OK, thanks. Now I understand it. This is all related to the taxonomic homogeneous/heterogeneous thing. One thing I should caution, using your example data below:
If we assume that JohnDeckGutSample1 was extracted from JohnDeck after JohnDeck was extracted from nature, then we have to be careful about inferring that the organism Bacteria501 has an occurrence related to the place & time where JohnDeck was extracted from nature. In other words, we can’t reliably connect Bacteria501 with the Occurrence of JohnDeck in nature, because Bacteria501 might have entered the gut of JohnDeck at some later time (e.g., during decomposition).
I also disagree that the location where the gut sample was taken is fundamentally different where the organism was extracted from nature. We definitely need be able to distinguish between Occurrences representing “natural” place+time+organism instances, from “articifical” instances. However, you can’t simply say “extracting a tissue in a lab is fundamentally different from extracting an organism in nature” The reason is that there is a very rich spectrum between those two end points, and no clear place along that spectrum where a line can be drawn. What about a specimen of a “naturalized” species in a certain location? What about an organism taken from nature that was born of parents that were brought to that place by humans? What about the organisms that were themselves brought by humans, then released, then recaptured? What about captive organisms or plans in a person’s garden? This spectrum continues all the way down to extracting a gut sample from a specimen collected in Moorea, in a lab at Berkeley. The degree of “naturalness” of an Occurrence is certainly important, but it’s not Boolean, and it’s only one axis of interest, so we shouldn’t simply assume dc:location represents some kinds of locations, but not others.
I think the basic problem is that, as has already been stated, DwC emerged from the collections-based world, where one specimen = one occurrence, and that occurrence is naturally regarded as being the occurrence when+where the specimen was extracted from nature. Now that we have such a diversity of data we are trying to manage, this Occurrence-centric approach (with its overloaded notion of an “Occurrence”) is being stretched to the breaking point.
I think we should trend towards leaving DwC as a simple data exchange paradigm, and focus these more complex conversations on a next-gen ontology for biodiversity data. I realize that’s already happening; but it seems like the “center of mass” for conversation should shift from DwC to the biodiversity ontology domain.
Aloha,
Rich
From: jdeck88@gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck
Sent: Friday, May 31, 2013 9:17 AM
To: Richard Pyle
Cc: TDWG Content Mailing List; Robert Whitton; Ramona Walls
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
Since it was a gut sample, we'll be seeing lots of stuff in there, maybe even 1000 different taxa each one can be a distinct occurrence as JohnDeckOccurrence124 and JohnDeckOccurrence125 are different taxa.
Now, in the sense of Event/location i'm taking the location details to be when it was isolated from nature and thus the location would be the same as the wholeorganism location. In our recent workshop on this same issue recently in Copenhagen we went around about this issue for awhile but decided that we should take "location" to mean the the location at which whatever parent organism was isolated in nature. Certainly the location where the gut contents were extracted (e.g. in the lab) is important too but that is something different and not represented by dc:location or in dwc in general. This is something of an interpretation of the actual term but it since our implementation model of DwCA is still using "occcurrence" at the core we probably don't have much choice since GBIF does not use a graph-based parser. The other option is to represent this all using event/location at the core of a DwCA but felt this introduced yet more complexities and breaks other cases where we would want to hang data off of occurrence (e.g. Identification), and would not be able to do so if event/location lived at the core.
John
On Fri, May 31, 2013 at 12:02 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote:
Thanks, John – this is REALLY helpful!
A couple questions – can you expand a bit on the differences between JohnDeckOccurrence123, 124,and 125? I’m assuming that JohnDeckOccurrence123 is associated with the Event representing the time & place when JohnDeckTissueSample1 was removed from JohnDeck. I’m guessing that JohnDeckOccurrence124 is associated with the Event representing the time & place when JohnDeckGutSample1 was removed from JohnDeck. What I don’t understand is why there needs to be a JohnDeckOccurrence125. What Occurrence does that represent? Later you suggest that JohnDeck (WholeOrganism) was extracted from nature. Is the extraction-from-nature Occurrence one of these three Occurrences?
What you describe below is consistent with our approach to treating materialSample as a subclass of Individual (assuming a hierarchical Individual, which means that ParentIndividualID of both JohnDeckTissueSample1 and JohnDeckGutSample1 is IndividualID=JohnDeck). The nice thing about the hierarchical approach is that deals with the problem you describe in the last paragraph.
Rich
From: jdeck88@gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck
Sent: Friday, May 31, 2013 7:54 AM
To: Richard Pyle
Cc: Markus Döring; Jason Holmberg; TDWG Content Mailing List; Robert Whitton; Ramona Walls
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
Yep--- that reference point for aggregation can be really powerful: To provide a working example of how these identifiers would work, and how they can act to aggregate data elements, consider the following:
IndividualID = JohnDeck
MaterialSampleID = JohnDeckTissueSample1
OccurrenceID = JohnDeckOccurrence123
Taxon = "Homo sapiens"
IndividualID = JohnDeck
MaterialSampleID = JohnDeckGutSample1
OccurrenceID = JohnDeckOccurrence124
Taxon = "Bacteria500"
IndividualID = JohnDeck
MaterialSampleID = JohnDeckGutSample1
OccurrenceID = JohnDeckOccurrence125
Taxon = "Bacteria501"
JohnDeckTissueSample1 is representative of the Individual itself, while JohnDeckGutSample1 is still associated with the same Individual but notice the taxon has changed and it is a new Occurrence as well. This approach allows for some sense to be constructed using a flat file approach if desired. Providing a Material Sample BoR for OccurrenceID's 124 and 125 provides further context. Meanwhile, we can consider the implications of, for example, habitat descriptions (... for JohnDeckOccurrence123 maybe i'd put http://purl.obolibrary.org/obo/ENVO_01000193, "temperate grassland biome") but the distinct occurrence records for the gut samples could be listed as (http://purl.obolibrary.org/obo/ENVO_01000162, "organ").
Another use for the identifier MaterialSampleID -- lets assume we've expressed an equivalent identifier for a genbank sample using MIxS:source_mat_id, a term which references the same OBI:MaterialSample we're referencing, which allows. If they're URIs we can model this in RDF using the MaterialSampleID's as either subjects or objects... this gets us a step closer for representing contextual information in genbank and DwC without duplicating metadata across systems (genbank for sequencing metada; DwC for environmental context)
There are some issues with this approach of course, for example, if we provide a lat/lng for an occurrence that is a gutsample are we taking the lat/lng where the gutsample was removed from the organism (may be different than where a parent organism was isolated from nature). In this case, we need to assume that we're referring to where the parent organism was isolated from nature to be consistent with DwC and implementations in use. However, the notion of habitat should vary with the occurrence of the actual organism (e.g. "organ" vs. "temperate grassland biome"). Thus, we can still aggregate properties around MaterialSample BoR's that are useful but we need to think carefully about what exactly the properties mean that we assign to these things.... but this is no different than issues we've encountered between other BoR's (Fossil, PreservedSpecimen, or Human/MachineObservation).
John
On Thu, May 30, 2013 at 11:48 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote:
Yes, that’s a fair point! In a sense, the ID has intrinsic value on its own if for no other reason than to represent a reference point for aggregation.
Nevertheless, I still maintain that if it fulfills that purpose, then it implies a “thing” (around which other “things” are aggregated), and I can’t imagine such a “thing” that we would care about for aggregating purposes, about which we would not associate other property values.
I say all this quite deliberately in reference to “dwc:individualID”, of course…. J
Aloha,
Rich
From: Markus Döring [mailto:m.doering@mac.com]
Sent: Thursday, May 30, 2013 7:56 PM
To: Jason Holmberg
Cc: Richard Pyle; TDWG Content Mailing List; Robert Whitton; John Deck; Ramona Walls
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
The id value is actually very useful and the only trustworthy way of grouping records, e.g. all occurrences of the same whale.
Markus
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