[tdwg-tag] dwcterms (was: Embedding specimen (and other) annotations in NeXML)

John R. WIECZOREK tuco at berkeley.edu
Wed Feb 25 21:44:24 CET 2009

Comments inline...

On Tue, Feb 24, 2009 at 10:52 AM, Hilmar Lapp <hlapp at duke.edu> wrote:
> On Feb 23, 2009, at 5:55 PM, John R. WIECZOREK wrote:
>> On Mon, Feb 23, 2009 at 8:29 AM, Hilmar Lapp <hlapp at duke.edu> wrote:
>>> Thanks John - this now works and loads into Protege. Great!
>>> A couple of random comments from a first inspection:
>>> - There are lots of individuals that seem to correspond to classes
>>> and
>>> object properties (and seem to be replaced by them, which sounds
>>> odd). Is
>>> this by intention?
>> I don't know what you mean by this. Can you give me an example?
> As far as I can see the replaces relationships to classes have gone
> away. For object properties, an example is AcceptedTaxon:
> <rdf:Description rdf:ID="AcceptedTaxon">
>   <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
> "/>
>   <rdfs:domain rdf:resource="http://rs.tdwg.org/dwc/terms/Taxon"/>
>   <rdfs:replaces rdf:resource="http://rs.tdwg.org/dwc/terms/AcceptedTaxon-2008-11-19
> "/>
> </rdf:Description>
> This seems fine.
> BTW note that unless I'm missing something the base URLs http://rs.tdwg.org/dwc/terms/
>  and http://rs.tdwg.org/dwc/rdf/dwcterms.rdf result in different URIs
> for concepts (hence making them effectively different) for what you
> may want to be the same (the URLs seem to be used interchangeably -
> but maybe the idea behind this is different?).

I think this is a result of not including
xmlns="http://rs.tdwg.org/dwc/terms/ in the rdf:RDF section. Now all
of those terms with IDs and no namespaces should have the
xmlns="http://rs.tdwg.org/dwc/terms/ namespace and the unintended
collision will go away. Correct?

>> [...]
>>> - seeAlso often has the value 'not in ABCD', which is probably the
>>> wrong
>>> kind of value for this annotation.
>> None of those values is technically very useful, as they are
>> references to xpaths in a schema. As such, "not in ABCD" is no
>> different functionally speaking from any of the other values. If
>> seeAlso is not appropriate for this type of content (where is the
>> reasoning for that?)
> According to the RDF Schema spec, rdfs:seeAlso is "[...] used to
> indicate a resource that might provide additional information about
> the subject resource." The value of the property is supposed to be a
> rdfs:Resource (i.e., a URI to/for a resource).
> See http://www.w3.org/TR/rdf-schema/#ch_seealso

Changed this to a dwc-defined attribute abcdEquivalence, defined in a
new version of http://rs.tdwg.org/dwc/terms/attributes/dwcattributes.rdf

>> [...]
>>> - There are two classes with label 'Taxon' (but different URIs).
>>> Intentional?
>> I see only one. What are the URIs?
> Now there are actually three:
> http://rs.tdwg.org/dwc/rdf/dwcterms.rdf#Taxon
> http://rs.tdwg.org/dwc/rdf/dwcterms.rdf#Taxon-2008-11-19
> http://rs.tdwg.org/dwc/terms/Taxon
> All three have label "Taxon", and are classes, and there is no
> asserted relationship between them.

Should only be Taxon and it's historical version Taxon-2008-11-19,
both in the namespace http://rs.tdwg.org/dwc/terms now. The labels are
intentionally the same.

>>> - Same properties and some classes have the date suffix in their
>>> label.
>>> Intentional?
>> Every one of them has a date suffix in its label as far as I can see.
>> What are the exceptions?
> There are no classes anymore now with a suffix in the label, but many
> of the properties have it. For example:
> SamplingEvent-2008-11-19
> LivingSpecimen-2008-11-19
> PreservedSpecimen-2008-11-19
> For those there seems to be another term without the suffix.

Vocabulary has been removed to its own file

>> [...]
>> Again, all of them have the date suffix as far I I can see. Yes, term
>> versioning is the motivation. They are all in the one document so that
>> the entirety of the documentation, including history, can be produced
>> from it. It isn't so much that there are a lot of updates expected as
>> that there is a lot of historical nonsense to resolve unequivocally.
>> Here it is all in one place.
> Maybe it would be worth producing two versions - one with the history
> that allows the maintainers to resolve issues, and one for public
> consumption that has the cruft removed?

Good suggestion. That;s what I have done. There are now three files:
http://rs.tdwg.org/dwc/rdf/dwctype.rdf  for types
http://rs.tdwg.org/dwc/rdf/dwcterms.rdf  for the current terms, and
http://rs.tdwg.org/dwc/rdf/dwctermshistory.rdf   for all terms with
their historical versions

>> [...] The solution, I think, is to add each base term without
>> version information and give these terms rdfs:replaces with the
>> value of the term with the version number. This would give a
>> complete progression for any term up to the one currently
>> in use. I have done that in a copy of the file just committed. Does
>> that solve the problem adequately? Does it create any new ones?
> Looks a lot better now - thanks!
> BTW note that the server returns the ontology with mime-type text/html
> rather than application/rdf+xml. Not a big deal, just the browser will
> try to display it rather than downloading.

Updated the mime-types in the rs.tdwg.org repository. These had only
been set in the development repository.

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