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

[John R. WIECZOREK]

Comments inline...

On Mon, Feb 23, 2009 at 11:49 AM, Hilmar Lapp <hlapp at duke.edu> wrote:
>
> On Feb 23, 2009, at 2:26 PM, Kevin Richards wrote:
>
>> Was this particular question answered?
>
> No, not yet.
>
>>
>> "2) Is there a TDWG vocabulary (in RDF or OWL) that has a relation for
>> referring to a specimen record, or are you aware of another one that
>> has this?"
>>
>> Is the Occurrence RDF vocab at http://rs.tdwg.org/ontology/voc/
>> TaxonOccurrence what you are looking for?
>> I'm not sure I fully understood what you are after, but have a look
>> and see if it matches your requirements.
>
> Thanks for the link. It seems nearly identical to DwC or shares at
> least a lot of the terms, no? But it doesn't seem to have an
> appropriate relation either.

It is no accident that they have a lot in common. The idea of a
TaxonOccurrence as a concept was at the core of Darwin Core, which the
TDWG Ontology used as a model for its properties. At the time the
Ontology was actively developed Darwin Core had no notion of classes,
so its elements consisted of what are now properties of several Darwin
Core classes.

> What I am looking for, formally speaking, is an object property that
> would have a specimen as its range, and hence allows me to relate a
> specimen record to some entity (a class or an individual). Am I
> making sense?
>
> There are some pieces along those lines in the DwC terms, but they
> don't (seem to) connect:
>
> - There are classes PreservedSpecimen, FossilSpecimen, and
> LivingSpecimen, but they don't have a supertype (other than
> owl:Thing) that you could make the range.
>
> - There is a class Sample, but that doesn't have any of the Specimen
> classes as subtypes. Maybe that's correct since a sample and a
> specimen aren't really the same thing (rather, the former is obtained
> from the latter).

Following what Dublin Core does with type vocabulary for dcterms:type,
the classes PreservedSpecimen, FossilSpecimen, LivingSpecimen, and
others are terms that act as the controlled vocabulary for
dwcterm:BasisOfRecord (see
http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).
FossilSpecimen refines PreservedSpecimen as PreservedSpecimen refines
dcterms:PhysicalObject. FossilSpecimen has neither PreservedSpecimen
nor Sample (the class equivalent to a specimen in Darwin Core) as its
range because it is a controlled vocabulary term. Instances of Samples
having PreservedSpecimen, LivingSpecimen, or FossilSpecimen as the
BasisOfRecord could be considered specimens, as they all refine
dcterms:PhysicalObject. PhysicalObjects as Samples in Darwin Core are
specimens.

> - There is an object property Sample-2008-11-19 (domain is the class
> 'none'), but there is no further annotation as to what that property
> should mean.

I have removed all references to the domain class 'none'. In Darwin
Core Sample has no domain. The details of the relationship of Sample
to other classes is left to implementation as there is more than one
reasonable viewpoint - a Sample could be a property of a SamplingEvent
(something resulting from an event) or a SamplingEvent could be a
property of a Sample (the place where is the Sample was gathered).
Darwin Core makes no commitment to one viewpoint or the other outside
of implementation.

> - There are object properties LivingSpecimen-2008-11-19 and
> PreservedSpecimen-2008-11-19 that have PhysicalObject as their super-
> property (why not Specimen?), and there is FossilSpecimen-2008-11-19
> which has PreservedSpecimen (no date suffix) as super-property.

These are refinements showing the relationships between the options
for controlled vocabulary of the BasisOfRecord property, nothing more
(see also http://dublincore.org/documents/dcmi-type-vocabulary/).