organism and MaterialSample: derivatives.

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 Individual was parentIndividual. We did this mostly to accommodate tissue samples derived from vouchers. We treated each of them (the voucher and the tissue sample) as distinct Individual (=Organism) instances, and the child would inherit properties from the parent. This meant we could attach a Taxonomic identification directly to the parent instance, and the child would inherit it. But things started getting confusing when the taxonomic identification was actually attached to the child (e.g., via a DNA sequence derived from the tissue sample). Long story short: we came to realize that instances of Individual/Organism should not be represented through hierarchical relationships. Sure, a given Organism can and does have one or more (usually two) biological "parents", and this is certainly a relationship that needs to be accommodated in any good data model, this is a different kind of parent/child relationship than the informatic kind, which involves more implicit "inheritance" (of the informatic sort, not the genetic sort).

The point is: instances of MaterialSample can have derivatives and sub-derivatives and so on (implying the need for parentMaterialSample), but not instances of Organism.

That, then raises a couple of questions related to parent/child relationships among MaterialSample instances:

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 MaterialSample instance, and all three of the preparations (skin, meat, bones) represents a separate child? If so, then do I also need three MaterialSample instances for the fish example (the parent being the whole fish with all fins intact, and the two children being the fin clip and the voucher-sans-fin)? Perhaps it's handled on a case-by-case basis, following some sort of standard(ish) guidelines, such that the fish can be represented as two MaterialSample instances (voucher parent and tissue child) but the bird example benefits from manufacturing a single "parent" MaterialSample instance for the whole dead bird, which is then destructively processed into the three children (retaining the data record for the parent for informatic purposes).

Second: If we agree that MaterialSample instances inherit their Taxon Identifications and associations with Occurrences through instances of Organism, then does each each instance in a parent-child hierarchy of MaterialSample instances need to individually link to the associated Organism? Or does only the "parent" need to be linked to the Organism, and all the "child" MaterialSample instances inherit this link? This may well be an implementation detail that does not need to be answered for the DwC standard, but I think it's still valuable to discuss and understand this, to help explain how the eventual standard can be applied from actual CMSs.

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" MaterialSample instance is a lot of 5 specimens, and only one of those 5 is sequenced, then you can't apply the sequence to all five specimens; only the one that was actually sequenced. The point here is that any notion of inheritance across MaterialSamples and their derivatives will probably need to be explicitly indicated (hinting at the need for additional properties to record such indications).

Many of these problems may become more evident in the next chapter...

[deepreef]

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:

1. The event when/where the organism died; and
2. The event where/when the fossil was taken into custody by a human.

I gather that most fossilologists are focused primarily on the second (fair enough -- although I still maintain that the first is also important, and dwc:Occurrence records should be generated to capture this information). But I think it would be helpful to present a use-case to tease these issues apart:

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 Organism vs. MaterialSample, but the one that most kept me up last night was when the critters stopped being "Organisms". My epiphany was that the Organisms continue to exist. As already explained in an earlier chapter, we already accept 100% turnover in molecular/atomic composition of an Organism, so I see no reason why that logic cannot continue beyond organic molecule turnover while the critter was alive into mineralization after it's dead. In other words, I think the critters maintained their abstract essence of being an Organism throughout the fossilization process.

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:

dwc:Event instances through Time -->
Sperm meets egg    Captured    Dies    Preserved    Subsampled    Analyzed    Disintegrated
<------------------------------------------ dwc:Organism --------------------------------------->
                                    <-------------------------- dwc:MaterialSample------------------------>

dwc:Event instances through Time -->
Sperm meets egg    Dies                    Fossilized                    Collected     Disintegrated
<------------------------------------ dwc:Organism -------------------------------------->
                                                                                             <-- dwc:MaterialSample-->

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 Organism equals or exceeds that of its associated MaterialSample manifestations, and that there is never a case where an extant MaterialSample exists without its corresponding Organism. The other important implication of this is that we don't need another class of thing to represent the direct intersection of a MaterialSample an an Event, because the Organism is always there to bridge that gap.

Of course, there are other implications of this as well, such as: "Is an Organism always the sum of its extant physical parts?" I'm thinking "yes" -- which applies to the bird dropping a feather in the forest example, and the eDNA sample of a cougar downstream of where it crossed the river, and various other edge cases we've discussed on related issues.

[deepreef]

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 Organism and MaterialSample. But I have other things I need to do today, and I think I've already gone way out of bounds in terms of the volume of text one should ever dump into a GitHub post (at least in rapid succession like this). I may eventually post the final two chapters, but for now I'll wait to see if the above is helpful, or just a whole lotta textual noise.

[deepreef]

One more thing, just to add the derivative MaterialSample instances to the timeline:

dwc:Event instances through Time -->
Sperm meets egg    Captured    Dies    Preserved              Subsampled              Analyzed                    Disintegrated
<------------------------------------------------------ dwc:Organism ---------------------------------------------------|
                                    ↳- dwc:MaterialSample-| (1)
                                                                            ↳------------------------- dwc:MaterialSample----------------------| (2)
                                                                            ↳---------------- dwc:MaterialSample--------------| (3)
                                                                            ↳------------------- dwc:MaterialSample-----------------| (4)
                                                                                          ↳- dwc:MaterialSample-| (5)

For example, MaterialSample (1) could be the whole dead bird, that ceases to exist when the three derivatives (skin, bones, meat; 2, 3, 4) are parsed out. These each might survive for different lengths of time. MaterialSample (5) could be a tissue sample extracted from the meat that is destructively sampled for DNA analysis. But the point is, as long as some instance of MaterialSample exists, so too does the corresponding Organism exist (and it can continue to participate in various Occurrence instances along the way, when any one of the MaterialSample instances participate in an Event). After all physical manifestations of the Organism cease to exist, the Organism instance itself ceases (and can no longer participate in any future Occurrence instances).

Of course, the Organism can live beyond the disintegration of all associated MaterialSample instances, as would be the case of a tree in nature from which these MaterialSample instances were taken, and all the MaterialSamples and their derivatives disintegrated while the tree in nature (or its fossilized future) continues to exist.

[Jegelewicz]

@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.

maybe the whole/intact dead bird was its own MaterialSample instance, and all three of the preparations (skin, meat, bones) represents a separate child? If so, then do I also need three MaterialSample instances for the fish example (the parent being the whole fish with all fins intact, and the two children being the fin clip and the voucher-sans-fin)?

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.

we already accept 100% turnover in molecular/atomic composition of an Organism, so I see no reason why that logic cannot continue beyond organic molecule turnover while the critter was alive into mineralization after it's dead

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.

[deepreef]

Many thanks, @Jegelewicz
...and sincere apologies for the massive dump. Maybe I should have just written it all up in a whitepaper somewhere and posted a link here.

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.

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).

I don't know about these [cellular turnover in a living thing vs. mineralization of a fossil] being equal. One is due to the life process of the "organism" and the other is not.

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 dwc:Organism. For one thing we can do away with the non-organism thing place-holder on earlier timelines; and also we have no need to come up with a new class to represent the intersection of MaterialSample and Event (or maybe we still do?)

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.

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 dwc:Organism) to the point where they maintain adherence to their definitions, but allow broader use-cases to be accommodated.

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).

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 dwc:Occurrence if an instance of dwc:Organism was there -- hence my desire to treat the fossil as representing the instance of Organism.

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 dwc:Occurrence to represent the collection of the scat?

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.

100% agreed. And with respect to the other post by @baskaufs : we don't want to change the definition of dwc:Organism; we just want to clarify that definition.

[Jegelewicz]

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 dwc:Occurrence to represent the collection of the scat?

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?

[Jegelewicz]

we don't want to change the definition of dwc:Organism; we just want to clarify that definition.

Agree - we want to clarify the meaning of "organism" in the definition of dwc:Organism

[dagendresen]

Another important distinction between an instance of Organism and an instance of MaterialSample is that the former is, by definition, constrained to a single taxon; whereas the latter may represent many different taxa (e.g., soil or water sample); or even no taxa at all (abiotic MaterialSample instance).

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 dwc:Organism. For one thing, we can do away with the non-organism thing place-holder on earlier timelines; and also we have no need to come up with a new class to represent the intersection of MaterialSample and Event (or maybe we still do?)

it can only be a dwc:Occurrence if an instance of dwc:Organism was there -- hence my desire to treat the fossil as representing the instance of Organism.

Or do we need some way besides dwc:Occurrence to represent the collection of the scat?

I think that is my point. We do want to track both and they are different kinds of things.

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?

[deepreef]

OK, so it seems are quandary boils down to this:

1. DwC clearly defines dwc:Occurrence as the intersection of dwc:Organism and dwc:Event (=specific place and time, assuming the "action" part represents the documentation thereof).
2. We don't want to mess too much with the existing definition of dwc:Organism, but we're open to clarifying what that definition is.
3. We definitely want to clarify the definition of dwc:MaterialSample.
4. We want to be able to track instances of dwc:MaterialSample as they participate in dwc:Events,

Some of the options that have been thrown on the table include:

1. Relaxing the definition of dwc:Occurrence such that instances of both dwc:Organism and dwc:MaterialSample can be documented as existing at a particular place at a particular time.
2. Clarifying a particularly liberal/broad definition of dwc:Organism such that it can accommodate fossilized impressions of once-living things and scat found on porches (so that such physical things can be tracked as dwc:Occurrences by linking through an instance of dwc:Organism).
3. Defining a new idea/class/collection of properties/whatever to explicitly represent the intersection of an instance of dwc:MaterialSample and an instance of dwc:Event.
4. Resurrecting the idea of an "Evidence" class to somehow help solve this conundrum.

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.

[Jegelewicz]

closing for focus on MaterialSample and properties