Re: [tdwg-content] Implementing Darwin Core in RDF

28 Aug 2016

      I looked at the tdwg-content archives to try to figure out which of the 
last two emails that I wrote were actually sent out to the list.  This 
one below does not show up in the archives because "An HTML attachment 
was scrubbed...", apparently the actual email.  I'll try sending it 
again in hopes that the message actually survives.  The other message 
that contained comments about Douglas' example files (and which actually 
had attachments) never came to me, but shows up in the archives at 
http://lists.tdwg.org/pipermail/tdwg-content/2016-August/003642.html
I'm not sure what is going on with the listserv, my spam filter, or both.
Steve
-------- Original Message --------
Subject: 	Re: [tdwg-content] Implementing Darwin Core in RDF
Date: 	Fri, 26 Aug 2016 10:44:45 -0500
From: 	Steve Baskauf steve.baskauf@vanderbilt.edu
Organization: 	Vanderbilt University Dept. of Biological Sciences
To: 	Douglas Campbell Douglas.Campbell@tepapa.govt.nz, 
"tdwg-content@lists.tdwg.org" tdwg-content@lists.tdwg.org
References:
Douglas (and the list),
I took some time to look at your Turtle file, but will have to come back 
to it again later when I have more time before giving you specific 
feedback.
However, I wanted to make a few general comments to express how I think 
about the use of RDF in the biodiversity informatics context.  Before 
embarking down the path of exposing metadata as RDF, I think that one 
needs to ask the question: "Why do I want to expose RDF?"  There are 
several things that you get with RDF:
1. It's machine-readable.
2. It's a W3C standard that enables linking resources described by 
different data providers as a graph.
3. RDF triples from different sources can easily be aggregated in a 
triplestore and be queried using SPARQL.
4. It is compatible with machine reasoning.
If all you care about is item #1, then RDF is probably more trouble than 
it is worth.  There are more conventional means for providing access to 
data without requiring human intervention, with vanilla JSON being a 
prime example.
If your primary concern is breaking down data silos (i.e. you like the 
idea of Linked Data), then item #4 is probably more trouble that it's 
worth.  Machine reasoning is possible, but carrying out effective, 
non-trivial reasoning, requires a clear idea of what kind of reasoning 
you want to undertake and careful thought about how to structure the RDF.
RDF isn't the only way to achieve item #2.  Although JSON-LD can be 
valid RDF, it doesn't have to be.  There also other popular non-RDF 
graph database options may be less troublesome if all you care about is 
linking data as a graph.
It seems to me that item #3 is the sweet spot where the potential 
benefits of using RDF could outweigh its hassles.  IF multiple data 
providers exposed their data using a consistent graph topology, a 
machine could harvest triples from the various providers, throw them 
into a standard triplestore, and other machines could query the 
aggregated data using SPARQL to ask interesting questions.  All of this 
could be done in an automated fashion, with little or no human 
intervention.  (There is the additional problem of providers 
disciplining themselves to using consensus URIs to identify resources 
that would be linked across data silos rather than minting their own new 
ones, but that's a different issue that I won't get into in this email.)
However, if the multiple providers each use their own graph topology, 
then there are problems.  Simply merging the triples into a single graph 
would be no problem.  However, constructing a query that would work with 
every possible graph model that providers dream up would be virtually 
impossible.
So if one aspires to merge RDF triples from multiple providers, the 
burden of enabling querying that will work with all data can fall at 
three places in the workflow:
1. The burden could fall on *providers* to discipline themselves to 
follow a consensus graph model.  This requires them to express their 
triples as a graph that might not correspond to their native data model, 
but once that is done, no further action would be required down the 
pipeline.
2. The burden could fall on *aggregators* to "clean up" triples as they 
are ingested into the triplestore.  For example, it's not difficult to 
create SPARQL construct queries that would add nodes that aren't present 
in the providers data but that are needed for consistency with the graph 
model used by the aggregator.  However, that would depend on the 
aggregator to create a sort of "mapping" for each provider that uses a 
different graph model.  It's likely that would require at least some 
human intervention, which is at odds with the goal of automated machine 
discovery and ingestion. 
3. The burden could fall on the *users* who want to query the aggregated 
triples.  The "dirty" triples from multiple providers following 
differing graph models could just be thrown together in a triplestore.  
Those who want to query the data would have to create complex queries 
that were designed to catch all of the variations in graph topologies 
that providers might reasonably dream up, or else risk missing some 
results that might be important.  It seems likely that this approach 
would be doomed to failure.  Who would want to waste their time doing 
all that work when there would be a high probability of missing some 
results anyway?
Although the second option would probably be feasible, in order to 
achieve the real promise of RDF for our community, it seems to me like 
option #1 would be the way to go.
Bringing this back to the specific example of Douglas' data and 
Darwin-SW, Darwin-SW was designed with the intention of facilitating 
aggregation of RDF metadata from diverse sources: traditional museum 
specimens, event-oriented occurrences (bioblitzes, trawls), 
mark-recapture, repeated samples, collection of tissues/DNA without 
collecting the organism, camera traps, observations without collection 
(e.g. birder observations), etc.  Every one of these categories of data 
providers are going to have some part of the Darwin-SW model that they 
don't care about.  Museums may care about specimens but not organisms.  
Birders may care about organisms but not specimens.  Bioblitzers may 
care passionately about events with many occurrences, while 
mark-recapture people may think that events are useless since every 
occurrence happens at a separate event.  In order for Darwin-SW to work 
as intended, each kind of provider is going to just have to bite the 
bullet and create nodes for every kind of resource in the Darwin-SW 
model whether they like it or not.  This is very much NOT in the 
wild-west spirit of RDF where Anybody can say Anything about Any 
resource.  But if one cares about standardization, one will follow the 
template even if it doesn't fit perfectly with the provider's situation.
In writing Darwin-SW, we rigged it (some would say poisoned it) with 
semantics that cause a graph to become inconsistent if the Darwin-SW 
object properties are used to join classes in a way that's inconsistent 
with the Darwin-SW model.  I won't go into the details here - you can 
read about them in section 3.2 of the paper [1].  We've received some 
criticism for doing that, and perhaps it was a bad idea.  But that's the 
way things stand at the present.  It's a sort of veiled threat that 
says, "there's nothing to stop you from using the Darwin-SW object 
properties inappropriately, but if you do, you will create a graph that 
a reasoner will flag as inconsistent".  If a provider is bothered by 
that, it's better to mint its own object properties and not use the 
Darwin-SW ones.
I'll try to provide a more direct response about Douglas' sample data 
later on.  One thing that I might say now is that I'm not sure that I 
understand what Douglas means when he says "it would be impossible to 
create an Organism entity. And in fact we will not create Organism 
entities as we don’t need them in our context".  If the problem is a 
reluctance to mint and maintain URIs for resources that don't play an 
important role in the data, it's quite possible to just let them be 
blank nodes without URIs.  If the issue is that the Organism doesn't 
have an identification, that's no problem.  An Organism can have zero to 
many identifications at any particular time.  New identifications can be 
added at any point in the future.
Steve
[1] 
http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-term...
Douglas Campbell wrote:
...
Thank you all for your feedback.
I am hopeful there will eventually be a ‘standard’ vocabulary for the 
DwC associations.  In the meantime it looks like DSW will suit us the 
best.  dwcFP is quite loose (and having version numbers in the IRI 
means the namespace has broken once already).  BCO is quite 
bewildering – I like the solidity of underlying OBO framework, but BCO 
has a steep learning curve and doesn’t seem to tie into well-known LD 
ontologies.
The downside of DSW for us is the extra abstract Occurrence and 
Organism entities.  We basically hold specimens from field collection 
events that we identify – that is the data in our collection 
management system, so the other entities would just be fabricated for 
data exchange (not because we specifically model or store them).
I have mocked up a herbaria record starting from the specimen point of 
view (the core things that we hold in our collections).  This is 
attached as turtle and also our original JSON-LD (converted at 
http://json-ld.org/playground/ ).
*I had to go to Occurrence directly from the Specimen/Token using 
dsw:evidenceFor (rather than via Organism and dsw:hasOccurence) as it 
may not have been identified - meaning it would be impossible to 
create an Organism entity. And in fact we will not create Organism 
entities as we don’t need them in our context.

The Occurrence is just a placeholder (since we don’t have data for

it), which means I have associated the Agent to the Event rather than 
the Occurrence – it so happens that this is valid as the domain isn’t 
specified in dwciri:recordedBy.
*I have include properties of linked-to entities because we need them 
populated as part of the web API for searching, etc.  This is similar 
to the DwC concept of convenience properties.

There’s a few other messy parts like what IRIs we will create for

the Occurrence and Identification entities.
I’d be interested in any comments about whether this is on the right 
track and/or would be considered conformant DwC RDF J
Cheers,
Douglas
*From:* tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.org] *On 
Behalf Of *John Deck
*Sent:* Thursday, 18 August 2016 4:02 a.m.
*To:* tdwg-content@lists.tdwg.org
*Subject:* Re: [tdwg-content] Implementing Darwin Core in RDF
Another angle to consider here is using the Biological Collections 
Ontology (https://github.com/BiodiversityOntologies/bco), which is 
part of the OBO Foundry framework (http://www.obofoundry.org/), and 
for which development and work has been done in integrating with 
Darwin Core and Audubon Core 
(e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511409/).  The OBO 
community has a longer history with the biomedical community but 
gaining traction in biodiversity.  Since these are all ontologies, 
there should be less confusion on the meaning of classes. For example, 
the notion of Observation in DwC is broken down into at least some of 
the following classes: "Observing process", "Material target of 
observation",  "Material target of observation role".  Relations are 
well specified as well and drawn from the Relations Ontology 
(http://www.obofoundry.org/ontology/ro.html).  BTW, along with the PPO 
(plant phenology ontology 
-- https://github.com/PlantPhenoOntology/PPO) team, i'm working on 
annotating instance data with BCO and PPO now, an ongoing project and 
we will have more information on this effort at the upcoming TDWG 
meeting.   Happy to answer additional questions you have.
John Deck
On Wed, Aug 17, 2016 at 7:59 AM, Paul J. Morris <mole@morris.net 
mailto:mole@morris.net> wrote:
While commenting on the RDF guide, I wrote implementations of delivery
of flat Darwin Core in RDF into Symbiota and the Harvard University
Herbaria web search using content negotiation.  Symbiota, when an
occurrence (or agent record) is requested with an accept header of
text/turtle; will deliver the occurrence record in a turtle
serialization (an example is below), when requested with an accept
header of application/rdf+xml will return flat Darwin Core in RDF/XML
For structured relations beyond flat Darwin Core, there is another
alternative to darwin-sw (which is also in use in the wild), dwcFP:
http://filteredpush.org/ontologies/FP/2.0/dwcFP.owl  Bob Morris can
probably comment further, but one of the design goals of dwcFP was
fewer added inferences than darwin-sw (object properties have ranges
specified, but not domains).
dwcFP defines a set of object properties for making relations between
core Darwin Core classes that we've been using in annotations:
owl:ObjectProperty rdf:about="dwcFP:hasIdentification"
owl:ObjectProperty rdf:about="dwcFP:usesTaxon"
owl:ObjectProperty rdf:about="dwcFP:hasCollectingEvent"
owl:ObjectProperty rdf:about="dwcFP:hasLocality"
owl:ObjectProperty rdf:about="dwcFP:hasGeologicalContext"
owl:ObjectProperty rdf:about="dwcFP:hasGeoreference"
owl:ObjectProperty rdf:about="dwcFP:hasAssociatedMedia"

One object property we added specifically to simplyfy SPARQL queries on
taxonomic trees:
owl:ObjectProperty rdf:about="dwcFP:descendantTaxonOf"

And additional object properties that cover more possible relations:
owl:ObjectProperty rdf:about="dwcFP:relationProperty"
owl:ObjectProperty rdf:about="dwcFP:hasAcceptedNameUsage"
owl:ObjectProperty rdf:about="dwcFP:namePublishedIn"
owl:ObjectProperty rdf:about="dwcFP:hasOriginalNameUsage"
owl:ObjectProperty rdf:about="dwcFP:hasParentNameUsage"
owl:ObjectProperty rdf:about="dwcFP:hasScientificName"
owl:ObjectProperty rdf:about="dwcFP:hasTaxonConcept"
owl:ObjectProperty rdf:about="dwcFP:taxonomicAuthorityFor"
owl:ObjectProperty rdf:about="dwcFP:nomenclaturalCode"
owl:ObjectProperty rdf:about="dwcFP:nomenclaturalStatus"

Attached is an example RDF document (which is a commented extract from
the body of an annotation in a new occurrence annotation document)
that describes an occurrence.  There were about 350,000 such occurrence
records wrapped in annotations generated in the NEVP project.  This
representation preceeded the Darwin Core RDF guide, and I've added a
couple of comments about things we would do differently now.
In using dwcFP, we encountered the same kind of questions you are
raising about where to place datatype properties that might go in more
than one place.  We ended up hanging dwc:scientificName,
dwc:scientificNameAuthorship, etc, off of the Identification, and then
a Taxon (through dwcFP:usesTaxon) off the Identification, with only a
guid hung off the Taxon.  Bob can probably comment further, but I think
our motivation for this was that the new occurrence annotation
documents are intended to describe transcription of data off of
specimens (and container (herbarium sheet and folder)), and that
conceptually these scientfic names were properties of transcriptions of
identifications.  If I recall correctly, we are doing the opposite in
new identification annotations (hanging dwc:scientificName off of a
Taxon instance).
-Paul
--
Example flat Darwin Core occurrence record as RDF produced by Symbiota:
http://symbiota4.acis.ufl.edu/scan/portal/collections/individual/index.php?o... 
http://symbiota4.acis.ufl.edu/scan/portal/collections/individual/index.php?occid=16950169&clid=0
with
HTTP Accept (through, for example, the Modify Headers firefox plugin):
text/turtle;q=1.0,text/xml,application/xml,application/xhtml+xml,text/html;
q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5
Delivers:
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns# 
http://www.w3.org/1999/02/22-rdf-syntax-ns> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema# 
http://www.w3.org/2000/01/rdf-schema> .
@prefix owl: <http://www.w3.org/2002/07/owl# 
http://www.w3.org/2002/07/owl> .
@prefix foaf: http://xmlns.com/foaf/0.1/ .
@prefix dwc: http://rs.tdwg.org/dwc/terms/ .
@prefix dwciri: http://rs.tdwg.org/dwc/iri/ .
@prefix dc: http://purl.org/dc/elements/1.1/ .
@prefix dcterms: http://purl.org/dc/terms/ .
@prefix dcmitype: http://purl.org/dc/dcmitype/ .
urn:uuid:00032bdf-8862-4ca1-b8a6-ba35ee59f56a
    a dwc:Occurrence  ;
    dwc:institutionCode "ASNP" ;
    dwc:collectionCode "ENT" ;
    dwciri:inCollection
urn:uuid:af7140c3-4aa2-41ac-b3e9-4c7415b3ce90 ; a
dcmitype:PhysicalObject ; dwc:basisOfRecord  "PreservedSpecimen" ;
    dwc:catalogNumber "735" ;
    dwc:kingdom "Animalia" ;
    dwc:phylum "Arthropoda" ;
    dwc:class "Insecta" ;
    dwc:order "Hemiptera" ;
    dwc:family "Miridae" ;
    dwc:scientificName "Phytocoris" ;
    dwc:scientificNameAuthorship "Fallén, 1814" ;
    dwc:genus "Phytocoris" ;
    dwc:identifiedBy "G. W. Cowper 2008" ;
    dwc:recordedBy "G. W. Cowper" ;
    dwc:eventDate  "2008-10-18" ;
    dwc:year  "2008" ;
    dwc:month  "10" ;
    dwc:day  "18" ;
    dwc:startDayOfYear "292" ;
    dwc:fieldNumber "-" ;
    dwc:individualCount "1" ;
    dwc:preparations "Academy Drawer" ;
    dwc:country "United States" ;
    dwc:stateProvince "New Jersey" ;
    dwc:county "Burlington" ;
    dwc:municipality "Woodland" ;
    dwc:locality "SW of Chatsworth Beat Pinus along sandy road in
upland pine & oak woodland.; 1 individual(s) collected; Way Point
[-]" ; dwc:decimalLatitude "39.806067" ; dwc:decimalLongitude
"-74.545333" ; dwc:verbatimCoordinates "N+39º48.364' W-074º32.720'" ;
    dwc:disposition "ANSP" ;
    dcterms:modified "2015-04-25 17:13:22" ;
    dcterms:license http://creativecommons.org/licenses/by-nc/3.0/ ;
    dcterms:rightsHolder <Academy of Natural Sciences> ;
    dcterms:accessRights "CC BY-NC (Attribution-Non-Commercial)" ;
    dcterms:references
"http://symbiota4.acis.ufl.edu/scan/portal/collections/individual/index.php?o...".
On Wed, 17 Aug 2016 06:02:01 +0000
Douglas Campbell <Douglas.Campbell@tepapa.govt.nz 
mailto:Douglas.Campbell@tepapa.govt.nz> wrote:
...
Thanks for taking the time to bring me up to speed, Steve.
I'm familiar with the complexities of preparing specifications and
realise I've come in mid-way.  I'll spend some time reading up on the
containers and occurrences history.  But I'm unclear whether it is
better to use DSW terms in anticipation of them having longevity, or
just to mint our own in the meantime?
For the taxon convenience fields...
I thought I read in the DwC RDF schema that properties like taxonRank
were in the Taxon class (so using them in Identification conflicts
with their definition), but looking again I see that the spec uses
"dwcattributes:organizedInClass" which specifically does not imply
domain or range.  So now I'm at peace with that. :)
However, I am pointing to our own RDF versions of taxon
classification terms that we use, and using DwC properties to define
these taxon terms, plus I am combing these all together in a single
JSON-LD API result.  So at this point I don't think I need to repeat
the convenience properties in Identification (as they are available
directly in the Taxon object).  While this seems to fit our purpose I
can see that this may be sub-optimal for others who download the data
and use it separately - I'll need to contemplate that scenario some
...
more.
Cheers,
Douglas
From: Steve Baskauf [mailto:steve.baskauf@Vanderbilt.Edu
mailto:steve.baskauf@Vanderbilt.Edu]
...
Sent: Wednesday, 17 August 2016 6:32 a.m.
To: Douglas Campbell
Cc: tdwg-content@lists.tdwg.org mailto:tdwg-content@lists.tdwg.org
Subject: Re: [tdwg-content] Implementing Darwin Core in RDF
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.t...
...
[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-term...
...
[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/lea...
...
[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_convenienc...
...
[16]
http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#3.5_Darwin_Core_convenienc...
...
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:

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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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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Paul J. Morris
Biodiversity Informatics Manager
Museum of Comparative Zoölogy, Harvard University
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The email message together with the accompanying attachments may be 
*CONFIDENTIAL*. If you have received this message in error, please 
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immediately and delete the original message. The views expressed in 
this message are those of the individual sender, except where the 
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employs strict virus checking measures and accepts no liability for 
any loss caused either directly or indirectly by a virus arising from 
the use of this message or any attached file.

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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