[tdwg-content] Implementing Darwin Core in RDF

Douglas Campbell Douglas.Campbell at tepapa.govt.nz
Wed Aug 24 07:39:52 CEST 2016

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 ☺


From: tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of John Deck
Sent: Thursday, 18 August 2016 4:02 a.m.
To: tdwg-content at 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 at morris.net<mailto:mole at 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).



Example flat Darwin Core occurrence record as RDF produced by Symbiota:

HTTP Accept (through, for example, the Modify Headers firefox plugin):


@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/> .
    a dwc:Occurrence  ;
    dwc:institutionCode "ASNP" ;
    dwc:collectionCode "ENT" ;
<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)" ;

On Wed, 17 Aug 2016 06:02:01 +0000
Douglas Campbell <Douglas.Campbell at tepapa.govt.nz<mailto:Douglas.Campbell at 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 at Vanderbilt.Edu<mailto:steve.baskauf at Vanderbilt.Edu>]
> Sent: Wednesday, 17 August 2016 6:32 a.m.
> To: Douglas Campbell
> Cc: tdwg-content at lists.tdwg.org<mailto:tdwg-content at 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.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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> http://vanderbilt.edu/trees
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Paul J. Morris
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Museum of Comparative Zoölogy, Harvard University
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John Deck
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