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

[Steve Baskauf]

Rich,
Thanks for clarifying that "individual" as you are using the term 
corresponds to dsw:IndividualOrganism rather than THeE.  I didn't read 
carefully enough.  With regards to the term "Individual", as you note, 
its origin is from the term dwc:individualID.  The original DwC term 
addition proposal was to create the term dwc:Individual to follow the 
pattern of the other ID terms in DwC.  When Cam and I were writing DSW 
in Web Ontology Language (OWL), we realized that "individual" had a 
particular meaning in OWL: it effectively means "instance".  So that 
made creating a class called dsw:Individual particularly confusing.  For 
that reason, Cam suggested dsw:IndividualOrganism to indicate that we 
were talking about individuals sensu organisms rather than individuals 
sensu OWL.  As you know, we never intended for it to apply only to 
individual organisms. 

I think that pretty much everybody agrees that "individual" is a 
confusing term name for a number of reasons.  If at some point there is 
a DwC term which corresponds to what we are talking about 
(TaxonomicallyHomogeneousEntity, THoE, or whatever), the solution may be 
to deprecate dwc:individualID and change it to 
dwc:taxonomicallyHomogeneousEntityID or whatever corresponds to the new 
class name with "ID" tacked on the end.  For convenience, in this email 
I'll refer to "Individual" with the understanding that it's not a good name.

Although there is potentially significant overlap between the proposed 
dwc:MaterialSample class and Individual, I think that there are at least 
two ways that they differ significantly.  One is that I'm pretty sure 
that there is no requirement that a dwc:MaterialSample must be a 
biological material (i.e. derived from a living thing).  I think that 
it's pretty clear from what Rich has said that Individual (to include 
the range from tissue samples up to herds) must consist of biological 
materials.  The other is that a material sample must be physically 
sampled (i.e. removed from the environment and subjected to some kind of 
processing).  An important feature of an Individual (at least to me!) is 
that it can be observed, photographed, or recorded without necessarily 
having all or part of it being removed from its environment and 
subjected to processing.  My reading of the definition of 
dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID ) 
is that the "individual or named group of individual organisms" (e.g. 
"Orca J 23") might be observed repeatedly without physical sampling.  
The definition of dwc:individualID says "resampling", but I think 
"sampling" there was being used more broadly than just "physically 
removing part or all of the organism".  I've been thinking about whether 
it is a problem for DwC type vocabulary terms to overlap.  There is 
nothing in the current definitions of the type vocabulary terms that 
require its classes to be disjoint.  I think it is possible that 
something could be both a dwctype:PreservedSpecimen and a 
dwctype:FossilSpecimen, and if dwctype:MaterialSample is accepted as a 
term there would undoubtedly be things that were both 
dwctype:PreservedSpecimen and dwctype:MaterialSample.  So I don't think 
it is necessarily a problem if there is overlap between 
dwctype:MaterialSample and an Individual class.  Certainly RDF allows a 
resource to have two (or more) rdf:type declarations.

With regards to Ramona's objection "Making one root class to cover lots 
of different types of entities is poor ontological practice", I would 
just note that Darwin Core is "glossary of terms ... intended to 
facilitate the sharing of information about biological diversity" 
(http://www.tdwg.org/standards/450/ ) and that the mission of TDWG in 
general is to "Develop, adopt and promote standards and guidelines for 
the recording and exchange of data about organisms" 
(http://www.tdwg.org/about-tdwg/ ) and not ontology building per se.  So 
in the context of TDWG and Darwin Core, the primary criterion for 
judging a proposed term is whether it effectively facilitates the 
sharing and exchange of information about biological diversity, and not 
whether it fits well into an ontology.  Don't get me wrong - I'm fully 
in support of ontology-building as a means to clarify the relationships 
among entities of interest to TDWG.  What I'm saying is that there will 
probably be terms in DwC that have a utilitarian purpose in promoting 
data exchange that will never be part of an ontology.  It is possible 
(perhaps likely) that Individual will be such a term.  It was once 
described as "more of a database join than a real thing" (or something 
like that) which is perhaps an overstatement because it does correspond 
roughly to a certain set of real things.  But I think its purpose is 
really more for linking sets of resources that have shared properties 
and shared connections to identifications, observations, etc.

Steve

Richard Pyle wrote:
> Hi Ramona,
>
> I apologize for the long emails, but this stuff is complex and unfortunately
> requires lots of words (to avoid - or at least minimize - misunderstanding).
> I will try to keep my responses to your points short.
>
>   
>> Using the word "individual" to describe collections of organisms - 
>> whether they are taxonomically homogenous or heterogeneous - makes no
>>     
> sense. 
>   
>> Yes, I know it is just a label, but seriously, just make a better label.
>>     
>
> Yes, I agree.  But it's what we already have in DWC
> (http://rs.tdwg.org/dwc/terms/index.htm#individualID)  I have no problem
> using a different term, but before we choose terms, we should first define
> what the concepts are.
>
>   
>> A single organism and a collection of organisms are fundamentally
>>     
> different things. 
>
> Actually, not really different things.  Many natural history collections
> maintain their specimens as "lots", which may have a single individual
> specimen, or multiple specimens.  Regardless of whether it's a single
> specimen or multiple specimens, the basic properties are the same (same
> collecting event, sme taxonomic identification, and many other identical
> properties).  This becomes especially true for colonial organisms (like
> corals, where the "individual" could be interpreted as a single polyp). It's
> also true for other use cases we deal with that are outside the DWC/TDWG
> scope.
>
>   
>> If you need a class that can cover both of them under certain
>>     
> circumstances, 
>   
>> you need to use a logical definition to define the circumstances (just
>>     
> like the 
>   
>> class material sample does by using the criterion of having a material
>>     
> sample role). 
>   
>> In order to do this, you also need to have separate classes for individual
>>     
> organism 
>   
>> and collection of organisms.
>>     
>
> We have tried to do this by distinguishing instances as "Lot" or "Whole
> Organism" -- which could be thought of as distinct subclasses (though again,
> they generally share the same properties).  The same is true for tissue
> samples, and other "parts".
>
>   
>> I agree whole-heartedly with the need to clearly track stakeholders needs 
>> for different classes of things, using a logical system to decide how
>>     
> these 
>   
>> things relate to one another, examining alternative systems for creating 
>> the classes of things, and testing them against use cases (Steve's points
>>     
> 1-4). 
>   
>> This is precisely what we are trying to do with the bio-collections
>>     
> ontology 
>   
>> (BCO). The suggestion to use the term material sample came out of just 
>> such a process. It is important to remember that the stakeholders include 
>> more than just the community using DwC. 
>>     
>
> It seems we are all in full agreement on these points.  In my case, I am
> especially in agreement with the last point, as much of our thinking has
> been independent of the TDWG/DWC thinking, but still keeping that set of
> use-cases in mind.
>
> Aloha,
> Rich
>
>
> .
>
>   

-- 
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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