[tdwg-content] Add a Full Example: Re: Public comment on the Darwin Core RDF Guide

Sat Dec 13 18:52:39 CET 2014

OK, I think I get what you are saying. 

Just to clarify, in general, the basic Darwin Core vocabulary includes 
very few machine-interpretable semantics (domain, range, subclass, 
subproperty, sameAs).  I think that the subproperty declarations for the 
"ID" terms are just about all that is left.  The RDF Guide similarly 
remains silent on these kinds of relationships, except where they exist 
in "adopted" terms from Dublin Core.  The guide really just attempts to 
frame known best-practices in terms of how they would apply to the DwC 
vocabulary, and to deal with the quirks that have been introduced by DwC 
originally being designed to facilitate spreadsheets and flat database 
tables. 

My feeling was that there was a consensus that once the basic layer (the 
vocabulary itself) was cleaned up with clearer definitions and the guide 
(a second layer) was in place to apply well-known best practices to that 
layer, there would be a subsequent attempt to determine how these two 
"layers" could be used by higher level layers (i.e. ontologies) to 
generate actual usable RDF graphs.  This determination would be based 
primarily on use cases and how successful various possible approaches 
would be at facilitating those use cases.  So the question of whether 
there are valid reasons why ontologies should impose rdfs:domain 
properties should be part of that next discussion, and on the level of 
the RDF Task Group rather than the whole tdwg-content list.  We already 
have this as an open issue in the RDF Task Group issue tracker: 
https://code.google.com/p/tdwg-rdf/issues/detail?id=10

So I think this is an important issue, but I think it's veering out of 
scope for the discussion about the guide.  Returning to the original 
question of examples, my feeling is that it just isn't practical to 
include what are likely to be highly mutable examples in what's going to 
become a non-normative part of the standard.  As you suggested in a 
later email, I think having back links from the examples on GitHub to 
particular sections of the guide would be the way to go. 

Steve

Bob Morris wrote:
> Sorry if what I wrote was either irrelevant or unclear, or both. My
> intent was to say this:  You gave examples where there have been
> ongoing arguments in favor of  two answers to a question of the form
> "to what class should a predicate P be applied."  But in my view there
> is often no reason to settle that question in a guidance document or
> spec, perhaps unless the intent is to settle the arguments. To me,
> your discussion of dwc:EventDate  seems like an example of such, at
> least because there have been arguments on the table that have not(?)
> been successfully contradicted. The point I too cryptically mean to
> raise is: it is a common problem that such arguments are, in the case
> of rdfs reasoning, often settled de-facto when ontologies impose
> rdfs:domain. Settling an extensive argument in an ontology should not
> be taken lightly, if for no other reason than that forestalling
> arguments is one of the main accomplishments of a well-crafted
> ontology.
>
> Hope that is clearer.  If so, it doesn't bother me if it is declared irrelevant.
> Bob
>
> On Sat, Dec 13, 2014 at 7:49 AM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu> wrote:
>   
>> Umm.  I don't understand why what you said is relevant. Nobody that I know
>> of has assigned domains to any of the existing Darwin Core terms.  If you
>> have Darwin-SW in mind, it only assigns domains to object properties that it
>> mints and I don't see how that would prevent supporting either or both kinds
>> of use.  The problem in my mind is figuring out how to do queries that would
>> catch both kinds of uses, e.g.
>>
>> SELECT ?Occurrence WHERE {
>>   ?Occurrence dwc:eventDate "2014-12-13"^^xsd:date.
>>   ?Occurrence dwc:locality "Smith Pond".
>>   }
>>
>> which would work for the simple version, but not Darwin-SW.  Obviously, one
>> could easily create a more complex query that would work in simple cases
>> like this example, but the complexity would expand greatly if one wanted to
>> require matches with 3 or more patterns.
>> Steve
>>
>>
>> Bob Morris wrote:
>>
>> Ah, Steve, your examples well illustrate the reason to avoid assigning
>> rdfs:domain, as well as why both are perfectly good illustrations
>> neither of which should be deprecated.  Communities of practice can
>> exploit either or both, and the only communities that are nailed are
>> those that labor under an rdfs:domain for such things as dwc:EventDate
>>
>> Bob
>>
>> On Fri, Dec 12, 2014 at 10:59 PM, Steve Baskauf
>> <steve.baskauf at vanderbilt.edu> wrote:
>>
>>
>> Paul,
>> That's exciting that you are trying to generate RDF using real data!
>>
>> I think we initially considered including something in the guide like
>> what you have suggested, but the problem is that what constitutes "an
>> Occurrence record" varies depending on the model one has in mind when
>> serializing the record as RDF.  Historically, "occurrences" were
>> considered to be a superclass that included specimens, and any property
>> remotely related to a specimen could be included as part of an
>> occurrence record.  A provider exposing an occurrence record might give
>> it properties such as dwc:eventDate, dwc:preparations, and
>> dwc:locality.  However, a different provider might consider
>> dwc:eventDate to be the property of a dwc:Event instance,
>> dwc:preparations to be the property of a dwc:PreservedSpecimen, and
>> dwc:locality to be the property of a dcterms:Location instance and link
>> those instances to a separate Occurrence instance via object properties.
>>
>> Which of these is correct?  At this point there is no consensus as to
>> whether one of these approaches is better than the other.  We avoided
>> putting extensive examples within the guide document itself, since the
>> guide will become part of the standard and will probably not be changed
>> frequently, whereas best practices for deciding the types of resources
>> with which properties should be associated is likely to develop over
>> time and with the experience of usage.  For that reason, we have
>> included examples in the ancillary documents that are associated with
>> the guide, but which do not form part of the standard.  The "examples
>> using 'pure' Darwin Core" [1] and "Examples using Darwin-SW object
>> properties" [2] illustrate the extremes that I've described above.
>>
>> Steve
>>
>> [1] https://code.google.com/p/tdwg-rdf/wiki/DwcRdfOccurrences
>> [2] https://code.google.com/p/tdwg-rdf/wiki/DwcRdfExamplesDarwinSW
>>
>> Paul J. Morris wrote:
>>
>>
>> As I've been working through implementing RDF generation in a few
>> applications and seeking to conform to the guide, I've found myself
>> spending a good bit of time hunting through the document looking for
>> guidance on particular situations, this leads me to a suggestion for
>> the guide: Include, at the end of the guide, a single comprehensive
>> example of an Occurrence record, annotated to point to relevant
>> sections in the guide.  This could serve both to quickly answer
>> questions and as a visual index to the rest of the guide.
>>
>> -Paul
>>
>>
>>
>> --
>> Steven J. Baskauf, Ph.D., Senior Lecturer
>> Vanderbilt University Dept. of Biological Sciences
>>
>> postal mail address:
>> PMB 351634
>> Nashville, TN  37235-1634,  U.S.A.
>>
>> delivery address:
>> 2125 Stevenson Center
>> 1161 21st Ave., S.
>> Nashville, TN 37235
>>
>> office: 2128 Stevenson Center
>> phone: (615) 343-4582,  fax: (615) 322-4942
>> If you fax, please phone or email so that I will know to look for it.
>> http://bioimages.vanderbilt.edu
>> http://vanderbilt.edu/trees
>>
>> _______________________________________________
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>> tdwg-content at lists.tdwg.org
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>>
>>
>>
>>
>>
>> --
>> Steven J. Baskauf, Ph.D., Senior Lecturer
>> Vanderbilt University Dept. of Biological Sciences
>>
>> postal mail address:
>> PMB 351634
>> Nashville, TN  37235-1634,  U.S.A.
>>
>> delivery address:
>> 2125 Stevenson Center
>> 1161 21st Ave., S.
>> Nashville, TN 37235
>>
>> office: 2128 Stevenson Center
>> phone: (615) 343-4582,  fax: (615) 322-4942
>> If you fax, please phone or email so that I will know to look for it.
>> http://bioimages.vanderbilt.edu
>> http://vanderbilt.edu/trees
>>
>>     
>
>
>
>   

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

postal mail address:
PMB 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
http://vanderbilt.edu/trees

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