[tdwg-content] Of Evidence and Individuals (Was Plea for competency questions)

[Steve Baskauf]

Responses inline.

Richard Pyle wrote:
>> So then what IS an actual individual organism like the wildebeest calf?  
>> It is a BiologicalEntity if it has been documented as an Occurrence or 
>> assigned an Identification.  It is a CollectionObject if it was 
>> collected for a zoo, or shot and mounted in a museum.  Or it can be 
>> both simultaneously if it is both documented and collected.  If none 
>> of these things were done, then it's neither a BiologicalEntity nor a 
>> CollectionObject - it's simply a wildebeest calf.  Define the 
>> class/type of the thing by the properties that you wish to assert for 
>> it (or the competency questions that you can answer for it).
>>     
>
> I think I get where you are coming from here, but I'm very queasy about this
> notion that the same "thing" (a mass of flesh & bones) can be represented as
> an instance of two different DwC classes, depending merely on what
> attributes about the "thing" are emphasized.  
Well, I have to say I had a problem with this at first.  Because most of 
the existing classes in Darwin Core are disjoint with other classes (as 
in http://www.w3.org/TR/2004/REC-owl-guide-20040210/#DisjointClasses), I 
was predisposed to thinking that it was "bad" to have two classes that 
were not mutually exclusive.  But actually we have such classes all the 
time.  A person can be a member of the class Father, class Teacher, and 
class ElectedOfficial depending on which set of properties we can 
appropriately apply to that person.  In fact, most of the things that we 
could consider as "evidence" (i.e. instances of the proposed class 
CollectionObject) could probably be members of other classes as well, 
such as foaf:Image, foaf:Document, acterms:MultiMediaObject, etc.  An 
image could be an instance of dwc:CollectionObject because it had 
properties such as dwc:catalogNumber and dwc:collectionCode that it 
shares with other types of CollectionObjects while at the same time 
being a acterms:MultiMediaObject because it has properties like 
dcterms:format, xmpRights:UsageTerms, Iptc4xmpExt:creditLine that it 
shares with other types of MultiMediaObjects.  There isn't anything 
wrong with that as far as I know, other than getting used to the idea.
> For example, during my recent
> trip to South Africa, we took the opportunity of one of our non-diving days
> to visit a game park where we saw (among other things), numerous wildebeest
> (coincidentally enough).  I took video images of these wildebeest with my
> GPS-enabled camera, and therefore documented the presence of a specific
> individual wildebeest at a particular date and time. Clearly there is a
> dwc:Occurrence record there, so it's certainly a BiologicalEntity (by your
> definition; i.e., documented as an Occurrence and assigned an
> Identification).  But does a Game Park constitute the same thing as a zoo?
> There are electric fences around the perimeter of the park, so I'm inclined
> to think so.  Is it also a CollectionObject? Would this be an example of
> something that is both?
>   
Well, I've thought about this question quite a bit.  My opinion is that 
the wildebeest you photographed would not be a CollectionObject.  It 
seems to me that implicit in the idea of a CollectionObject is an 
understanding that someone is "keeping track" of the object and that 
there is a reasonable expectation that the particular object could be 
produced at will (or at least accounted for if it no longer exists in 
the collection).  That's what we are doing when we assign catalogNumbers 
to things, put them in particular pens, jars, or cabinets, and keep 
track of their dwc:disposition.  If the game park were tracking that 
wildebeest by means of an ear tag, radio collar, unique color patterns, 
etc., assigned the wildebeest an identifying number, kept track of which 
electric fence unit the wildebeest was located in, and put this all in a 
database, then I would say the wildebeest was a CollectionObject that 
was a LivingSpecimen.  If you could walk into the park office with the 
wildebeest's ID number and ask "what's going on with this wildebeest" 
and get an answer, it would be a CollectionObject.  I really had to come 
to grips with this when thinking about the Bicentennial Oak at 
Vanderbilt.  It is clearly a CollectionObject in the Vanderbilt 
Arboretum because it has an ID number, is on the arboretum's map, and 
has a record in the arboretum's database.  But Vanderbilt didn't "do" 
anything physically to make it become a CollectionObject (i.e. didn't 
move or plant it - it was there long before the University).  It became 
a CollectionObject of type LivingSpecimen when the arboretum started 
accounting for it by assigning it a catalogNumber and keeping track of 
its status in the collection.  That's different from some other random 
bur oak that I happen across in the forest.  Even if I assign it a GUID 
and record it's latitude and longitude, I'm not asserting to anybody 
that I will know what is going on with that tree or if it even continues 
to exist after I make a record of its Occurrence.  It does NOT have a 
dwc:catalogNumber, dwc:collectionCode, or dwc:disposition because it 
isn't in a collection over which I assert control - it does not have 
properties in common with other CollectionObjects. 
> The more I think about it, the less confident I am that we really need
> *both* new classes.  With such potential overlap between them, should we not
> simply generalize them both into the same class, and provide whatever
> properties are known/relevant in a DwC instance of it?
>   
Well you could say this about any non-disjoint classes.  Why not combine 
the classes Teacher and ElectedOfficial if a person can be an instance 
of both?  We don't do that because there are instances where persons are 
Teachers and not ElectedOfficials and other instance where people are 
ElectedOfficials and not Teachers.  Instances of the class Teacher share 
properties like numberOfStudents and schoolOfEmployment, while instances 
of ElectedOfficial share properties like votesReceived and yearElected. 
> You said that the CollectionObject class is fully capable of doing much of
> what I want to accomplish with my vision of "Individual".  Could I not say
> the exact same thing that a broader definition of CollectionObject (i.e.,
> one that doesn't attempt to distinguish the disposition of the same mass of
> flesh & bones in the context of human-mitigated captivity/preservation vs.
> nature) could be fully capable of accomplishing what you want to accomplish
> with Individual?  Namely, the three competency questions you established for
> the "Individual" (=BiologicalEntity) class.
>   
If we do as you have suggested here, we would limit CollectionObjects to 
individual organisms, their pieces, and aggregations that include them. 
That definition would not include all kinds of things which can serve as 
evidence (which I think is what John was suggesting in his proposal) 
because it would exclude Images, Sounds, and Documents.  It actually 
would make sense to define a class of things for "biological material" 
that could include individual organisms, their pieces, and aggregations 
that include them.  That class doesn't currently exist as far as I 
know.  Perhaps it could be a superclass of LivingSpecimen, 
PreservedSpecimen, tissue sample, DNA sample, cell culture, herd, mixed 
flock, etc.  and disjoint with other classes like Image and Document 
that could also serve as CollectionObjects.  Whether that "biological 
material" class would be synonymous with BiologicalEntity would be a 
subject for discussion.  Perhaps it does just boil down to the same thing. 
>   
>> An actual single, live organism can serve both as a unit for 
>> resampling and "attachment" of Identifications, AND as an 
>> organizational unit that is part of and which has parts that are 
>> biological samples.  Some other entities, such as cohesive pack/herds 
>> and clonal organisms can also serve both purposes.  Other entities 
>> cannot: it doesn't make sense to resample dead organisms or pieces of 
>> organisms,
>>     
>
> I guess it depends on what you mean by "resample".  Surely a tissue sample
> can be removed from a dead organism, and used for DNA sequencing that can
> lead to a new Identification instance.  I agree that a dead organism cannot
> represent the basis for future Occurrence instances, 
That's what I meant.
> but I don't really see
> the relevance of that.
>   
I guess it would depend on the agreed definition.  If the 
BiologicalEntity class only needed to facilitate some of the three 
functions that I outlined, then it's not relevant whether the organism 
is dead or not (i.e. whether it could potentially be the subject of 
additional future Occurrence records).  If it needs to always be capable 
of facilitating all three functions, then the entity would probably have 
to be alive.  The most important thing to me is that we are clear about 
the definition.
>   
>> Personally, I would like for the third function ("inferring 
>> duplicates"; linking multiple Identifications to the same entity and 
>> being assured that all Identifications of the same Individual would 
>> apply to all artifacts associated with that Individual) to be 
>> accommodated by the definition,
>>     
>
> I definitely support this, and on this basis, I am willing to abandon my
> earlier defense for what you would call taxonomic heterogeneity.  I still
> feel the need to not limit the rank at which a taxon identification may be
> applied, but I am ready to abandon my original notion that a rock with
> multiple phyla of organism attached should ever be represented as a single
> instance with Identification "Animalia".  In other words, I've come around
> to your perspective on this.  I think the power of implied "taxon
> identification inheritance" that you advocate in your function #3 overrides
> my advocacy for taxonomically heterogenous organisms to be lumped together
> with the same instance of the class.
>
> Thus, I now agree with you on the following:
>
>   
>> When I used that term, I intended for it to mean that the entity is 
>> believed to be homogeneous to the lowest possible level in the way 
>> that one knows that two branches from the same tree or two parts of 
>> the same clonal organism are guaranteed to have the same taxonomic
>>     
> identify at every level.
>
> So, from my perspective, we can put that part of the debate to rest.
>   
OK, cool.  I think that simplifies the matter considerably.
>   
>> This email is now at or has exceeded the length of an email that many 
>> people will take the time to read.  So I will draw it to a close and 
>> post a separate email on the topic of competency questions for John's 
>> proposed class "CollectionObject" which I believe address Rich's 
>> desire to track "real-world" objects (samples, re-samples, etc.).
>>     
>
> Rather than respond separately to the other post, I've just made this single
> response with the new subject heading, because I think we're narrowing down
> the scope of the debate in such a way that we should now focus on the
> difference between the two proposed new classes
> ("Individual"/"BiologicalEntity", and "Evidence"/"CollectionObject").
>
> For a while, I thought I saw the difference as being the "Evidence" was more
> like an instance of "Documentation" (e.g., an image, a label on a preserved
> specimen, etc.); rather than the flesh-and-bones organism itself.  But with
> your suggestion that this class may serve the function(s) of my desires for
> the "Individual" class, the waters have been muddied a bit in my own mind.
>
> I guess if there are to be two separate classes, then I would favor a more
> generalized "Organism" class to serve the functions of what Steve has
> described for both the "CollectionObject" and "BiologicalEntity" classes,
> but then define a separate "Documentation" class that serves as the basis of
> "proof" for an Occurrence.
>   
I think there is probably more than one way of sorting this out.  In my 
email I've suggested one method of defining the classes, which more or 
less corresponds to the approach Cam and I suggested with darwin-sw.  
This method is implemented on my website, e.g. for a particular tree in 
the UNC-Greensborough campus having GUID 
http://bioimages.vanderbilt.edu/uncg/39
Using the terminology of the current discussion, the tree is an instance 
of BiologicalEntity (called IndividualOrganism in darwin-sw).  It's 
existence is documented by 17 instances of CollectionObject (called 
Tokens in darwin-sw): 15 that are StillImages, one that is a 
PreservedSpecimen in the NCU herbarium, and one that is a LivingSpecimen 
in the UNC-G arboretum (i.e. the tree itself).  It would be painful to 
pick through the RDF (located in the files 
http://bioimages.vanderbilt.edu/uncg/39.rdf for the tree, 
http://bioimages.vanderbilt.edu/specimen/ncu592804.rdf for the specimen, 
http://bioimages.vanderbilt.edu/kirchoff/em2535.rdf and 14 other files 
for the 15 images) but suffice it to say that the BiologicalEntity (the 
tree)  has the properties hasIdentification, hasOccurrence, 
foaf:depiction (relating it to the images), and dcterms:hasPart 
(relating it to the specimen) as would be expected based on the three 
"purposes" I outlined for BiologicalEntity.  The 17 CollectionObjects 
have the properties dwc:institutionCode, dwc:collectionCode, 
dwc:catalogNumber, evidenceFor [an Occurrence], and derivedFrom [the 
BiologicalEntity] as would be expected based on how I described 
CollectionObject instances.  Not all of these properties are from Darwin 
Core in part because DwC doesn't have any object properties relating the 
classes (we had to make those up).  So what I would like to see is what 
particular properties (DwC and otherwise) would be held in common by 
instances of each of the two classes that Rich suggests: "Organism" and 
"Documentation". 
> On a semi-related topic, I don't think it's appropriate to create a DwC
> class simply to establish a Many-to-Many relationship between instances of
> other classes.  That function (in my mind) is already elegantly fulfilled by
> the existing dwc:ResourceRelationship class (another major discussion that
> will need to take place on this list).  While it's true that certain DwC
> classes do serve a M:M function (e.g., Occurrence), I think that classes
> should represent "things" that are unambiguously different, with very
> specific sets of properties.
>   
Well, "many-to-many relationship" was the way Kevin described it and I 
liked that because it described succinctly the way that "Individual" fit 
into the "crow's feet" and block diagram that you included in 
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html 
and which I used as the basis for the Fully Normalized Model diagram at 
the bottom of 
http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels .  
That doesn't mean that the class BiologicalEntity (a.k.a. "Individual" 
or dsw:IndividualOrganism) doesn't actually represent a real "thing".  
The BiologicalEntity instance that is the tree 
http://bioimages.vanderbilt.edu/uncg/39 is an actual "thing", not just 
an abstract database artifact.  It just can have the relationships "one 
tree:many Occurrences" and "one tree:many Identifications".  The same 
would be true of all BiologicalEntity instances which would have 
specific sets of properties that would differ from the specific 
properties of CollectionObjects as I outlined in the paragraph above. 
> On a final, somewhat encouraging note, I *really* like the diagram
> represented in the link that Cam sent earlier:
>
> http://code.google.com/p/darwin-sw/
>
> During one of our non-diving days in South Africa, Rob Whitton and I spent
> some time thinking about the BiSciCol project (BCC'd on this post), and we
> studied this diagram and both agreed it represents an *excellent* foundation
> to both this discussion on proposed new DwC classes, and the BiSciCol
> project in particular.
>   
Cool!  Go BiSciCol!

Steve

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

postal mail address:
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