[tdwg-content] Implementing Darwin Core in RDF

Bob Morris morris.bob at gmail.com
Wed Aug 17 18:55:03 CEST 2016

Paul beat  me  to  it, but I would add that the version of dwcFP found
in  http://filteredpush.org/ontologies/FP/2.01/  corrects some minor
trivial errors (some instantces of "lang=en" should be "xml:lang=en" )
Most important it appears that @Douglas agrees with my oft-offered
rant that rdfs:domain (and perhaps rdfs::range ) are typically
misunderstood by users of rdfs reasoners to little or no  value.

Another application of dwcFP is at
https://github.com/plazi/TreatmentOntologies. I'm helping Terry
Catapano use dwcFP in modelling taxon treatments. Take care, some of
the proposed plazi use of dwcFP in the github is presently wishes, not
yet correct models.  More interesting is the ultimate rdfs modelling
for the current stable, active  taxon treatment bank searchable at

Both of the applications using dwcFP can probably use any rdfs-based
model of DwC that quarantees tractable SPARQL1.1  queries

Bob Morris

On Wed, Aug 17, 2016 at 10:59 AM, Paul J. Morris <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).
> -Paul
> --
> Example flat Darwin Core occurrence record as RDF produced by Symbiota:
> 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#> .
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix 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?occid=16950169".
> On Wed, 17 Aug 2016 06:02:01 +0000
> Douglas Campbell <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]
>> Sent: Wednesday, 17 August 2016 6:32 a.m.
>> To: Douglas Campbell
>> Cc: 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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>> 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:
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>> http://vanderbilt.edu/trees
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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>> The email message together with the accompanying attachments may be
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> --
> Paul J. Morris
> Biodiversity Informatics Manager
> Museum of Comparative Zoölogy, Harvard University
> mole at morris.net  AA3SD  PGP public key available
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Robert A. Morris

Emeritus Professor  of Computer Science
100 Morrissey Blvd
Boston, MA 02125-3390

Filtered Push Project
Kurator Project
Harvard University Herbaria
Harvard University

email: morris.bob at gmail.com
web: http://efg.cs.umb.edu/
web: http://wiki.filteredpush.org

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