[tdwg-content] Implementing Darwin Core in RDF
Steve Baskauf
steve.baskauf at vanderbilt.edu
Tue Aug 16 20:32:06 CEST 2016
Douglas,
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.
*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.
*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].
*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 http://rs.tdwg.org/dwc/terms/Organism) 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:
http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004
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.
*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:
a collection item linked by dwciri:inCollection to an IRI-identified
collection
an identification instance linked by dwciri:toTaxon to an IRI-identified
taxon (a.k.a. taxon concept)
a location instance linked by dwciri:inDescribedPlace to an
IRI-identified geographic place (a.k.a. "feature")
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
dwc:collectionCode="Mamm"
dwc:institutionCode ="MVZ"
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
dwc:genus="Hersiliiadae"
dwc:specificEpithet="yaeyamaensis"
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:
a collection item linked by dwciri:inCollection to
http://grbio.org/cool/0rht-pj95
an identification instance linked to
http://zoobank.org/75C9EA16-72B1-44C9-AD40-3C3D41323AB9
although I don't think either of these IRIs currently dereference to
meaningful machine-readable RDF (although they have human-readable web
pages).
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.
Steve Baskauf
[1] https://github.com/tdwg/rdf
[2] http://groups.google.com/group/tdwg-rdf
[3]
https://github.com/tdwg/vocab/blob/master/code-examples/darwin-core/dwciri.ttl
[4] https://github.com/tdwg/vocab/blob/master/documentation-specification.md
[5] https://github.com/tdwg/vocab/blob/master/maintenance-specification.md
[6] https://github.com/tdwg/rdf/blob/master/DwCAncillary.md
[7] https://github.com/darwin-sw/dsw
[8]
http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1
[9] https://github.com/darwin-sw/dsw/wiki/TdwgContentEmailSummary
[10] https://github.com/darwin-sw/dsw/blob/master/img/acs-dsw-poster.pptx
[11] http://rdf.library.vanderbilt.edu/sparql?view
[12]
https://github.com/HeardLibrary/semantic-web/blob/master/learning-sparql/learning-sparql-ch3-part2-answers.md
[13] https://github.com/darwin-sw/dsw/wiki/ClassOccurrence
[14] http://bioimages.vanderbilt.edu/org-jorgem/rec13_0004.rdf
[15]
http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#2.7_Darwin_Core_convenience_terms
[16]
http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#3.5_Darwin_Core_convenience_terms_that_are_expected_to_be_used_o
Douglas Campbell wrote:
>
> Hi all,
>
>
>
> 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.
>
>
>
> The areas of confusion I have include:
>
> * Best practice for connecting containers together
>
> * Dereferencing of the DwC IRI namespace
>
> * The overlapping scope of the Occurrence and Specimen types
>
> * Conflicting usage of Taxon fields in the Identification object.
>
>
>
> I'm hoping for suggestions:
>
> 1. Are there any implementations of DwC RDF data online that I could
> look at as examples to follow?
>
> 2. What/to whom is the best way to ask specific questions about DwC RDF?
>
>
>
> At this stage our API prototype is only available internally but there
> is some documentation available publicly at:
>
> https://github.com/te-papa/collections-api/wiki
>
>
>
> Thanks in advance,
>
> Douglas
>
>
>
> *Douglas Campbell*
>
> Business Analyst
>
> Collections Information Services
>
> Museum of New Zealand Te Papa Tongarewa
>
>
>
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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
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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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