Request for vote on proposals to add Individual as a Darwin Core class and to add the term individualRemarks as a term within that class
I am pleased with the significant and thoughtful discussion that has taken place on the tdwg-content email list regarding the relationships among Occurrences, Individuals, and other entities that are a part of the community's thinking about biodiversity metadata and the way that those metadata are structured. It appears from the discussion that there is widespread acceptance of the idea that Individual as a concept has a place in the structuring of biodiversity metadata and that there is some consensus of what "Individual" means (i.e. an entity ranging from actual biological individuals to small coherent populations that can reliably be asserted to represent a single taxon). Whether that acceptance and consensus constitutes a compelling need for adding two new terms (the class dwc:Individual and dwc:individualRemarks) to the Darwin Core standard or not is the point of a TAG "vote". Given the discussion that has occurred, it seems to me that there are two reasons why there is an actual need for those terms. One reason is that if members of the Darwin Core constituency intend to structure their metadata in a fully normalized manner that includes grouping Occurrences by Individuals (and it appears that there are at least several who intend to do this), the term dwc:individualRemarks is needed to provide a means indicate the nature of the individual (i.e. is it a biological individual, clonal individuals, a small population, etc.?) and the class dwc:Individual is needed as the category within which to put individualRemarks so as to indicate that individualRemarks is a property of Individuals. The second reason for explicitly recognizing Individual as a class is that it would place a term representing the concept of "Individual" within a "well-known vocabulary". I feel that would be critical for facilitating the ultimate development of a recommendation for the representation of Darwin Core as RDF.
At this point, it is not clear to me that there are any other existing DwC terms that should be moved to a new Individual class. Originally, I suggested that individualCount should be placed in that class, but I no longer think so. Counting the number of individuals is really something that happens when an Occurrence takes place and a small cohesive group of a single taxon (e.g. wolf pack or plant population) could have an individualCount that changes over time. As was discussed earlier in on the email list, the xxxxxxID terms probably really belong in the Record-level terms category rather than being listed within particular classes. So I don't believe that dwc:individualID should be in the proposed class either. As I detailed in my Biodiversity Informatics paper, an Individual is really an entity that serves primarily as a node that allows the grouping of other resources (namely Occurrences and Identifications). As such, it really has few (or no) properties that can be known outside of Occurrences.
Thus I would like to "call the question" on the issue of the proposal. I would suggest that the issue of adding the class dwc:Individual and the term dwc:individualRemarks within it be addressed in a single vote, since there little point in having one term without the other. I would also hope that those on the TAG who choose to vote would review the list discussion carefully first. Given that the question of "what exactly is an Individual?" came up a few times after that question was clearly answered in the thread is an indication that some people entered the thread later on without the benefit of having read some of the earlier posts.
Steve
At this point, it is not clear to me that there are any other existing DwC terms that should be moved to a new Individual class.
My feeling is that, if an Individual class was established, it would be a logical place for dwc:preparations, dwc:previousIdentifications, dwc:associatedSequences, and possibly dwc:disposition (depending on how, exactly, that term is scoped).
I was tempted to also add dwc:catalogNumber and dwc:otherCatalogNumbers; but now I'm wondering why those two terms are not included among the "Record-level Terms". Does anyone know the logic behind why things like dwc:institutionCode and dwc:collectionCode (and related terms) are in "Record-level Terms", while dwc:catalogNumber and dwc:otherCatalogNumbers are in the Occurrence class?
Originally, I suggested that individualCount should be placed in that class, but I no longer think so. Counting the number of individuals is really something that happens when an Occurrence takes place and a small cohesive group of a single taxon (e.g. wolf pack or plant population) could have an individualCount that changes over time.
Hmmm...I'm not sure. If "Individual" can range fron a single organism, to several organisms, to a single colony of organisms, to a defined population of organisms (possibly up to an entire taxon), then how would you indicate the "scope" of organisms represented by a single instance of "Individual"? Wouldn't individualCount serve this function? Or, maybe you're right that individualCount should describe the Occurrence, and another term (e.g., "individualScope") would be needed to define the scope of the "Individual" instance.
As was discussed earlier in on the email list, the xxxxxxID terms probably really belong in the Record-level terms category rather than being listed within particular classes. So I don't believe that dwc:individualID should be in the proposed class either.
I missed that conversation. This doesn't seem right to me, but if the consensus is that the xxxID terms are all best treated as "Record-level Terms", then certainly "individualiD" should be treated accordingly.
Aloha, Rich
Not sure if this has been mentioned as I have struggled to keep up with this thread, but it sounds to me like the benefit of the Individual class/properties is to be able to link together various web resources that refer to data obtained from the same individual in some manner, so we probably need terms that allow the description of how these individuals, or parts of individuals relate to each other. The Scope idea will help, but maybe there is a need for terms like "partOfIndividual", "derivedFromIndividual"?
Then, I suppose we are heading into interaction territory, so we then need to model how interactions between individuals can be defined - eg "foundOnHostIndividual" ...
This is starting to sound quite appealing, as I think the "Individual" resources could be seen as the atoms to defining occurrences, in the same way that NameUsages are the atoms for defining Taxon Names and Concepts.
Kevin
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: Monday, 1 November 2010 7:46 a.m. To: 'Steve Baskauf'; tdwg-content@lists.tdwg.org; tdwg-tag@lists.tdwg.org Subject: Re: [tdwg-content] Request for vote on proposals to add Individual as a Darwin Core class and to add the term individualRemarks as a term within that class
At this point, it is not clear to me that there are any other existing DwC terms that should be moved to a new Individual class.
My feeling is that, if an Individual class was established, it would be a logical place for dwc:preparations, dwc:previousIdentifications, dwc:associatedSequences, and possibly dwc:disposition (depending on how, exactly, that term is scoped).
I was tempted to also add dwc:catalogNumber and dwc:otherCatalogNumbers; but now I'm wondering why those two terms are not included among the "Record-level Terms". Does anyone know the logic behind why things like dwc:institutionCode and dwc:collectionCode (and related terms) are in "Record-level Terms", while dwc:catalogNumber and dwc:otherCatalogNumbers are in the Occurrence class?
Originally, I suggested that individualCount should be placed in that class, but I no longer think so. Counting the number of individuals is really something that happens when an Occurrence takes place and a small cohesive group of a single taxon (e.g. wolf pack or plant population) could have an individualCount that changes over time.
Hmmm...I'm not sure. If "Individual" can range fron a single organism, to several organisms, to a single colony of organisms, to a defined population of organisms (possibly up to an entire taxon), then how would you indicate the "scope" of organisms represented by a single instance of "Individual"? Wouldn't individualCount serve this function? Or, maybe you're right that individualCount should describe the Occurrence, and another term (e.g., "individualScope") would be needed to define the scope of the "Individual" instance.
As was discussed earlier in on the email list, the xxxxxxID terms probably really belong in the Record-level terms category rather than being listed within particular classes. So I don't believe that dwc:individualID should be in the proposed class either.
I missed that conversation. This doesn't seem right to me, but if the consensus is that the xxxID terms are all best treated as "Record-level Terms", then certainly "individualiD" should be treated accordingly.
Aloha, Rich
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On Sun, Oct 31, 2010 at 4:21 PM, Kevin Richards < RichardsK@landcareresearch.co.nz> wrote:
Not sure if this has been mentioned as I have struggled to keep up with
this thread, but it sounds to me like the benefit of the Individual class/properties is to be able > to link together various web resources that refer to data obtained from the same individual in some manner, so we probably need terms that allow the description of > how these individuals, or parts of individuals relate to each other. The Scope idea will help, but maybe there is a need for terms like "partOfIndividual",
"derivedFromIndividual"?
Now you're talkin Kevin! Actually, now you're talking about ontology, and I plead: Go slow, develop use cases; develop competency questions; develop tools. I note that Steve was careful to separate the question of adding terms to the normative, representation free, DwC, from the problem(s) of making an RDF representation of same:
On Sun, Oct 31, 2010 at 10:38 AM, Steve Baskauf < steve.baskauf@vanderbilt.edu> wrote: >
I am pleased with the significant and thoughtful discussion that has taken
place on the tdwg-content email list
regarding the relationships among Occurrences, Individuals, and other entities that are a part of the community's
thinking about biodiversity metadata
and the way that those metadata are structured. [...] I feel that > would
be critical for
facilitating the ultimate development of a recommendation for the
representation of Darwin Core as RDF.
[...]
This separation is important, because what use one intends to make of an RDF representation has a lot of bearing on what "gotcha's" one has to take care about.
For example, if there is a desire to exploit formal semantics available for RDF stack ---which will probably emerge as a requirement once one starts talking about relations between properties---then different surprises will emerge from the pitfalls if one "merely" wishes to put SKOS relations on the properties and reason about the SKOS instead of the science. But I guess, for example, that Miranker's Morphster project [1] will benefit most in its current use cases, from good mereological ontologies for descriptive data, not just stuff like "more general than".
There are surprises even in the simplest use of RDFS and formalisms about classes. I've previously whined about premature assignment of rdfs:domain while conceding (did I???) that it can sometimes make a designer's intention clearer to humans. Perhaps more startling is that type assignment automatically "creates" an rdfs:class if one was not already available, due to the formal semantics of rdf:type [3]. Thus, in an earlier posting, Paul Murray has (unintentionally?) introduced a new class apni:TaxonName in 33407.rdf [2] via <rdf:type rdf:resource=" http://biodiversity.org.au/voc/apni/APNI#TaxonName%22/%3E
Then there is the question of adequate tools for the desired style of ontology architecture. The OWL community's important tools are not friendly even to DublinCore, whose style is(?) what DwC follows. (Steve Baskauf has complained to me in private email that the Manchester validators don't seem to even check rdfs vocabulary correctly; Paul complained that Protege4 makes a big mishmash of Properties when importing DwC. (Both of these are probably false positives in cases of insufficient typing of properties themselves, and the OWL community probably doesn't care about the origin or utility of such weak typing [4]. )
So the hard part is yet to come. But I agree with you. It is quite appealing.
Bob Morris
Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob@gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram http://www.cs.umb.edu/%7Eram phone (+1) 857 222 7992 (mobile)
[1] http://www.cs.utexas.edu/~miranker/studentWeb/MorphsterHomePage.htmlhttp://www.cs.utexas.edu/%7Emiranker/studentWeb/MorphsterHomePage.html [2] http://biodiversity.org.au/apni.name/33407.rdf [3] http://www.w3.org/TR/rdf-schema/#ch_type [4] https://mailman.stanford.edu/pipermail/p4-feedback/2009-October/002448.html
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participants (4)
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Bob Morris -
Kevin Richards -
Richard Pyle -
Steve Baskauf