[tdwg-content] New Darwin Core terms proposed relating to material samples

Chuck Miller Chuck.Miller at mobot.org
Sun May 26 23:23:25 CEST 2013

One observation I would like to inject into this thread is the role of English language semantics. In addition to the pursuit of a set of terms and their relationships with each other, I see Gregor and Rob saying things like " "individual" doesn't quite seem to capture the concept or usage" which I read as "the English word "individual" has a dictionary definition that doesn't match this usage and therefore will confuse the usual English speaker.

Perhaps one permutation in solving the puzzle of a complete semantic model is to look for alternate words that convey the semantic concept without causing ambiguity with standard English definitions, like the invention of THeE. Would a Latin term serve for instance?

Just a thought. Overcoming the ME and YOU conflicts, may require a third WE approach.


On May 26, 2013, at 8:07 AM, "Steve Baskauf" <steve.baskauf at vanderbilt.edu<mailto:steve.baskauf at vanderbilt.edu>> wrote:

I suppose that Rich and Rob W. have already looked at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity .  I think it pretty much encapsulates what they are talking about.  I should note that the way DSW defines dsw:IndividualOrganism does not require it to be a single organism.  It can be a collection of organisms (herd, colony, school) or part of an organism (tissue).  The basic requirement is that it is a "taxonomically homogeneous entity".  In a variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous entity" (THeE) which would basically include what Rich and Rob W. are talking about (lots of organisms which are seperatable and aren't necessarily from the same lowest taxonomic level).  It should be no surprise that THeE does what Rich wants because we included it in DSW because during the preceding discussion Rich said he wanted something like it.  In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to connect physical entities whose properties can be inferred by inheritance.  What this diagram includes that Rich did not mention are "tokens" (evidence).  We defined a class for evidence, but we also considered not having evidence being an explicit class.  Not defining an explicit Token class would have simplified the diagram at the bottom of the page - one could just say that there should be evidence and it should be linked to the resource it documents.  Token and THeE/IndividualOrganism are not disjoint classes - the physical entity can be the evidence if somebody "owns" it and makes it available for people to examine.  However, in DSW, Token and THeE are not synonymous because we allow evidence to include things that are not physically derived from the entity (e.g. images, sounds, string data records) in addition to physical specimens.

I think that we have to be careful when we say "we don't need X", "there is pressing value for X but not for Y", "X is too vaguely defined", etc.  MaterialSample does exactly what the metagenomics people need because they invented it to serve the purposes they want it to serve (handle material samples in which one may or may not ever know what all organisms are included or even if there are organisms in it).  Individual (sensu Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it to do with their lots and specimens, but is too vague for Rob G.  IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I want it to do with our images, specimens, DNA samples, and data records, and the requirement that IndividualOrganism be taxonomically homogeneous allows us to infer that a determination applied to one resource also applies to other resources which are derived from the same IndividualOrganism (a requirement not stated by the others) but it's too restrictive for both Rob G and Rich.  If we start in on the game of saying "WE need the features that I think are important but not the features that YOU think are important" then we are in for another month of massive email traffic on this list and will end up no better off than we were when we started.

I think that it is clear from this and preceding discussions that there is a need for some system of tracking things that are like individuals/organisms/samples/lots.  It is my believe that what needs to happen is:
1. define clearly what the various stakeholders want to accomplish by their version of individuals/organisms/samples/lots (i.e. use cases/competency questions)
2. use set theory or some other kind of logical system to describe clearly how the various versions of individuals/organisms/samples/lots are related to each other
3. examine alternative mechanisms for defining the relationships among the variously defined individuals/organisms/samples/lots terms and determine how each approach can or cannot satisfy the use cases/competency questions.
4. use one or more mechanisms which pass test #3 to define the terms that are deemed necessary and include them in some TDWG standard which may or may not be Darwin Core.

In September 2011, John Wieczorek had packaged several of the proposed class additions to Darwin Core into a concrete proposal: http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html .  This proposal was deferred by the Executive Committee (see the last comment at http://code.google.com/p/darwincore/issues/detail?id=117 ) "... until we can further examine broader changes including the new classes and any insights that might come out of the RDF Interest Group."  So the RDF Task Group has specifically been charged with the task of examining the addition of additional classes to Darwin Core and their implications.  The RDF TG has assembled competency questions http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions and use cases http://code.google.com/p/tdwg-rdf/wiki/UseCases but has not moved beyond that.  So that's a start on Item #1 in the list above.  However, the process has not moved beyond that.  I recently made an appeal to the TG for someone to take up work on delivering some concrete progress on deliverables, but got no responses.  I cannot be the person to move this forward for two reasons.  One is that I already have my hands full with the DwC RDF guide (which doesn't address these issues) and the other is that I have reached the limits of my technical skills and am not able to take leadership on items #2-#4.  Who will champion this?

At the risk of making this email too long, I will add one more comment.  There seems to be a developing consensus that an OWL ontology structured according to the OBO Foundry (http://www.obofoundry.org/) principles is the answer to #2 and #3 above.  However, I have yet to see the evidence that the complexity introduced by a formal OWL ontology is necessary or any actual concrete examples of how an OBO-style ontology would be used to satisfy the use cases.  We have shown with DSW that some use cases can be met using only simple RDF and SPARQL (i.e. no actual reasoner involved).  I presume that Rich and Rob W. have in hand a technical solution to their use cases that doesn't involve RDF at all.  So I think that there need to be some iterations of defining and testing before we adopt a technology by acclimation.  We've been down that road before with the TDWG Ontology and look how that turned out.


Robert Guralnick wrote:

I agree with John and Gregor.  The term "individual" doesn't quite seem to capture the concept or usage.  However, I think there is more general agreement that there is a pressing need - and immediate value - for a term to represent "material sample" and derivaties.  It seems that the proposal on the table serves that need with the right definition, that is explicit, and that provides necessary linkages to other related domains.

Best, Rob

On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn <g.m.hagedorn at gmail.com<mailto:g.m.hagedorn at gmail.com>> wrote:
> Basically, we’ve been running with the idea of an “Individual” class – as
> originally proposed by Steve and discussed at some length on this list a
> while ago.  This has been documented for DSW:
> https://code.google.com/p/darwin-sw/wiki/ClassIndividual

> We define an “Individual” as the physical “something” that underpins an
> Occurrence.  In the case of organisms, this can be a group (herd, school,
> flock, etc.), specimen (either a single specimen, or a lot of multiple
> specimens), or any sort of derivative of a specimen (part, tissue sample,
> dna extraction, etc.).  It corresponds to the intended meaning of

I disagree with using "Individual" for sets of objects. It is
surprising, and lacking any clear definition when to stop, that means
a taxon is an individual, a collection is an individual, etc.
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Steven J. Baskauf, Ph.D., Senior Lecturer
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