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Douglas,<br>
I was the lead author on the DwC RDF Guide, so I can try to answer your
questions about it. The TDWG RDF Task Group is still in operation,
although it hasn't been very active for the past several years. The
RDG TG has an online "home" at the TDWG Github site.[1] However, the
content didn't survive the migration from Google Code very well, so it
takes some effort at this point to sort through it. The TG also has an
email list [2] but there has been little traffic on it recently.<br>
<br>
*Dereferencing of the DwC IRI namespace* - Unfortunately, the dwciri:
namespace terms don't dereference at the present time. This needs to
be corrected. I've created a Turtle serialization [3] of how I think
the RDF should be written for the dwciri: terms, but it isn't served
when one attempts to dereference the terms and hasn't been incorporated
into the official DwC repository. Part of the problem here is that the
guidelines for documenting terms in machine-readable form are still
going through the adoption process.[4] I'm hopeful that when the
Documentation Specification is ratified, we can make sure that all
existing DwC terms dereference in a consistent manner.<br>
<br>
*Best practice for connecting containers together* - By this, I'm
assuming you mean linking instances of the various Darwin Core classes,
or in RDF terms, linking nodes. The RDF Guide is silent on how to do
this. That's not great from the standpoint of actually turning Darwin
Core records into RDF, but it was a way to complete the guide in a
finite amount of time. What is missing is a consensus domain model
that would lay out how instances of the Darwin Core classes would be
linked. Such a model should be developed, but that has not yet
happened. Again, there is a draft standard submitted for review [5],
which if adopted will specify (in Section 4) a process for developing
such a model. When we wrote the RDF Guide, we provided ancillary
documents [6], which included examples that followed the RDF Guide and
linked instances using various proposed models. There are links to web
pages containing examples using TaxonConcept, BiSciCol, and Darwin-SW
object properties to link class instances. I am not sure whether there
is any RDF "in the wild" for the first two examples. I'm more familiar
with Darwin-SW, as I was involved in its development [7]. There is a
Semantic Web Journal article about Darwin-SW [8], so I won't go into
detail about it here, except to say that its data model was developed
following an extensive discussion on the tdwg-content email list [9]
about how members of the community understood the Darwin Core classes.
The relationship between Darwin-SW model and the historical 1993 ACS
Model can be viewed at [10]. There are a bit over a million triples of
data "in the wild" modeled on Darwin-SW in accordance with the DwC RDF
guide, accessible at a SPARQL end point. [11] Some examples showing
how to play around with SPARQL queries of these data are at [12].<br>
<br>
*The overlapping scope of Occurrence and Specimen types* - There is a
long history behind the meaning of "Occurrence". There is an
out-of-date-summary of some of the discussion around this topic in the
Darwin-SW documentation [13]. I
think that at the time when Darwin Core was originally adopted, an
Occurrence was considered a sort of superclass of the Specimen and
Observation classes. However, after a lot of discussion, the meaning
of dwc:Occurrence was clarified by changing it to its current
definition: "An existence of an Organism (sensu
<a class="moz-txt-link-freetext"
href="http://rs.tdwg.org/dwc/terms/Organism">http://rs.tdwg.org/dwc/terms/Organism</a>)
at a particular place at a
particular time." In this view, an Occurrence isn't a concrete thing
like a Specimen - it's more like a database join between an Event
instance (time and place) and an Organism, which allows for a
one-to-many relationship between a Organism and Occurrences, and a
one-to-many relationships between an Event and Occurrences. It also
allows for a single occurrence of an organism at a time and place to be
documented by one-to-many forms of evidence, which could include
PreservedSpecimens, HumanObservation data, or images of various sorts.
In RDF terms, an Occurrence could be thought of as a node that is
linked to Event, Organism, and evidence instances nodes. You can see
this represented graphically at [7], where "dsw:Token" refers to a
generic class for evidence. In any case, separating Occurrence (as a
node linking Events to Organisms) from Specimen allows an Occurrence to
be documented by one to many instances of any kind of evidence, or even
multiple kinds of evidence. For example, an Occurrence could be
documented by a PhysicalSpecimen as well as several images. Here is an
example of an organism with two Occurrences: <br>
<a class="moz-txt-link-freetext"
href="http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004">http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004</a><br>
The first occurrence on 2013-07-24 was documented by 42 camera trap
images, and the second occurrence on 2013-07-25 was documented by 21
camera trap images. You can see how this was represented in RDF at
[14]. In most cases, specimen records will be much simpler than this,
with one organism, documented at one occurrence, with evidence of one
PreservedSpecimen. Such a simpler case could be represented with a
simpler model. But the more complex model allows specimen-derived
occurrence records to be merged with other kinds of occurrence records,
such as the camera trap example I gave, mark-recapture bird banding
observations, iNaturalist occurrences documented by photos of the
organism, etc.<br>
<br>
*Conflicting usage of Taxon fields in the Identification object* - In
order to explain the rationale behind why what seem to be taxon-related
properties are assigned to Identification instances, I must refer to
the idea of "convenience terms" as expressed in Section 2.7 of the RDF
Guide.[15] In a perfect world, we would have the following:<br>
<br>
a collection item linked by dwciri:inCollection to an IRI-identified
collection<br>
an identification instance linked by dwciri:toTaxon to an
IRI-identified taxon (a.k.a. taxon concept)<br>
a location instance linked by dwciri:inDescribedPlace to an
IRI-identified geographic place (a.k.a. "feature")<br>
<br>
If the linked IRI-identified object resources were described by RDF, it
would
not be necessary to include any of the Darwin Core "convenience"
properties included in Table 3.5 [16]. The information contained in
the values of those properties could be discovered by dereferencing the
object IRIs and traversing subsequent links from that RDF. However, if
those
IRIs don't exist, then the convenience properties provide a
string-based mechanism to relate the subject resource to other
resources that should be linked to the same (unidentified) object
resource. So for example, if we say a specimen has the convenience
properties and values <br>
<br>
dwc:collectionCode="Mamm"<br>
dwc:institutionCode ="MVZ"<br>
<br>
we are not saying that "Mamm" is the collection code of the specimen
and that "MVZ" is the institution code of the specimen. Rather, we
mean that the specimen should be linked to a collection (with unknown
IRI) whose code is MVZ and whose owning institution has the code
"MVZ". Similarly, if we say that an identification has the convenience
properties and values<br>
<br>
dwc:genus="Hersiliiadae"<br>
dwc:specificEpithet="yaeyamaensis"<br>
<br>
we are not saying that "yaeyamaensis" is the specific epithet of the
identification and that "Hersiliiadae" is the genus of the
identification. Rather, we mean that the identification should be
linked to a taxon (with unknown IRI) for which the specificEpithet part
of its name string is "yaeyamaensis", which is included in the genus
"Hersiliiadae". This may seem odd, particularly if you are used to
thinking of genus and specific epithet as properties of a taxon. But
the sets of DwC convenience properties are intended to be a temporary,
string-based way to describe an unidentified resource to which the
subject resource should be linked. At some future time, if IRIs can be
discovered, those sets of convenience properties might be dropped if
dereferencing the IRIs provides the same information. In these
examples, one might replace with:<br>
<br>
a collection item linked by dwciri:inCollection to
<a class="moz-txt-link-freetext" href="http://grbio.org/cool/0rht-pj95">http://grbio.org/cool/0rht-pj95</a><br>
an identification instance linked to
<a class="moz-txt-link-freetext" href="http://zoobank.org/75C9EA16-72B1-44C9-AD40-3C3D41323AB9">http://zoobank.org/75C9EA16-72B1-44C9-AD40-3C3D41323AB9</a><br>
<br>
although I don't think either of these IRIs currently dereference to
meaningful machine-readable RDF (although they have human-readable web
pages). <br>
<br>
I hope that this has provided you with some answers, or at least a
starting point for additional exploration or questions. Please feel
free to reply if there were parts of what I wrote that weren't clear.<br>
<br>
Steve Baskauf<br>
<br>
[1] <a class="moz-txt-link-freetext" href="https://github.com/tdwg/rdf">https://github.com/tdwg/rdf</a><br>
[2] <a class="moz-txt-link-freetext"
href="http://groups.google.com/group/tdwg-rdf">http://groups.google.com/group/tdwg-rdf</a><br>
[3]
<a class="moz-txt-link-freetext"
href="https://github.com/tdwg/vocab/blob/master/code-examples/darwin-core/dwciri.ttl">https://github.com/tdwg/vocab/blob/master/code-examples/darwin-core/dwciri.ttl</a><br>
[4]
<a class="moz-txt-link-freetext"
href="https://github.com/tdwg/vocab/blob/master/documentation-specification.md">https://github.com/tdwg/vocab/blob/master/documentation-specification.md</a><br>
[5]
<a class="moz-txt-link-freetext"
href="https://github.com/tdwg/vocab/blob/master/maintenance-specification.md">https://github.com/tdwg/vocab/blob/master/maintenance-specification.md</a><br>
[6] <a class="moz-txt-link-freetext"
href="https://github.com/tdwg/rdf/blob/master/DwCAncillary.md">https://github.com/tdwg/rdf/blob/master/DwCAncillary.md</a><br>
[7] <a class="moz-txt-link-freetext"
href="https://github.com/darwin-sw/dsw">https://github.com/darwin-sw/dsw</a><br>
[8]
<a class="moz-txt-link-freetext"
href="http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1">http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1</a><br>
[9] <a class="moz-txt-link-freetext"
href="https://github.com/darwin-sw/dsw/wiki/TdwgContentEmailSummary">https://github.com/darwin-sw/dsw/wiki/TdwgContentEmailSummary</a><br>
[10]
<a class="moz-txt-link-freetext"
href="https://github.com/darwin-sw/dsw/blob/master/img/acs-dsw-poster.pptx">https://github.com/darwin-sw/dsw/blob/master/img/acs-dsw-poster.pptx</a><br>
[11] <a class="moz-txt-link-freetext"
href="http://rdf.library.vanderbilt.edu/sparql?view">http://rdf.library.vanderbilt.edu/sparql?view</a><br>
[12]
<a class="moz-txt-link-freetext"
href="https://github.com/HeardLibrary/semantic-web/blob/master/learning-sparql/learning-sparql-ch3-part2-answers.md">https://github.com/HeardLibrary/semantic-web/blob/master/learning-sparql/learning-sparql-ch3-part2-answers.md</a><br>
[13] <a class="moz-txt-link-freetext"
href="https://github.com/darwin-sw/dsw/wiki/ClassOccurrence">https://github.com/darwin-sw/dsw/wiki/ClassOccurrence</a><br>
[14] <a class="moz-txt-link-freetext"
href="http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004.rdf">http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004.rdf</a><br>
[15]
<a class="moz-txt-link-freetext"
href="http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#2.7_Darwin_Core_convenience_terms">http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#2.7_Darwin_Core_convenience_terms</a><br>
[16]
<a class="moz-txt-link-freetext"
href="http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#3.5_Darwin_Core_convenience_terms_that_are_expected_to_be_used_o">http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#3.5_Darwin_Core_convenience_terms_that_are_expected_to_be_used_o</a><br>
<br>
Douglas Campbell wrote:
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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am implementing Darwin Core in RDF as part of
our API at Te Papa (Museum of New Zealand). My aim is to map our
specimen metadata to rich Darwin Core RDF using JSON-LD, then 'dumb
down' to Simple Darwin Core to contribute to virtual herbariums. I
have mocked-up some records, however there are some areas where I'm not
quite sure how to interpret the Darwin Core RDF Guide.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The areas of confusion I have include:<o:p></o:p></p>
<p class="MsoNormal">* Best practice for connecting containers
together<o:p></o:p></p>
<p class="MsoNormal">* Dereferencing of the DwC IRI namespace<o:p></o:p></p>
<p class="MsoNormal">* The overlapping scope of the Occurrence and
Specimen types<o:p></o:p></p>
<p class="MsoNormal">* Conflicting usage of Taxon fields in the
Identification object.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I'm hoping for suggestions:<o:p></o:p></p>
<p class="MsoNormal">1. Are there any implementations of DwC RDF data
online that I could look at as examples to follow?<o:p></o:p></p>
<p class="MsoNormal">2. What/to whom is the best way to ask specific
questions about DwC RDF?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">At this stage our API prototype is only
available internally but there is some documentation available publicly
at:<o:p></o:p></p>
<p class="MsoNormal"><a class="moz-txt-link-freetext"
href="https://github.com/te-papa/collections-api/wiki">https://github.com/te-papa/collections-api/wiki</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance,<o:p></o:p></p>
<p class="MsoNormal">Douglas<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="">Douglas Campbell<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="">Business Analyst<o:p></o:p></span></p>
<p class="MsoNormal"><span style="">Collections Information Services<o:p></o:p></span></p>
<p class="MsoNormal"><span style="">Museum of New Zealand Te Papa
Tongarewa<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p> </p>
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<pre class="moz-signature" cols="72">--
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.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
<a class="moz-txt-link-freetext" href="http://vanderbilt.edu/trees">http://vanderbilt.edu/trees</a>
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